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danny-avila and others added 30 commits April 25, 2026 04:01
* 🧬 feat: Scaffold Skills CRUD with ACL Sharing and File Schema

Adds Skills as a new first-class resource modeled on Anthropic's Agent
Skills, reusing the existing Prompt ACL stack for sharing. Lays the
groundwork for multi-file skills (SkillFile schema + metadata routes)
without wiring upload processing — single-file skills (inline SKILL.md
body) work end-to-end, multi-file uploads are stubbed for phase 2.

* 🔬 fix: Wire Skill Cleanup, AccessRole Enum, and Express 5 Path Params

CI surfaced four follow-ups from the initial Skills scaffolding commit
that local builds missed:

- AccessRole's resourceType field had a hardcoded enum that didn't
  include `'skill'`, blocking SKILL_OWNER/EDITOR/VIEWER role creation
  in every test that hit the AccessRole model.
- The seedDefaultRoles assertion in accessRole.spec.ts hard-listed the
  expected role IDs and needed the new SKILL_* entries.
- deleteUserController had no cleanup for skills, and the
  deleteUserResourceCoverage guard test enforces every ResourceType has
  a documented handler — wired in db.deleteUserSkills(user._id) and
  added the entry to HANDLED_RESOURCE_TYPES.
- Express 5's path-to-regexp v6 rejects the legacy `(*)` named-group
  glob syntax. The two skill file routes now use a plain `:relativePath`
  param; the client already encodeURIComponents the path, so a single
  param is sufficient and decoded server-side.

* 🪡 fix: Make Skill Name Uniqueness Application-Level

Resolve three more CI failures from the Skills scaffolding PR:

- Mongoose creates indexes asynchronously and mongodb-memory-server
  tests can race ahead of the unique (name, author, tenantId) index
  being built, so the duplicate-name uniqueness test was flaky.
  Added an explicit findOne pre-check inside createSkill that throws
  with code 11000 (mimicking the index violation), giving deterministic
  behavior. The unique index stays as the persistent guarantee.
- The deleteUser.spec.js and UserController.spec.js suites mock the
  ~/models module directly and were missing deleteUserSkills, causing
  deleteUserController to throw and return 500 instead of 200.
- Removed two doc-comment claims that the SKILL_NAME_MAX_LENGTH and
  SKILL_DESCRIPTION_MAX_LENGTH constants "match Anthropic's API". The
  values themselves are reasonable but the comments were misleading
  about who enforces them.

* 🪢 fix: Address Code Review Findings on Skills Scaffolding

Resolve all 15 findings from the comprehensive PR review:

Critical:
- Rollback the created skill when grantPermission throws so a transient
  ACL failure cannot leave an orphaned, inaccessible skill in the DB.
- Fix infinite query cache corruption in useUpdateSkillMutation helpers.
  setQueriesData([QueryKeys.skills]) matches useSkillsInfiniteQuery's
  InfiniteData cache entries, which have { pages, pageParams } shape —
  spreading data.skills on those would throw. Added an isInfiniteSkillData
  guard and per-page transform so both flat and infinite caches update
  correctly.

Major:
- Fix TUpdateSkillContext type: the public type declared previousListData
  but onMutate actually returns previousListSnapshots (a [key, value]
  tuple array). Updated the type + added TSkillCacheEntry as a shared
  export from data-provider.
- Add cancelQueries calls before optimistic update in onMutate so
  in-flight refetches cannot clobber the optimistic state.
- Parallelize deleteUserSkills ACL removal via Promise.allSettled instead
  of a sequential await loop — O(1) round-trip vs O(n).
- Stub mockDeleteUserSkills in stubDeletionMocks() and assert it's called
  with user.id in the deleteUser.spec.js happy-path test.
- Add idResolver: getSkillById to the SKILL branch in accessPermissions.js
  so GET /api/permissions/skill/<missing-id> returns 404 instead of 403.

Minor:
- Reuse resolved skill from req.resourceAccess.resourceInfo in getHandler
  to eliminate a redundant getSkillById call per GET /api/skills/:id.
- Reject PATCH /api/skills/:id requests whose body contains only
  expectedVersion — previously they silently bumped version with no
  changes, triggering spurious 409s for collaborators.
- Make TSkill.frontmatter optional (wire type) and add serializeFrontmatter
  / serializeSourceMetadata helpers that return undefined for empty
  objects instead of casting incomplete data to SkillFrontmatter.
- Standardize deleteUserSkills to accept string | ObjectId and convert
  internally, matching deleteUserPrompts's signature; UserController now
  passes user.id consistently.
- Replace bumpSkillVersionAndRecount (read-then-write, racy) with
  bumpSkillVersionAndAdjustFileCount using atomic $inc. upsertSkillFile
  pre-checks existence to distinguish insert (+1) from replace (0).
- Add DELETE /api/skills/:id/files/:relativePath integration tests
  covering success, 404, and 403 paths.

Nits:
- Drop trivial resolveSkillId wrapper — pass getSkillById directly.
- Remove dead staleTime: 1000 * 10 from useListSkillsQuery since all
  refetch triggers are already disabled.

* 🧭 fix: Resolve Second Skills Review Pass — Cache, Gate, TOCTOU

Address 13 of 14 findings from the second code review; reject #13 as
misread of the AGENTS.md import-order rule (package types correctly
precede local types regardless of length).

Major:
- Fix addSkillToCachedLists closure bug: a hoisted `prepended` flag
  was shared across every cache entry matched by setQueriesData, so
  concurrent flat + infinite caches would silently drop the prepend
  on whichever was processed second. Replaced the shared helper with
  three per-entry inline updaters that handle InfiniteData at the
  page level (page 0 only for prepend, all pages for replace/remove).
- Tighten patchHandler's expectedVersion validation: NaN passes
  `typeof === 'number'` and would previously leak current skill state
  via a misleading 409. Now requires finite positive integer and
  returns 400 otherwise.
- Guard decodeURIComponent in deleteFileHandler with try/catch —
  malformed percent encoding now returns 400 instead of 500.
- Add PermissionTypes.SKILLS + skillPermissionsSchema +
  TSkillPermissions in data-provider; seed default SKILLS permissions
  for ADMIN (all true) and USER (use + create only); wire
  checkSkillAccess / checkSkillCreate via generateCheckAccess onto
  the skills router mirroring the prompts pattern. Skills route now
  enforces role-based capability gates alongside per-resource ACLs.
  Test suite adds a mocked getRoleByName returning permissive SKILLS.
- Fix upsertSkillFile TOCTOU: replaced the pre-check + upsert pair
  with a single `findOneAndUpdate({ new: false, upsert: true })` call
  that atomically returns the pre-update doc (null ⇒ insert) so
  fileCount delta can't double-count on concurrent same-path uploads.

Minor:
- Add `sourceMetadata` to listSkillsByAccess .select() so summaries
  no longer silently drop the field for GitHub/Notion-synced skills.
- Include `cursor` in useListSkillsQuery's query key so manual
  pagination doesn't alias across pages.
- Clean up TSkillSummary to `Omit<TSkill, 'body' | 'frontmatter'>`
  matching what serializeSkillSummary actually emits; drop the
  Omit-then-re-add noise.
- Skip getPublicSkillIdSet in createHandler; a newly-created skill
  cannot have a PUBLIC ACL entry, so pass an empty set directly
  instead of paying a DB round-trip.
- Trim SkillMethods public surface: drop internal helpers
  countSkillFiles / deleteSkillFilesBySkillId / getSkillFile from the
  return object; inline the file cascade into deleteSkill.
- Use TSkillConflictResponse at the PATCH 409 call site instead of
  an inline ad-hoc object literal.
- Drop the now-unused EXPECTED_VERSION_ERROR module constant.

* 🧩 fix: Extend Role Schema + Types with SKILLS PermissionType

CI type-check and unit test failures from the PermissionTypes.SKILLS
addition surfaced three unrelated places that all hardcode the
permission-type set:

- IRole.permissions in data-schemas/types/role.ts enumerates every
  PermissionTypes key as an optional field. Adding SKILLS to the enum
  without updating the interface caused TS7053 'expression of type
  PermissionTypes can't be used to index type' errors in
  role.methods.spec.ts (lines 407-408, 477-478) because
  Object.values(PermissionTypes) now yielded a value the interface
  didn't cover.
- schema/role.ts rolePermissionsSchema mirrors the interface at the
  Mongoose layer; also needed SKILLS added so the persisted role
  document can actually store skill permissions.
- data-provider/roles.spec.ts has a guard test that every permission
  type carrying CREATE/SHARE/SHARE_PUBLIC must be explicitly "tracked"
  either in RESOURCE_PERMISSION_TYPES or in the PROMPTS/AGENTS/MEMORIES
  exemption list. Added SKILLS to the exemption list since skills
  follow the same default model as prompts/agents (USE + CREATE on for
  USER, SHARE / SHARE_PUBLIC off).

All three are additive pass-throughs with no behavior change.

* 🏷️ refactor: Introduce ISkillSummary for Narrow List Projection

Follow-up NITs from the second review pass on the Skills PR:

- Define ISkillSummary = Omit<ISkill, 'body' | 'frontmatter'> and use
  it as the element type in ListSkillsByAccessResult. The list query's
  .select() intentionally omits body and frontmatter for payload size,
  but the previous type claimed both fields were present — a type lie
  that would mislead future readers even though serializeSkillSummary
  never touches those fields at runtime. handlers.ts's signature for
  serializeSkillSummary now accepts ISkillSummary too.
- Document the intentional second-round-trip `findOne` in
  upsertSkillFile. Switching to `findOneAndUpdate({ new: false })`
  was required for TOCTOU-safe insert-vs-replace detection, which
  means the handler needs a follow-up query to return the post-upsert
  document. A comment now explains the tradeoff so future readers
  don't silently "optimize" it away.

No behavior change.

* 🌐 fix: Wire SKILL into SHARE_PUBLIC Resource Maps

Address codex comment #1 — making a skill public was blocked on two
hardcoded resource→permission-type maps that didn't know about SKILL:

- api/server/middleware/checkSharePublicAccess.js's
  resourceToPermissionType map was missing ResourceType.SKILL, so
  PUT /api/permissions/skill/:id with { public: true } would fall
  through to the 400 "Unsupported resource type for public sharing"
  path even though PermissionTypes.SKILLS exists and ADMIN has
  SHARE_PUBLIC configured. Added the mapping.
- client/src/hooks/Sharing/useCanSharePublic.ts has an identical
  client-side map used to gate the "Make Public" UI toggle. Without
  the SKILL mapping the hook returned false for everyone, so the
  toggle wouldn't render for skills once the sharing UI lands in
  phase 2. Added the mapping.

Codex comment #2 (create/update cache writes inject skills into
unrelated filtered lists) is invalid — it flags a pattern that
mirrors useUpdatePromptGroup (which the PR description explicitly
cites as the model) and is a deliberate optimistic-update tradeoff.
Trying to match each cache key's embedded filter would couple the
mutation callback to query-key internals, which is exactly what
setQueriesData is designed to avoid. No change there.

* 🧪 feat: Frontmatter Validation, Reserved-Name Fixes, Coaching Warnings

Address the follow-up review notes on the Skills PR. This commit closes
the gap between the wire-type promise and what the backend actually
enforces, tightens the reserved-name rules, and adds a non-blocking
coaching tier for validators.

Frontmatter validation (new):
- Add `validateSkillFrontmatter` in data-schemas/methods/skill.ts with
  strict mode — unknown keys are rejected so expanding the allowed set
  is an intentional code change. Known keys are type-checked against a
  `FrontmatterKind` table derived from Anthropic's Agent Skills spec
  (name, description, when-to-use, allowed-tools, arguments,
  argument-hint, user-invocable, disable-model-invocation, model,
  effort, context, agent, paths, shell, hooks, version, metadata).
- `hooks` and `metadata` get a shallow JSON-safety check (max depth 4,
  max string 2000, max array 100) instead of a full schema, since their
  full shapes live outside this module.
- Wired into BOTH createSkill AND updateSkill so the PATCH path can't
  smuggle invalid frontmatter past the validator.

Validation warning tier (new):
- Add optional `severity: 'error' | 'warning'` to `ValidationIssue`
  (defaults to error). `partitionIssues` splits an issue list into
  blocking errors and non-blocking warnings.
- `createSkill` / `updateSkill` filter on errors for the throw check
  and return warnings in a new `warnings: ValidationIssue[]` field on
  their result objects (`CreateSkillResult` / `UpdateSkillResult`).
- `validateSkillDescription` now emits a `TOO_SHORT` warning for
  descriptions under 20 chars — the primary triggering field, so a
  little coaching goes a long way.
- `createHandler` / `patchHandler` in packages/api surface the warnings
  via a new `attachWarnings` helper that decorates the serialized
  response with a `warnings?: TSkillWarning[]` field.
- `TSkill` gains an optional `warnings?: TSkillWarning[]` field
  documented as "present on POST/PATCH, never on GET".

Reserved-name filter (tightened):
- Replace the substring match (`.includes('anthropic')`) with prefix
  matching on `anthropic-` and `claude-` plus exact-match rejection of
  CLI slash-command collisions (help, clear, compact, model, exit,
  quit, settings, plus the bare `anthropic` / `claude` words). Both
  the pure validator (`methods/skill.ts`) and the Mongoose schema
  validator (`schema/skill.ts`) updated in lockstep; comments on
  each reference the other to prevent drift.
- `research-anthropic-helper` and `about-claude` are now allowed;
  `anthropic-helper`, `claude-bot`, and `settings` are still rejected.

Documentation:
- Add docstrings on `ISkill`, `schema/skill.ts`, and `TSkill` explaining
  the semantics of `name` (Claude-visible identifier, kebab-case,
  stable), `displayTitle` (UI-only cosmetic label, NOT sent to Claude),
  `description` (highest-leverage trigger field), and `source` /
  `sourceMetadata` (reserved for phase 2+ external sync).
- Add a detailed consistency comment on `bumpSkillVersionAndAdjustFileCount`
  explaining that it runs as a separate MongoDB operation from
  upsertSkillFile/deleteSkillFile, so `fileCount` can drift if the
  second op fails — options listed, tradeoff documented, phase 1
  risk window noted as closed because upload is still stubbed.

Tests:
- data-schemas skill.spec.ts: destructure `{ skill, warnings }` from
  createSkill at every call site; add a TOO_SHORT warning test, a
  frontmatter strict-mode test, reserved-prefix tests (including
  positive cases for substring names that should pass), CLI reserved
  word tests, and a full `validateSkillFrontmatter` describe block
  covering unknown keys, type mismatches, and deep-nesting rejection.
- api/server/routes/skills.test.js: bump default test description
  above the 20-char threshold, add a warning-emission test, add
  reserved-prefix + reserved-CLI-word tests, add an unknown-frontmatter-
  key test asserting the 400 response carries `issues` with `UNKNOWN_KEY`.

* 📦 fix: Export CreateSkillResult from data-schemas Methods Index

`CreateSkillResult` was defined in `methods/skill.ts` and consumed by
`packages/api/src/skills/handlers.ts` but never re-exported from the
methods barrel, so the type-check job failed with TS2724
"'@librechat/data-schemas' has no exported member named 'CreateSkillResult'".

Rollup's bundle-mode build picked up the type via its internal resolver,
but the standalone `tsc --noEmit` type-check ran against the package's
public entrypoint and couldn't see it. Added the type import + export
alongside the existing `UpdateSkillResult` export, which fixes the
CI type-check without any runtime change.
* 🎨 feat: Skills UI — Create/Edit/Share/List with Conditional File Tree

First-pass UI on top of the CRUD API scaffolding (#12613). Ships the full
user-facing flow for inline, single-SKILL.md skills and leaves a clean
drop-in for phase-2 multi-file support.

- Create a skill from /skills/new with name (kebab-case, validated),
  description, and SKILL.md body — wired to the real `useCreateSkillMutation`
  and `TCreateSkill` payload.
- List skills in a sidebar (SkillsSidePanel) via `useListSkillsQuery` with
  live search filtering.
- Edit any skill the caller has EDIT permission on — `useUpdateSkillMutation`
  passes `expectedVersion` for optimistic concurrency and surfaces 409
  conflicts as a warning toast + cache refetch.
- Non-blocking `TSkillWarning[]` (e.g. "description too short") are shown
  inline above the form after a successful create/patch.
- Read-only mode when the current user lacks EDIT — the form still renders
  but inputs are marked `readOnly` and the save/reset buttons are hidden.
- Share via ACL using the existing `GenericGrantAccessDialog` — the
  `ShareSkill` button is gated on the SHARE permission.
- Delete with confirmation, driven by `useDeleteSkillMutation({ id })`.
- Conditional file tree: only rendered when `useListSkillFilesQuery`
  returns > 0 files. The tree groups flat `relativePath` strings into a
  nested view (no `react-arborist` dependency) and supports per-file
  deletion via `useDeleteSkillFileMutation`. Upload is intentionally
  deferred — the backend stubs it at 501 in phase 1.

- New routes: `/skills`, `/skills/new`, `/skills/:skillId`.
- Sidebar accordion (`SkillsAccordion` wrapping `SkillsSidePanel`) added
  to `useSideNavLinks` gated on `PermissionTypes.SKILLS` USE.

The initial UI branch (#12580) shipped a lot of exploration code on top of
a now-superseded placeholder backend. Kept as complementary: the `Skills/`
component tree, translation keys, role descriptions, `PublicSharingToggle`
SKILL mapping, `resources.ts` SKILL config, `useCanSharePublic` SKILL
mapping, and `data-provider/roles.ts` `useUpdateSkillPermissionsMutation`.

Deferred out of this first pass:
- Skill favorites (`useSkillFavorites`, `getSkillFavorites` endpoint) —
  the backend route doesn't exist yet; saving for a follow-up.
- AgentConfig `SkillSelectDialog` integration — the UI branch had this
  gated behind `false &&`; rolled back with the config.
- `InvocationMode` / `CategorySelector` / `parseSkillMd` / tree-node
  mutations — not in the Anthropic skill spec and not in the CRUD API.
- `react-arborist` dependency — replaced with a hand-rolled recursive
  tree built from flat `TSkillFile[]`.

- 38 data-schemas skill model tests: pass
- 25 api skill route tests: pass
- 16 user-controller cleanup tests: pass

* 🔐 feat: Default-On Skills in Interface Config and Role Seeder

The skills accordion was registered in the side nav gated on
`PermissionTypes.SKILLS` USE, but no one was actually seeding that
permission on startup, so a fresh install had the USER role with
zero skill permissions and the accordion never rendered.

Fixes three gaps:

1. `interfaceSchema` in data-provider's `config.ts` had no `skills`
   field at all. Added it alongside the existing agents/prompts shape
   (boolean | { use, create, share, public }) and a default of
   `{ use: true, create: true, share: false, public: false }`.

2. `loadDefaultInterface` in data-schemas passed every interface key
   through to the loaded config EXCEPT `skills`. Added the one-line
   passthrough so `appConfig.interfaceConfig.skills` is actually
   populated on boot.

3. `updateInterfacePermissions` in packages/api/src/app/permissions.ts
   seeds role permissions from the interface config on every restart.
   Added:
   - `SKILLS` case to `hasExplicitConfig`
   - `skillsDefaultUse/Create/Share/Public` extraction (mirrors
     prompts/agents)
   - `PermissionTypes.SKILLS` block in `allPermissions` that falls
     through config → roleDefaults → schema default, same pattern as
     AGENTS and PROMPTS
   - `SKILLS` entry in the share-backfill array so that pre-existing
     SKILL role docs missing SHARE/SHARE_PUBLIC get them filled on the
     next restart

Test expectations updated: seven `expectedPermissionsFor(User|Admin)`
blocks in `permissions.spec.ts` now include SKILLS, matching the
role-default values (USER: use+create true, share/public false;
ADMIN: all true).

Result: on a fresh install, a regular USER gets skill USE/CREATE
and the "Skills" accordion shows up in the chat side panel without
any yaml config. Admins can lock it down per role or per tenant via
`interface.skills` in librechat.yaml.

Tests:
- 34 packages/api permissions.spec.ts: pass
- 151 packages/api app tests: pass
- 38 data-schemas skill.spec.ts: pass
- 928 data-provider tests: pass
- 25 api skills.test.js: pass

* ♻️ fix: Resolve Skills UI Review Findings

Addresses the 13 findings from the PR review against the prior commit.

1. **canEdit consistency** — extracted `useSkillPermissions(skill)` as the
   single source of truth for owner/admin/ACL gating. `SkillsView`,
   `SkillForm`, `ShareSkill` all consume it; `SkillFileTree`'s per-file
   delete button now honors admin + EDIT-bit permissions instead of just
   ownership. Unit tests cover owner, admin, editor-ACL, viewer-ACL,
   owner-ACL, loading, and undefined-skill cases.

2. **Disabled submit buttons** — create/edit form submit buttons now set
   native `disabled` (not just `aria-disabled`) during `isLoading`.
   `onSubmit` also guards with an early return when the mutation is still
   in-flight so a duplicate enter-key submit can't create two skills.

3. **Wrong maxLength error message** — description/name `maxLength` rules
   no longer re-use `com_ui_skill_*_required`. Added dedicated
   `com_ui_skill_name_too_long` and `com_ui_skill_description_too_long`
   keys with the literal limit interpolated (`{{0}}`).

4. **Search debouncing** — `SkillsSidePanel` now threads the filter input
   through the existing `useDebounce` hook (250ms) so typing "skills" no
   longer fires six separate list queries.

5. **Frontend test coverage** — added:
   - `tree.test.ts` (9 tests) covering `buildTree` / `nodeKey` edge cases:
     empty input, single root file, multiple roots, nested folders,
     deeply-nested trees, lexicographic sort, empty paths, stable keys
   - `useSkillPermissions.test.ts` (7 tests) covering every precedence
     branch (owner / admin / EDIT / VIEW / owner-ACL / loading / undef)

   Form integration tests proved flaky against react-hook-form's async
   `isValid` with our jest-dom mock setup; deferred to a follow-up PR
   with a proper `@librechat/client` test harness.

6. **Shared `SKILL_NAME_PATTERN`** — promoted the regex plus the four
   length constants (`SKILL_NAME_MAX_LENGTH`,
   `SKILL_DESCRIPTION_MAX_LENGTH`, `SKILL_DESCRIPTION_SHORT_THRESHOLD`,
   `SKILL_DISPLAY_TITLE_MAX_LENGTH`, `SKILL_BODY_MAX_LENGTH`) out of
   `packages/data-schemas/src/methods/skill.ts` and into
   `packages/data-provider/src/types/skills.ts`. The data-schemas
   module now aliases the shared exports so the backend validator and
   the frontend form share one source of truth. Also fixed a latent bug:
   the client regex was stricter than the backend
   (`^[a-z0-9]+(?:-[a-z0-9]+)*$` vs. the real `^[a-z0-9][a-z0-9-]*$`),
   which would have rejected valid names like `foo--bar` client-side.

7. **Removed hardcoded "Claude"** — replaced `com_ui_skill_description_help`
   ("Claude uses this to...") with a new `com_ui_skill_create_subtitle`
   for the form header and `com_ui_skill_description_field_hint`
   ("This is what the model reads to decide...") for the inline hint.
   LibreChat is LLM-agnostic; the old copy misled GPT/Gemini users.

8. **Lifted tree mutation hook** — `useDeleteSkillFileMutation` is now
   instantiated once in `SkillFileTree` (not per `TreeRow`). A
   `TreeContext` provides `onDeleteFile` + `isDeleting` + `canEdit` to
   rows. A 60-node tree used to instantiate 60 mutation hooks; it now
   instantiates one.

9. **List O(n) re-render** — `SkillListItem` no longer reads
   `useParams()` directly. `SkillList` reads the active id once and
   passes `isActive` as a prop, so navigation only re-renders the two
   items whose `isActive` flipped (memo'd), not all N items.

10. **Deduped help text** — the field-level hint and form-level subtitle
    now use different translation keys with distinct copy instead of
    showing the same sentence twice on the same page.

11. **Removed ineffective `useCallback`** — `DeleteSkill.handleDelete`,
    `CreateSkillForm.onSubmit` / `.handleCancel`, `SkillForm.onSubmit`,
    and `SkillFileTree.handleDeleteFile` all wrapped closures around
    React Query `mutation` refs, whose identities change every render.
    Their dep arrays invalidated every render, making the memo a no-op
    with extra overhead. `SkillFileTree` now destructures the stable
    `mutate` function and inlines the arrow inside the memoized
    `contextValue` — one stable reference per deps change.

12. **Import order** — fixed shortest→longest package ordering and
    longest→shortest local ordering across all touched skill files per
    AGENTS.md. `react` always first where imported.

13. **Memoization principle** — documented the rule with inline comments:
    `memo` on components that appear in repeated contexts (`TreeRow`,
    `SkillListItem`) or as children of frequently-re-rendering parents
    (`ShareSkill` / `DeleteSkill` under `SkillForm`'s per-keystroke
    form-state updates). Removed `memo` from `SkillFileTree` since its
    parent `SkillDetailPanel` only re-renders on query-data changes.

- 38 data-schemas skill.spec.ts
- 34 packages/api permissions.spec.ts
- 25 api skills.test.js
- 16 client unit tests (9 buildTree + 7 useSkillPermissions)
- All type-checks + eslint clean on touched files

* 🧹 fix: Skills Duplication, Input Styling, Remove LLM-specific Copy

Three UI fixes from an in-chat review pass:

1. **Sidebar duplication** — `SkillsView` was rendering its own
   `SkillsSidePanel` aside alongside the chat side panel's
   `SkillsAccordion`, so on `/skills` the user saw the skill list
   twice. Fixed by mirroring the `InlinePromptsView` pattern: the
   route content is now just the detail / create panel and the
   chat side panel is the sole list. Added `/skills → /skills/new`
   redirect and a `/skills/new` literal route so `useParams().skillId`
   is `undefined` for "new" (matches prompts).

2. **Name Input styling** — the big floating-label pattern used by
   prompts/agents for the primary name field was replaced with a
   conventional `<Label>` + `<Input>` above it, diverging from the
   rest of the app. Restored the prompts-style `text-2xl` input with
   the peer-focus animated label on both `CreateSkillForm` and
   `SkillForm`. Kept the conventional pattern for description and
   body since they're textareas.

3. **Remove LLM-specific copy from skill translations** — dropped
   `com_ui_skill_description_help` ("Claude uses this to...") and
   the transitional "This is what the model reads..." phrasing.
   Field hint is now a neutral "Be specific about when this skill
   should apply." and the create-page subtitle is a neutral "Author
   a new skill your agents can invoke." LibreChat is LLM-agnostic;
   baking product names into user-facing copy is wrong outside the
   `com_endpoint_anthropic_*` keys where the setting actually only
   applies to Claude models.

Side-effect: the `SkillDetailView` wrapper in `SkillsView` now only
renders the file-tree aside when the skill has > 0 files — same
conditional-tree behavior as before, just scoped to this route
instead of also trying to also render a list sidebar.

- 16 client skill tests still pass
- Type-check + eslint clean on touched files

* 🎁 feat: Restore Skills UI from PR #12580

Brings back everything the original UI PR (#12580, commit da039917c)
shipped that my earlier rebase dropped. Verbatim restores where possible;
adapts the new hooks/types where the backend contract has shifted.

**Scoped-out / gated-off (now restored as inert UI scaffolding):**
- `hooks/useSkillFavorites.ts` + `utils/favoritesError.ts` + the
  `useGetSkillFavoritesQuery` / `useUpdateSkillFavoritesMutation` additions
  in `data-provider/Favorites.ts`. The backend route doesn't exist yet —
  the data-service functions resolve with empty arrays so the Star UI is a
  visual-only no-op until phase 2.
- `dialogs/SkillSelectDialog.tsx` + the "Add Skills" section in
  `SidePanel/Agents/AgentConfig.tsx` (still gated behind the original
  `false &&`) + `skills?: string[]` on `AgentForm` / `Agent` /
  `AgentCreateParams` / `AgentUpdateParams` + the `skills: []` entry in
  `defaultAgentFormValues`.
- `TUserFavorite.skillId` reserved on the shared favorites type.

**Concept-is-gone / deleted-types (restored as UI-only types + stubs):**
- `InvocationMode` enum and `TSkillNode`, `TSkillTreeResponse`,
  `TCreateSkillNodeRequest`, `TUpdateSkillNodeRequest` types in
  `packages/data-provider/src/types.ts`. UI-facing only; the backend flat
  `TSkillFile[]` contract is unchanged.
- `TSkill.invocationMode?: InvocationMode` as an optional field. Forms
  read/write it in local state and deliberately drop it from the PATCH
  payload until the backend column lands.
- `tree/SkillFileTree.tsx` (`react-arborist`-based), `SkillTreeNode.tsx`,
  `TreeToolbar.tsx`, `SkillFileEditor.tsx`, `SkillFilePreview.tsx` — full
  filesystem-style browser UI restored verbatim.
- `data-provider/Skills/tree-queries.ts` + `tree-mutations.ts` hooks
  (`useGetSkillTreeQuery`, `useCreateSkillNodeMutation`, etc.). The
  `data-service` stubs them: `getSkillTree` returns `{ nodes: [] }`,
  `createSkillNode` / `updateSkillNode` / `updateSkillNodeContent` return
  synthetic node shapes, `deleteSkillNode` resolves void. Hooks compile
  and run; tree is empty until phase 2 wires a real backend.
- `MutationKeys.createSkillNode` / `updateSkillNode` / `deleteSkillNode` /
  `updateSkillNodeContent` + `CreateSkillNodeBody` /
  `UpdateSkillNodeVariables` / `DeleteSkillNodeBody` /
  `UpdateSkillNodeContentVariables` types.
- `QueryKeys.skillTree` / `skillNodeContent` / `skillFavorites` /
  `favorites` and the `skillTree()` endpoint helper.

**Scope-simplified (restored with minimal adaptation):**
- `display/SkillDetailHeader.tsx` + `display/SkillDetail.tsx`. Header now
  falls back to `InvocationMode.auto` when `skill.invocationMode` is
  undefined.
- `forms/SkillContentEditor.tsx` — click-to-edit markdown preview toggle
  for the SKILL.md body field. Wired into both `CreateSkillForm` and
  `SkillForm` replacing the plain `<TextareaAutosize>`.
  (Needed `@ts-ignore` on `remarkPlugins` / `rehypePlugins` for the same
  `PluggableList` vs `Pluggable[]` shape drift `MarkdownLite.tsx` already
  works around.)
- `forms/InvocationModePicker.tsx` + `forms/CategorySelector.tsx` — the
  auto/manual/both dropdown and the skill category selector. Wired into
  both forms inside a `FormProvider` so the Controller-based widgets can
  read `useFormContext`. `category` flows to the PATCH / POST payload as
  before; `invocationMode` is UI-only per the type note above.
- `buttons/CreateSkillMenu.tsx` + `utils/parseSkillMd.ts` — dropdown with
  AI / Manual / Upload SKILL.md entries + the YAML frontmatter parser for
  the upload path. `CreateSkillForm.defaultValues` now accepts the parsed
  shape, so the upload → redirect → pre-populated form flow works again.
- `buttons/AdminSettings.tsx` — admin permissions dialog. Uses the
  existing `useUpdateSkillPermissionsMutation` which was already wired.
- `sidebar/FilterSkills.tsx` — restored filter + AdminSettings +
  CreateSkillMenu wrapper. `SkillsSidePanel.tsx` is back to the original
  `FilterSkills`-based layout.
- `lists/SkillList.tsx` + `lists/SkillListItem.tsx` — restored verbatim.
- `layouts/SkillsView.tsx` — restored the full tree + file editor + file
  preview layout. The chat side panel keeps its own accordion list; this
  view is the inline detail experience.
- `hooks/Generic/useUnsavedChangesPrompt.ts` — route-leave guard hook.

- `useGetSkillByIdQuery` is aliased to `useGetSkillQuery` so restored
  components (`SkillsView`, `SkillForm`) that import the old name resolve
  to the new hook.
- `SkillSelectDialog` + `AgentConfig` coerce `skillsData?.skills` instead
  of `.data` (list response shape drift from the CRUD PR).
- `CreateSkillForm` / `SkillForm` wrap their JSX in `FormProvider` so the
  restored `CategorySelector` and `SkillContentEditor` components —
  which read `useFormContext` — work inside the existing forms without
  another refactor.
- `CreateSkillForm.defaultValues` prop accepts `Partial<Values> &
  { invocationMode?: unknown }` so the upload flow's
  `{ name, description, invocationMode }` shape passes through cleanly.
- `SkillsView` route map gains `/skills/:skillId/edit` and
  `/skills/:skillId/file/:nodeId` so the tree-navigation URLs the original
  view produces actually resolve.
- `client/package.json` gains `react-arborist@^3.4.3`.
- ~60 translation keys the restored files reference — invocation labels,
  edit/create page titles, file editor chrome, tree toolbar tooltips,
  favorites, admin allow-settings, unknown-file-type, sr_public_skill,
  delete/rename _var variants — all added to `en/translation.json`.

- Prompts-style floating-label name input — kept from my earlier commit
  so it matches the rest of the app (user reviewed and approved that
  styling). Hidden skill-body textarea is replaced by `SkillContentEditor`
  in both forms.

- 38 data-schemas skill.spec.ts
- 34 packages/api permissions.spec.ts
- 25 api skills.test.js
- 7 client useSkillPermissions.test.ts
- Type-check: pre-existing error count (188) dropped to 120 because my
  restorations fixed some previously-broken field types.

* chore: Update package-lock.json to include react-arborist and memoize-one

* feat: Add support for react-arborist in Vite configuration

This update introduces a new condition in the Vite configuration to handle the 'react-arborist' package, ensuring it is properly recognized during the build process. This change enhances compatibility with the recently added 'react-arborist' dependency in the project.

* 🩹 fix: Hide InvocationMode, Fix SkillContentEditor Click-to-Edit

1. Hide InvocationModePicker from both CreateSkillForm and SkillForm.
   Component stays on disk for when the backend lands the column.

2. Fix "Click to edit" doing nothing on SkillContentEditor. The
   `onBlur={() => setIsEditing(false)}` on the TextareaAutosize was
   racing with `autoFocus` — React renders the textarea, autoFocus
   fires, then a layout/reconciliation blur fires immediately,
   bouncing back to preview mode before the user can interact.
   Removed onBlur; users toggle via the header button or Escape key.

* 🎨 feat: Reader-First Skills UI — Match Claude.ai Layout

Reworks the Skills UI from form-first to reader-first, matching
Claude.ai's skill detail pattern.

**Default view is now read-only.** Clicking a skill in the sidebar
navigates to `/skills/:id` which renders `SkillDetail` — a clean
content view with:
- Skill name as the primary heading
- Metadata row: "Added by" + "Last updated" (formatted date)
- Description block
- Rendered SKILL.md body in a bordered card with a source/rendered
  toggle (eye + code icons, matching Claude.ai's segmented control)

No form fields, no save/cancel buttons. The user reads the skill
first and takes action deliberately.

**Create is now a dialog.** The `/skills/new` route is gone.
`CreateSkillMenu` (the + dropdown in the sidebar) now opens
`CreateSkillDialog` — a minimal modal with name, description, and
instructions fields. Upload-from-file still works: parse → populate
dialog → create. Matches Claude.ai's "Write skill instructions"
modal.

**Edit is behind an action.** The detail view shows an "Edit" button
(permission-gated) that navigates to `/skills/:id/edit`, rendering
the existing `SkillForm`. The edit route is preserved for direct
linking.

**Navigation goes to detail, not edit.** `SkillListItem` now
navigates to `/skills/:id` (detail) instead of `/skills/:id/edit`.

- `display/SkillMarkdownRenderer.tsx` — shared ReactMarkdown
  component extracted from `SkillContentEditor`. Same remark/rehype
  plugins, no form dependency.
- `display/SkillDetail.tsx` — the reader-first view (replaces the
  old thin wrapper).
- `dialogs/CreateSkillDialog.tsx` — OGDialog modal for skill
  creation.

- `layouts/SkillsView.tsx` — gutted and rebuilt. Three states:
  no-skill (empty state), skillId (SkillDetail), skillId+edit
  (SkillForm). Removed full-page CreateSkillForm, removed TreeView.
- `buttons/CreateSkillMenu.tsx` — opens dialog instead of navigating
  to `/skills/new`. Upload flow: parse → set dialog defaults → open.
- `lists/SkillListItem.tsx` — navigate to detail, not edit.
- `routes/index.tsx` — removed `/skills/new` and file/nodeId routes;
  `/skills` renders SkillsView directly (empty state).
- `display/index.ts`, `dialogs/index.ts` — added new exports.
- `locales/en/translation.json` — added ~10 new keys for metadata,
  toggle labels, dialog title, empty state.

* 🩹 fix: SkillContentEditor click-to-edit z-index — button was z-0 behind rendered content

* 🩹 fix: Align Edit button size with Share/Delete (size-9)

* 🎨 feat: Claude.ai-Style Skill List Panel

Rewrites the skills sidebar to match Claude.ai's panel layout:

- Header: "Skills" title + search icon (toggles input) + add icon
  (opens CreateSkillDialog directly, no dropdown menu)
- Collapsible "Skills" section with chevron toggle
- Skill items: 24px icon badge (rounded square with ScrollText icon)
  + name only. No description text in the list — that lives in the
  detail view. Active item gets highlighted bg + bold font.
- Removed AdminSettings button from sidebar header — admin config
  is accessible via the admin dashboard, not cluttering every user's
  skill list.
- Removed FilterSkills wrapper (was Filter + AdminSettings +
  CreateSkillMenu). The search + create are now inline in the panel
  header.

Files changed:
- sidebar/SkillsSidePanel.tsx — full rewrite
- sidebar/SkillsAccordion.tsx — simplified wrapper
- lists/SkillList.tsx — collapsible section, no description
- lists/SkillListItem.tsx — icon badge + name, memo'd

* 🎨 fix: Align Skills UI Styling with Prompts Patterns

Style alignment pass based on direct comparison with claude.ai and
the existing prompts preview dialog.

SkillsSidePanel search now replaces the title in the header row when
toggled (search icon + input + X close), matching Claude.ai's pattern.
Previously it pushed a separate input below the header, wasting
vertical space. Close button clears the search term.

Replaced `text-text-tertiary` with `text-text-secondary` across
SkillDetail, SkillList, SkillForm, CreateSkillForm, CreateSkillDialog,
SkillContentEditor. Tertiary was too dark / low contrast.

SkillList section chevron label now reads "Personal skills" (matching
Claude.ai) via the existing `com_ui_my_skills` key, instead of the
generic "Skills" which duplicated the header.

Aligned with `PromptDetailHeader` styling:
- 48px round icon (ScrollText in bg-surface-secondary circle)
- Name + public badge in the icon row
- Metadata below the icon: User icon + author, Calendar icon + date
  (text-xs text-text-secondary with gap-3, matching prompts exactly)
- Description uses the same label-above-text pattern as prompts
- Content card uses `bg-transparent` border (not bg-surface-primary-alt)
- Toggle buttons use size-5 icons and text-text-secondary for inactive

Changed from `max-w-lg p-0` to `max-w-5xl` with the same max-height
and padding pattern as the prompts PreviewPrompt dialog:
`max-h-[80vh] p-1 sm:p-2 gap-3 sm:gap-4`. Close button now renders
via default OGDialogContent behavior (removed showCloseButton=false).

* 🩹 fix: SkillDetail fills parent height, tighter spacing (px-6 pb-6 gap-2)

* 🩹 fix: Align Skills panel header padding (px-4) with list content below

* 🩹 fix: Reduce Skills header top padding (pt-2) to align with sidebar icon strip

* 🩹 fix: Tighten Skills header (py-2) and detail top (py-2) to align with sidebar icons and match edit view

* 🩹 fix: Offset SidePanel Nav pt-2 with -mt-2 on SkillsAccordion so Skills header aligns with icon strip

* 🛠️ fix: Increase Node memory limit for production build in package.json

* 🩹 fix: Remove top padding from SkillDetail header row (py-2 → pb-2)

* 🏗️ refactor: Move pt-2 from SidePanel/Nav wrapper to each panel

Removed the global `pt-2` from `SidePanel/Nav.tsx` and pushed it
into each panel's own top-level wrapper. This lets each panel own
its vertical alignment independently — Skills can sit flush at the
top to align with the sidebar icon strip, while other panels keep
their original spacing.

Panels updated with `pt-2`:
- PromptsAccordion (via className on PromptSidePanel)
- BookmarkPanel
- FilesPanel
- MemoryPanel
- MCPBuilderPanel
- AgentPanel (form wrapper)
- AssistantPanel (form wrapper)
- ParametersPanel (already had pt-2)

SkillsAccordion: removed the -mt-2 hack, now naturally flush.

* 🧹 fix: Align CreateSkillDialog field styling + remove 19 unused i18n keys

Dialog fields: all three inputs now use consistent `rounded-xl
border-border-medium px-3 py-2 text-sm` styling. Replaced the
`<Input>` component with a plain `<input>` to avoid the component's
built-in `rounded-lg border-border-light` overriding the dialog's
border style. Labels use `font-medium` for consistency.

Removed 19 unused translation keys from translation.json:
com_ui_skill_body, com_ui_skill_body_placeholder,
com_ui_skill_create_subtitle, com_ui_skill_file_delete_confirm,
com_ui_skill_file_delete_error, com_ui_skill_file_deleted,
com_ui_skill_files_empty, com_ui_skill_files_multi_hint,
com_ui_skill_list, com_ui_skill_load_error,
com_ui_skill_resize_file_tree, com_ui_skill_select_file,
com_ui_skill_select_file_desc, com_ui_skills_load_error,
com_ui_add_first_skill, com_ui_create_skill_page,
com_ui_edit_skill_page, com_ui_save_skill, com_ui_no_skills_title

* 🎁 feat: Upload Skill Dialog + Simplified Create Menu

New `UploadSkillDialog` matching Claude.ai's upload modal:
- Dashed drop zone with drag-and-drop support
- Accepts .md, .zip, .skill files
- Phase 1: processes .md files (parses YAML frontmatter → creates
  skill with body as the full file content)
- Shows file requirements below the drop zone
- On success: navigates to the new skill's detail view

`CreateSkillMenu` now has two flat options (no sub-menu):
- "Write skill instructions" → opens `CreateSkillDialog`
- "Upload a skill" → opens `UploadSkillDialog`

Removed the disabled "Create with AI" option and the old file input
hidden-element approach. The sidebar `+` button now renders
`CreateSkillMenu` directly instead of a standalone create dialog.

- Removed 5 unused i18n keys (com_ui_skill_added_by,
  com_ui_skill_last_updated, com_ui_skills_add_first,
  com_ui_skills_filter_placeholder, com_ui_skills_new)
- Tightened metadata gap in SkillDetail (mt-1 → mt-0.5)
- Added 7 new upload-related i18n keys

* 🔒 feat: Zip/Skill File Upload Support with Safety Limits

Rewrites UploadSkillDialog to properly handle all three accepted
file types:

- `.md` — reads as text, parses YAML frontmatter, creates skill
- `.zip` / `.skill` — reads as ArrayBuffer, extracts with JSZip,
  finds SKILL.md (at root or one level deep), parses its content,
  creates skill. Shows spinner during processing.

Security guards against zip bombs:
- MAX_ZIP_SIZE: 50MB compressed file limit
- MAX_ENTRIES: 500 file limit inside the archive
- Path traversal rejection: skips entries with `..` or leading `/`
- SKILL.md search limited to depth ≤ 2 segments

Added `jszip@^3.10.1` to client dependencies (already in the
monorepo's node_modules from backend usage).

The name is inferred from the zip filename if SKILL.md frontmatter
doesn't have one (e.g. `skills-autofix.zip` → `skills-autofix`).

* 🚀 feat: Backend Skill Import + Live File Upload Endpoints

New endpoint that accepts a single multipart file (.md, .zip, .skill)
and creates a skill with all its files in one request:

- **.md**: parse YAML frontmatter → create skill with body
- **.zip / .skill**: extract with JSZip, find SKILL.md (root or one
  level deep), create skill from its content, then persist every
  additional file via `upsertSkillFile` + local file storage strategy.
  Returns the created skill + an `_importSummary` with per-file
  results.

Security:
- 50MB compressed file size limit (multer)
- 500 max entries in archive
- 10MB per individual file
- Path traversal rejection (no `..`, no absolute, validated charset)
- File type filter: only .md/.zip/.skill accepted
- Rate limited via existing `fileUploadIpLimiter` + `fileUploadUserLimiter`

Handler lives in `packages/api/src/skills/import.ts` with injectable
deps (`createSkill`, `upsertSkillFile`, `saveBuffer`) for testability.

Replaced the 501 stub with a real handler:
- Accepts multipart FormData with `file` + `relativePath`
- Saves file via local storage strategy
- Calls `upsertSkillFile` to persist the SkillFile record
- Returns the upserted document
- Rate limited, ACL-gated (EDIT permission required)
- 10MB per file limit

`UploadSkillDialog` now sends the file to `/api/skills/import` via
`dataService.importSkill(formData)` — no more client-side JSZip.
Removed `jszip` from client dependencies (only backend needs it).

Added `importSkill()` in data-service + `importSkill()` endpoint
builder in api-endpoints.

Updated the file upload test from expecting 501 stub to expecting
400 "no file provided" (live validation). All 25 skill route tests
pass.

* 🔒 fix: Complete Import Handler — Validation, Ownership, Error Surfacing

Fixes several gaps in the skill import flow:

1. **Skill validation now runs and surfaces properly.** The import
   handler calls the real `createSkill(CreateSkillInput)` which runs
   `validateSkillName`, `validateSkillDescription`, `validateSkillBody`.
   Validation errors (SKILL_VALIDATION_FAILED) are caught and returned
   as 400 with the issue messages. Duplicate-key errors return 409.
   Previously all errors were swallowed into a generic 500.

2. **`authorName` is now populated.** The `CreateSkillInput` requires
   `authorName` which was missing — resolved from `req.user.name ??
   req.user.username ?? 'Unknown'`, matching the existing create handler.

3. **SKILL_OWNER permission is granted after import.** Calls
   `grantPermission` with `AccessRoleIds.SKILL_OWNER` so the uploader
   can edit/delete/share the imported skill. This was entirely missing —
   imported skills would have been ownerless.

4. **`tenantId` propagated.** Both the skill and each SkillFile record
   receive `req.user.tenantId` for multi-tenant deployments.

5. **SkillFile records are created in the DB.** Each non-SKILL.md file
   in the zip is saved to file storage via `saveBuffer` and recorded
   via `upsertSkillFile`, which validates the relativePath, infers the
   category from the path prefix, and atomically bumps the skill's
   `fileCount` and `version`.

Import deps now include `grantPermission` from PermissionService,
injected in `api/server/routes/skills.js`.

* 🐛 fix: Import grant uses accessRoleId (not roleId) — fixes skill not appearing in list

* 🎨 fix: Cache invalidation, file tree, frontmatter rendering

Three fixes for the skill detail view:

1. **Cache invalidation after import.** UploadSkillDialog now calls
   `queryClient.invalidateQueries([QueryKeys.skills])` after a
   successful import so the sidebar list picks up the new skill
   without requiring a page refresh.

2. **File tree in detail view.** When a skill has `fileCount > 0`,
   the detail view now queries `useListSkillFilesQuery` and renders
   a file list below the body card — SKILL.md first, then folders
   and root files. Icons: Folder for directories, FileText for files.

3. **Frontmatter stripped and rendered as metadata.** YAML frontmatter
   (`---\nversion: 0.1.0\ntriggers: ...\n---`) is now parsed out of
   the body before markdown rendering. The `name` and `description`
   fields are skipped (already shown in the header). Remaining fields
   (version, triggers, dependencies, etc.) are displayed in a
   Claude.ai–style grid: label on the left, value on the right,
   above the rendered markdown content. Source view still shows the
   full raw body including frontmatter.

* 🩹 fix: Always fetch skill files — fileCount may be stale in cached skill object

* 🌳 feat: Inline File Tree in Sidebar Skill List

Moves the file tree from the bottom of SkillDetail into the sidebar
list, matching Claude.ai's pattern:

- Multi-file skills show a chevron toggle on the right side of the
  skill list item
- Clicking the chevron expands an inline file tree below the skill
  name: SKILL.md first, then folders (with folder icon + right
  chevron) and root files
- File list is fetched lazily (only when expanded) via
  useListSkillFilesQuery
- Clicking a file navigates to the skill detail view
- Files section removed from SkillDetail — the sidebar is now the
  sole file tree location, keeping the detail panel clean

SkillDetail cleaned up: removed groupFiles helper, file-related
state, useListSkillFilesQuery import, FileText/Folder icon imports.

* 🌲 feat: Virtualized inline file tree with react-vtree

Replace hand-rolled recursive FolderRow/FileRow buttons with a proper
virtualized FixedSizeTree from react-vtree for the sidebar skill list.
Dynamic height tracks open folders; capped at 350px with smooth
expand/collapse transitions.

* chore: Remove no longer used SkillFileTree and SkillTreeNode components

* chore: Update Vite config to replace 'react-arborist' with 'react-vtree' for module resolution

* feat: Skill file content viewing with lazy DB caching

- Add `skills` field to `fileStrategiesSchema` so operators can
  configure a dedicated storage backend for skill files. Falls back
  by type (image/document) when unset.
- Fix hardcoded `FileSources.local` in skill save/import — now uses
  the resolved strategy via `getFileStrategy(req.config, { context })`.
- Replace 501 download stub with real handler that streams from any
  storage backend and returns JSON `{ content, mimeType, isBinary }`.
- Binary detection (null-byte + non-printable ratio on first 8 KB)
  flags files on first read so they're never re-fetched.
- Text content ≤ 512 KB is cached in the SkillFile MongoDB document;
  subsequent reads skip storage entirely.
- Clicking a skill row now expands inline files (not just chevron).
- Clicking a file navigates to `?file=<path>` and renders content
  in a new SkillFileViewer (markdown, code, images, binary placeholder).

* chore: Remove react-window and its type definitions from package.json and package-lock.json

- Deleted `react-window` and `@types/react-window` dependencies from both `package.json` and `package-lock.json` to streamline the project and reduce unnecessary bloat.

* fix: Build errors — remove endpoints import, fix Uint8Array cast

- Replace `import { endpoints }` (not public) with inline URL in
  SkillFileViewer
- Remove `as Uint8Array` cast in stream chunk handling
- Extend getSkillFileByPath return type with content/isBinary to
  decouple from data-schemas build artifact resolution

* chore: Remove 8 unused i18next keys

com_ui_create_skill_ai, com_ui_create_skill_manual,
com_ui_delete_folder_confirm_var, com_ui_delete_skill,
com_ui_delete_skill_confirm_var, com_ui_delete_var,
com_ui_rename_var, com_ui_skill_files

* fix: Add configMiddleware to skills router, handle SKILL.md in viewer

- Add configMiddleware to skills router so req.config is populated
  when getLocalFileStream (or any strategy) reads file paths.
- Handle SKILL.md in download handler — serves skill.body directly
  from the Skill document instead of looking for a SkillFile record.
- Clicking SKILL.md in sidebar tree now opens the file viewer
  (matching Claude.ai behavior: file view vs default detail view).

* ci: Run unit tests on PRs to any branch

Remove the branches filter from both test workflows so contributor
PRs targeting feature branches (not just main/dev) get CI coverage.
Path filters are kept so tests only run when relevant files change.

* fix: Update skills route tests for download handler changes

- Mock configMiddleware (sets req.config for file storage access)
- Mock getStrategyFunctions and getFileStrategy (storage strategy deps)
- Replace 501 stub test with SKILL.md content test + 404 test

* fix: Auto-expand files, frontmatter parsing, select-none, prefetch

- Auto-expand file tree when navigating directly to a skill URL
- Prefetch files for the active skill (eliminates first-expand lag)
- Fix frontmatter parser to handle multi-line YAML list values
  (triggers field was missing because it uses list syntax)
- SkillFileViewer now parses frontmatter for .md files — shows
  structured grid + rendered body (matching SkillDetail's display)
  with source/rendered toggle
- Add select-none to all sidebar skill and file tree buttons

* refactor: Derive expanded state from isActive instead of useEffect

Replace useEffect sync with deterministic derivation:
expanded = hasFiles && (isActive || !collapsed)

Active skill is always open. collapsed is a manual toggle that
only takes effect on non-active items.

* fix: Remove empty space above body card — overlay view toggle

Move the rendered/source toggle from a dedicated row (40px of empty
space) to an absolute-positioned overlay in the card's top-right
corner, matching Claude.ai's layout.

* fix: Remove header bars from content editors — overlay action buttons

Collapse the full-width header bars ("Skill Content", "Text") in
SkillContentEditor, PromptTextCard, and PromptEditor. Action buttons
(edit/save toggle, copy, variables) are now absolute-positioned in
the card's top-right corner, reclaiming ~46px of vertical space.

* fix: Spinner visibility in file viewer — use text-text-secondary

* fix: Address review findings — security, correctness, code quality

Codex P1: Use $unset instead of undefined to clear cached content
and isBinary fields on file re-upload (Mongoose strips undefined).

Codex P2: Match skill-file validation errors by error.code instead
of error.message substring.

F1: Zip bomb defense — track cumulative decompressed bytes (500 MB
cap), check declared uncompressed size before buffering each entry.

F2: Remove misleading "atomically" from import handler JSDoc.

F3: Static import for isBinaryBuffer instead of dynamic import().

F4: Replace console.error with logger in upload handler.

F6: Add multer error handler middleware to skills router.

F7: Move React import to top of SkillDetail.tsx.

F9: Fix variable shadowing (trimmed → item) in parseFrontmatter.

F11: Replace JSON.parse(JSON.stringify()) with toJSON() for
Mongoose document serialization.

F12: Remove dead dynamic import('fs') fallback (memoryStorage
always provides file.buffer).

F13: Hoist MIME_MAP to module scope to avoid per-call allocation.

F16: Share single multer.memoryStorage() instance.

* fix: Follow-up review — close zip bomb gap, fix error handler

F1: Add post-decompression cumulative byte check with break (the
pre-decompression check relies on undocumented JSZip internals
that may be absent; this closes the gap unconditionally).

F2+F3: Multer error handler now forwards non-multer errors via
next(err) instead of swallowing them. Also catches file filter
rejections (plain Error, not MulterError) by message prefix.

F4: Move isBinaryBuffer import to local imports section per
CLAUDE.md import order rules.

F5: Simplify dead toJSON branch — createSkill returns a POJO.

* nit: Link filter error message to handler prefix check

* feat: Accordion expansion + active file highlight in sidebar

- Only one skill's file tree can be expanded at a time (accordion).
  Expansion state lifted from SkillListItem to SkillList.
- Selected file gets bg-surface-active highlight in the tree.
  Skill row uses subtle style (no background) when a file is active,
  matching Claude.ai's pattern where the file — not the skill —
  carries the selection state.

* style: Adjust margin for file tree in SkillListItem component

- Reduced left margin from 10 to 5 for improved layout consistency in the file tree display.

* fix: TS error on FileTreeNode, nested ternary, chevron collapse

- Make style prop optional to match react-vtree's NodeComponentProps
- Flatten nested ternary for skill row active styles
- Skill row click expands (but doesn't collapse) files + navigates
- Chevron click explicitly toggles collapse (matching Claude.ai
  where clicking the chevron is how you collapse files)

* fix: Upload basePath, reject SKILL.md uploads, add skills permission route

- Pass basePath: 'uploads' in per-file upload handler (was defaulting
  to 'images' path, inconsistent with the import flow).
- Reject uploads targeting SKILL.md (reserved path — download handler
  special-cases it to return skill.body, making an uploaded file
  unreachable via the API).
- Add skills entry to roles router permissionConfigs so PUT
  /api/roles/:roleName/skills actually reaches a handler instead
  of returning 404.

* feat: Expand content area, move controls to header, reduce padding

Default detail view:
- Remove rounded-xl bordered card wrapper — content flows directly
  into the article, capitalizing on full screen width
- Move eye/code toggle inline with the divider row
- Reduce px-6/pb-6 to px-4/pb-4

File viewer:
- Move eye/code toggle from card overlay to the header bar
- Add copy-to-clipboard button for text files in the header bar
- Remove rounded-xl bordered card wrapper for markdown content
- Remove bordered pre wrapper for non-markdown text
- Reduce px-6/py-4 to px-4/py-3

Both views maximize content space over decorative chrome.

* fix: Stable header height, restore some padding

- Fix layout shift in file viewer header: use fixed h-10 so the
  bar height stays constant whether the eye/code toggle renders
  (markdown) or not (plain text).
- Bump content padding from px-4/py-3 back to px-5/py-4 in both
  views — the previous reduction was too aggressive.

* fix: Grant rollback, path validation, error format, dead code cleanup

F2: grantOwnership now rolls back (compensating delete) on failure,
matching the create handler. Both markdown and zip import paths
check the result and return 500 on grant failure.

F4: Upload handler validates relativePath with regex + traversal
check before calling downstream upsertSkillFile.

F5: Document JSZip _data.uncompressedSize as best-effort; the
post-decompression cumulative check is the real safety net.

F10: Standardize all upload handler error responses to { error }
(was { message }, inconsistent with handlers.ts).

F13: Single-pass fileResults accumulation in import handler.

F1-5: Remove dead uploadFileStubHandler (no route references it).

Codex P2: Fix delete nav from /skills/new to /skills.

F12: Use cn() in UploadSkillDialog instead of template literals.

* perf: Stream-first binary detection + O(1) public skill check

F1: Download handler now reads only the first 8 KB for binary
detection. If binary, the stream is destroyed immediately without
buffering the remaining file. Text files continue reading for
caching. Eliminates buffering up to 10 MB per request for binary
files under concurrent load.

F7: Single-skill GET and PATCH now use hasPublicPermission (O(1)
ACL lookup) instead of getPublicSkillIdSet (queries ALL public
skill IDs). The list handler still uses the Set approach since it
serializes multiple skills. serializeSkill/serializeSkillSummary
now accept boolean | Set for flexibility.

* fix: Update test to match { error } response format

* fix: Critical stream truncation bug, grantedBy, error format

NF-1 (CRITICAL): Rewrite binary detection to single for-await loop.
Breaking out of for-await-of destroys the stream via iterator.return(),
so the previous two-loop approach silently truncated text files > 8KB.
Now: one loop collects chunks, checks binary after 8KB accumulated,
and either destroys+returns (binary) or continues reading (text).

NF-2: Add grantedBy to import handler's grantPermission call and
interface (was missing, inconsistent with create handler).

NF-3: Standardize all import handler error responses from { message }
to { error }, matching handlers.ts convention. Update client's
UploadSkillDialog to read response.data.error accordingly.

* fix: Prefer specific validation message over generic error field

* fix: YAML quote stripping, saveBuffer null guard, dot segment rejection

- Strip surrounding YAML quotes from frontmatter values so
  name: "my-skill" parses as my-skill (not "my-skill" with quotes
  that fails the name validator).
- Guard resolveSkillStorage against backends with saveBuffer: null
  (e.g. OpenAI/vector strategies) — throws a descriptive error
  caught by the handler's try/catch instead of a TypeError.
- Tighten upload path validation to reject . segments (e.g.
  docs/./a.md) matching the model-layer validator, preventing
  storage writes for paths the DB will reject.

* fix: Orphan cleanup, stream errors, malformed zip, cache latency

F1: Upload handler now deletes the stored blob if the subsequent
DB upsert fails, preventing orphaned files on disk/cloud.

F2: Multer error handler returns { error } (was { message }).

F3: Wrap JSZip.loadAsync in try/catch — malformed zip returns 400
instead of falling through to 500.

F4: Raw download stream gets an error handler — logs the error and
destroys the response if headers were already sent.

F8: Strip leading hyphens from inferred skill name so filenames
like _my-skill.zip don't produce -my-skill (invalid name pattern).

F9: Fire-and-forget all updateSkillFileContent cache writes so the
response is sent immediately. Cache failures are logged but don't
block or fail the read.

* fix: Import orphan cleanup + Content-Disposition sanitization

Finding A: Add deleteFile dep to ImportSkillDeps. The per-file loop
in handleZip now cleans up stored blobs when upsertSkillFile fails,
closing the second half of the F1 orphan fix (upload handler was
already fixed).

Finding B: Sanitize filename in Content-Disposition header for raw
downloads — strip quotes, backslashes, and newlines to prevent
header injection from user-uploaded filenames.

* security: Prevent stored XSS via raw file downloads

Non-image files served via ?raw=true now use Content-Disposition:
attachment (force download) instead of inline. An uploaded .html or
.svg file served inline from the LibreChat origin could execute
scripts with access to the user's session — this closes that vector.

Images stay inline (needed for <img> rendering in SkillFileViewer).
X-Content-Type-Options: nosniff added to prevent MIME sniffing.

* security: Block SVG XSS — allowlist safe raster MIME types for inline

SVG (image/svg+xml) passed the startsWith('image/') check and was
served inline, but SVG is a scriptable format — embedded <script>
tags execute in the LibreChat origin. Replace the prefix match with
a Set of safe raster-only MIME types (png, jpeg, gif, webp, avif,
bmp). SVGs and any future scriptable image/* subtypes now get
Content-Disposition: attachment (forced download).

* fix: Cap JSON text response at 1MB, consistent md name inference

F3: Text files > 1MB now return { isBinary: false } with no content
field, forcing the client to use ?raw=true for download. Prevents
buffering 10MB files into heap for JSON serialization. Frontend
shows a download fallback when content is absent.

F4: handleMarkdown now infers skill name from filename (same as
handleZip) when frontmatter has no name, instead of rejecting
with 400. Consistent behavior across import paths.

F1 (reviewer concern): upsertSkillFile is NOT affected — it uses
{ new: false } for insert-vs-replace detection but does a follow-up
findOne (lines 855-859) to return the post-upsert document.

* fix: deleteFile arg shape, raw URL base path, hoist SAFE_INLINE_MIMES

Codex P2: deleteFile expects { filepath } object, not a raw string.
Both upload handler cleanup and import handler cleanup now pass
{ filepath } to match the strategy contract (deleteLocalFile,
deleteFileFromS3 all expect a file object).

Codex P2: Raw download URL in SkillFileViewer now uses apiBaseUrl
prefix so subpath deployments (/chat, etc.) resolve correctly.

NIT: Hoist SAFE_INLINE_MIMES Set to factory scope — was re-allocated
per raw download request inside the if block.

* fix: Remove inert cache write for large text files, localize aria-label

N2: The { isBinary: false } cache write for text files > 1MB had no
effect — subsequent requests still fell through to stream read since
neither isBinary nor content provided a fast-path short-circuit.
Removed the pointless DB updateOne per request.

N4: Replace hardcoded "Back to skill" aria-label with localize().

* refactor: Extract shared parseFrontmatter, widen deleteFile type

N3: Extract parseFrontmatter into Skills/utils/frontmatter.ts —
single implementation shared by SkillDetail and SkillFileViewer.
Accepts optional skipKeys set so callers control which frontmatter
fields are excluded (SkillDetail skips name/description since
they're shown in the header; other .md files show all fields).

N5: Widen ImportSkillDeps.deleteFile file param from { filepath }
to { filepath; [key: string]: unknown } to signal extensibility
if strategies start accessing additional file properties.

* fix: Advance i past list items for skipped keys, DRY parseSkillMd

Finding A: parseFrontmatter now consumes multi-line YAML list items
before checking skipKeys — prevents list lines from leaking into
subsequent key parsing as spurious fields.

Finding B: parseSkillMd now delegates to the shared parseFrontmatter
instead of re-implementing the same frontmatter scanning loop.
Reduces client-side parseFrontmatter implementations from 3 to 1.

* fix: Call apiBaseUrl(), delete storage blob on file removal

- apiBaseUrl is a function, not a string — call it in the template
  literal so raw download URLs resolve correctly.
- deleteFileHandler now looks up the file record before deleting,
  then fire-and-forget deletes the storage blob via the strategy's
  deleteFile. Previously only the DB record was removed, leaving
  orphaned blobs in local/S3/Firebase/Azure storage.

* fix: Clean up storage blobs when deleting an entire skill

deleteHandler now lists all files for the skill before calling
deleteSkill, then fire-and-forget deletes each blob via the
storage strategy. Previously only per-file deletion cleaned up
blobs — deleting a whole skill left all associated files orphaned
in local/S3/Firebase/Azure storage.

* refactor: useImportSkillMutation hook, fix TSkill[] unsafe cast

- Create useImportSkillMutation in mutations.ts + ImportSkillOptions
  type. UploadSkillDialog now uses the mutation hook instead of
  calling dataService.importSkill directly with manual useState
  loading management. Eliminates unmounted-component state update
  risk and aligns with the React Query mutation pattern used by
  every other mutation in the codebase.

- SkillSelectDialog: replace as unknown as TSkill[] with proper
  TSkillSummary typing. SkillCard props updated to TSkillSummary.
  The dialog only uses summary-level fields (name, description,
  category, author) — the cast was hiding a type mismatch.

* fix: Use saved source for import cleanup, delete old blob on replace

Codex P2: Import cleanup now uses file.source (the backend the file
was actually saved to) instead of re-resolving from config. In mixed
strategy setups, the previous approach could target the wrong backend.

Codex P2: When re-uploading a file to an existing relativePath, the
old blob is now deleted after successful upsert. Previously only the
DB record was replaced, leaving the old storage object orphaned.

* fix: Register PUT /:roleName/skills route in roles router

* fix: Re-read skill after zip file processing for fresh metadata

The import response was built from the skill object created before
the file loop, but each upsertSkillFile bumps version and fileCount.
Clients caching the stale response would get 409 conflicts on first
edit and see incorrect file counts.

Now re-reads the skill via getSkillById after the loop so the
response reflects the current version, fileCount, and updatedAt.

* fix: Size-check SKILL.md before decompression, don't gate on fileCount

P1: SKILL.md was decompressed before any size accounting. A crafted
archive could expand SKILL.md past 10MB before validation ran. Now
checks declared size pre-decompression and actual size post, both
against MAX_SINGLE_FILE_BYTES.

P2: File list query was gated on cached fileCount which can be stale
after mutations. Now fetches files for the active skill regardless
of fileCount. hasFiles derived from fetched data with fileCount as
fallback, so newly uploaded files appear without hard refresh.

* fix: Move files declaration before hasFiles to avoid TDZ error

* security: Stream-decompress zip entries with enforced byte cap

Replace zipEntry.async('nodebuffer') (buffers entire entry before
checking limits) with zipEntry.nodeStream('nodebuffer') piped
through a byte counter that destroys the stream when the per-file
or cumulative limit is exceeded.

Previously, when JSZip's _data.uncompressedSize was absent (the
common case), a high-ratio entry could allocate hundreds of MB
before the post-decompression check caught it. Now decompression
is aborted mid-stream at the exact byte threshold — no entry can
exceed its limit regardless of compression ratio.

* refactor: Reorganize access check for prompts in useSideNavLinks hook

Moved the prompts access check to a new position in the code to improve readability and maintainability. This change ensures that the prompts link is added to the navigation only if the user has the appropriate access, without altering the existing functionality.

---------

Co-authored-by: Danny Avila <danny@librechat.ai>
…riming (#12649)

* feat: Skill runtime integration — catalog injection, tool registration, execute handler

Wires the @librechat/agents SkillTool primitive into LibreChat's agent runtime:

**Enums:**
- Add `skills` to AgentCapabilities + defaultAgentCapabilities

**Data layer:**
- Add `getSkillByName(name, accessibleIds)` — compound query that
  combines name lookup + ACL check in one findOne

**Agent initialization (packages/api/src/agents/initialize.ts):**
- Accept `accessibleSkillIds` param and `listSkillsByAccess` db method
- Query accessible skills, format catalog via `formatSkillCatalog()`,
  append to `additional_instructions` (appears in agent system prompt)
- Register `SkillToolDefinition` + `createSkillTool()` when catalog
  is non-empty (tool appears in model's tool list)
- Store `accessibleSkillIds` and `skillCount` on InitializedAgent

**Execute handler (packages/api/src/agents/handlers.ts):**
- Add `getSkillByName` to `ToolExecuteOptions`
- `handleSkillToolCall()` intercepts `Constants.SKILL_TOOL`:
  extracts skillName, loads body from DB with ACL check,
  substitutes $ARGUMENTS, returns ToolExecuteResult with
  injectedMessages (skill body as isMeta user message)

**Caller wiring:**
- initialize.js: query skill IDs via findAccessibleResources,
  pass to initializeAgent + store on agentToolContexts,
  add getSkillByName to toolExecuteOptions,
  pass accessibleSkillIds through loadTools configurable
- openai.js + responses.js: same pattern for their flows

Requires @librechat/agents >= 3.1.65 (PR #91 exports).

* feat: Skills toggle in tools menu + backend capability gating

Frontend:
- Add skills?: boolean to TEphemeralAgent type
- Add LAST_SKILLS_TOGGLE_ to LocalStorageKeys for persistence
- Add skillsEnabled to useAgentCapabilities hook
- Add skills useToolToggle to BadgeRowContext with localStorage init
- New Skills.tsx badge component (Scroll icon, cyan theme,
  permission-gated via PermissionTypes.SKILLS)
- Add skills entry to ToolsDropdown with toggle + pin
- Render Skills badge in BadgeRow ephemeral section

Backend:
- Extract injectSkillCatalog() into packages/api/src/agents/skills.ts
  (reduces initializeAgent module size, reusable helper)
- initializeAgent delegates to helper instead of inline block
- Capability-gate the findAccessibleResources query:
  - Agents endpoint: checks AgentCapabilities.skills in admin config
  - OpenAI/Responses controllers: checks ephemeralAgent.skills toggle
- ACL query runs once per run, result shared across all agents

* refactor: remove createSkillTool() instance from injectSkillCatalog

SkillTool is event-driven only. The tool definition in toolDefinitions
is sufficient for the LLM to see the tool schema. No tool instance is
needed since the host handler intercepts via ON_TOOL_EXECUTE before
tool.invoke() is ever called.

Removes tools from InjectSkillCatalogParams/Result, drops the
createSkillTool import.

* feat: skill file priming, bash tool, and invoked skills state

Multi-file skill support:
- New primeSkillFiles() helper (packages/api/src/agents/skillFiles.ts)
  uploads skill files + SKILL.md body to code execution environment
- handleSkillToolCall primes files on invocation when skill.fileCount > 0,
  returns session info as artifact so ToolNode stores the session
- Skill-primed files available to subsequent bash/code tool calls

Bash tool auto-registration:
- BashExecutionToolDefinition added alongside SkillToolDefinition when
  skills are enabled, giving the model a bash tool for running scripts

Conversation state:
- Add invokedSkillIds field to conversation schema (Mongoose + Zod)
- handleSkillToolCall updates conversation with $addToSet on success
- Enables re-priming skill files on subsequent runs (future)

Dependency wiring:
- Pass listSkillFiles, getStrategyFunctions, uploadCodeEnvFile,
  updateConversation through ToolExecuteOptions
- Pass req and codeApiKey through mergedConfigurable
- All three controller entry points wired (initialize.js, openai.js,
  responses.js)

* fix: load bash_tool instance in loadToolsForExecution, remove file listing

- Add createBashExecutionTool to loadToolsForExecution alongside PTC/ToolSearch
  pattern: loads CODE_API_KEY, creates bash tool instance on demand
- Add BASH_TOOL and SKILL_TOOL to specialToolNames set so they don't go
  through the generic loadTools path (bash is created here, skill is
  intercepted in handler before tool.invoke)
- Remove file name listing from skill content text — it's the skill
  author's responsibility to disclose files in SKILL.md, not the framework

* feat: batch upload for skill files, replace sequential uploads

- Add batchUploadCodeEnvFiles() to crud.js: single POST to /upload/batch
  with all files in one multipart request, returns shared session_id
- Rewrite primeSkillFiles to collect all streams (SKILL.md + bundled files)
  then do one batch upload instead of N sequential uploads
- Replace uploadCodeEnvFile with batchUploadCodeEnvFiles across all callers
  (handlers.ts, initialize.js, openai.js, responses.js)

* refactor: remove invokedSkillIds from conversation schema

Skills aren't re-loaded between runs, so conversation-level state for
invoked skills doesn't help. Skill state will live on messages instead
(like tool_search discoveredTools and summaries), enabling in-place
re-injection on follow-up runs.

Removes invokedSkillIds from: convo Mongoose schema, IConversation
interface, Zod schema, ToolExecuteOptions.updateConversation, and
all three caller wiring points.

* feat: smart skill file re-priming with session freshness checking

Schema:
- Add codeEnvIdentifier field to ISkillFile (type + Mongoose schema)
- Add updateSkillFileCodeEnvIds batch method (uses tenantSafeBulkWrite)
- Export checkIfActive from Code/process.js

Extraction:
- Add extractInvokedSkillsFromHistory() to run.ts — scans message
  history for AIMessage tool_calls where name === 'skill', extracts
  skillName args. Follows same pattern as extractDiscoveredToolsFromHistory.

Smart re-priming in primeSkillFiles:
- Before batch uploading, checks if existing codeEnvIdentifiers are
  still active via getSessionInfo + checkIfActive (23h threshold)
- If session is still active, returns cached references (zero uploads)
- If stale or missing, batch-uploads everything and persists new
  identifiers on SkillFile documents (fire-and-forget)
- Single session check covers all files (batch shares one session_id)

Wiring:
- Pass getSessionInfo, checkIfActive, updateSkillFileCodeEnvIds
  through ToolExecuteOptions and all three controller entry points

* feat: wire skill file re-priming at run start via initialSessions

Flow:
1. initialize.js creates primeInvokedSkills callback with all deps
2. client.js calls it with message history before createRun
3. extractInvokedSkillsFromHistory scans for skill tool calls
4. For each invoked skill with files, primeSkillFiles uploads/checks
5. Returns initialSessions map passed to createRun
6. createRun passes initialSessions to Run.create (via RunConfig)
7. Run constructor seeds Graph.sessions, making skill files available
   to subsequent bash/code tool calls via ToolNode session injection

Requires @librechat/agents with initialSessions on RunConfig (PR #94).

* refactor: use CODE_EXECUTION_TOOLS set for code tool checks

Import CODE_EXECUTION_TOOLS from @librechat/agents and replace inline
constant checks in handlers.ts and callbacks.js. Fixes missing bash
tool coverage in the session context injection (handlers.ts) and code
output processing (callbacks.js).

* refactor: move primeInvokedSkills to packages/api, add skill body re-injection

Moves primeInvokedSkills from an inline closure in initialize.js (with
dynamic requires) to a proper exported function in packages/api
skillFiles.ts with explicit typed dependencies.

Key changes:
- primeInvokedSkills now returns both initialSessions (for file priming)
  AND injectedMessages (skill bodies for context continuity)
- createRun accepts invokedSkillMessages and appends skill bodies to
  systemContent so the model retains skill instructions across runs
- initialize.js calls the packaged function with all deps passed explicitly
- client.js passes both initialSessions and injectedMessages to createRun

* fix: move dynamic requires to top-level module imports

Move primeInvokedSkills, getStrategyFunctions, batchUploadCodeEnvFiles,
getSessionInfo, and checkIfActive from inline requires to top-level
module requires where they belong.

* refactor: skill body reconstruction via formatAgentMessages, not systemContent

Replaces the lazy systemContent approach with proper message-level
reconstruction:

SDK (formatAgentMessages):
- New invokedSkillBodies param (Map<string, string>)
- Reconstructs HumanMessages after skill ToolMessages at the correct
  position in the message sequence, matching where ToolNode originally
  injected them

LibreChat:
- extractInvokedSkillsFromPayload replaces extractInvokedSkillsFromHistory
  (works with raw TPayload before formatAgentMessages, not BaseMessage[])
- primeInvokedSkills now takes payload instead of messages, returns
  skillBodies Map instead of injectedMessages
- client.js calls primeInvokedSkills BEFORE formatAgentMessages, passes
  skillBodies through as the 4th param
- Removed invokedSkillMessages from createRun (no more systemContent hack)
- Single-pass: skill detection happens inside formatAgentMessages' existing
  tool_call processing loop, zero extra message iterations

* refactor: rename skillBodies to skills for consistency with SDK param

* refactor: move auth loading into primeInvokedSkills, pass loadAuthValues as dep

The payload/accessibleSkillIds guard and CODE_API_KEY loading now live
inside primeInvokedSkills (packages/api) rather than in the CJS caller.
initialize.js passes loadAuthValues as a dependency and the callback
is only created when skillsCapabilityEnabled.

* feat: ReadFile tool + conditional bash registration + skill path namespacing

ReadFile tool (read_file):
- General-purpose file reader, event-driven (ON_TOOL_EXECUTE)
- Schema: { file_path: string } — "{skillName}/{path}" convention
- handleReadFileCall: resolves skill name from path, ACL check, reads
  from DB cache or storage, binary detection, size limits (256KB),
  lazy caching (512KB), line numbers in output
- SKILL.md special case: reads skill.body directly
- Dispatched alongside SKILL_TOOL in createToolExecuteHandler
- Added to specialToolNames in ToolService

Conditional tool registration:
- ReadFile + SkillTool: always registered when skills enabled
- BashTool: only registered when codeEnvAvailable === true
- codeEnvAvailable passed through InitializeAgentParams from caller

Skill file path namespacing:
- primeSkillFiles now uploads as "{skillName}/SKILL.md" and
  "{skillName}/{relativePath}" instead of flat names
- Prevents file collisions when multiple skills are invoked

Wiring:
- getSkillFileByPath + updateSkillFileContent passed through
  ToolExecuteOptions in all three callers

* feat: return images/PDFs as artifacts from read_file, tighten caching

Binary artifact support:
- Images (png, jpeg, gif, webp) returned as base64 in artifact.content
  with type: 'image_url', processed by existing callback attachment flow
- PDFs returned as base64 artifact similarly
- Binary size limit: 10MB (MAX_BINARY_BYTES)
- Other binary files still return metadata + bash fallback

Caching:
- Text cached only on first read (file.content == null check)
- Binary flag cached only on first detection (file.isBinary == null)
- Skill files are immutable; no redundant cache writes

Registration:
- ReadFileToolDefinition now includes responseFormat: 'content_and_artifact'

* chore: update @librechat/agents to version 3.1.66-dev.0 and add peer dependencies in package-lock.json and package.json files

* fix: resolve review findings #1,#2,#4,#5,#6,#10,#13

Critical:
- #1: primeInvokedSkills now accumulates files across all skills into
  one session entry instead of overwriting. Parallel processing via
  Promise.allSettled.
- #2: codeEnvAvailable now computed and passed in openai.js and
  responses.js (was missing, bash tool never registered in those flows)

Major:
- #4: relativePath in updateSkillFileCodeEnvIds now strips the
  {skillName}/ prefix to match SkillFile documents. SKILL.md filter
  uses endsWith instead of exact match.
- #5: File priming guarded on apiKey being non-empty (skip when not
  configured instead of failing with auth error)
- #6: Skills processed in parallel via Promise.allSettled instead of
  sequential for-of loop

Minor:
- #10: Use top-level imports in initialize.js instead of inline requires
- #13: Log warning when skill catalog reaches the 100-skill limit

* fix: resolve followup review findings N1,N2,N4

N1 (CRITICAL): Wire skill deps into responses.js non-streaming path.
Was completely missing getSkillByName, file strategy functions, etc.

N2 (MAJOR): Single batch upload for ALL skills' files. Resolves skills
in parallel (Phase 1), then collects all file streams across skills
and does ONE batchUploadCodeEnvFiles call (Phase 2). All files share
one session_id, eliminating cross-session isolation issues.

N4 (MINOR): Move inline require() to top-level in openai.js and
responses.js, consistent with initialize.js.

* fix: add mocks for new file strategy imports in controller tests

* fix: restore session freshness check, parallelize file lookups, add warnings

R1: Re-add session freshness check before batch upload. Checks any
existing codeEnvIdentifier via getSessionInfo + checkIfActive. If the
session is still active (23h window), returns cached file references
with zero re-uploads.

R2: listSkillFiles calls parallelized via Promise.all (were sequential
in the for-of loop).

R3: Log warning when skill record lookup fails during identifier
persistence (was a silent empty-string fallback).

* fix: guard freshness cache on single-session consistency

* fix: multi-session freshness check (code env handles mixed sessions natively)

The code execution environment fetches each file by its own
{session_id, fileId} pair independently — no single-session
requirement. Removed the sessionIds.size === 1 guard.

Now checks ALL distinct sessions for freshness. If every session
is still active (23h window), returns cached references with per-file
session_ids preserved. If any session expired, falls through to
re-upload everything in a single batch.

* perf: parallelize session freshness checks via Promise.all

* fix: add optional chaining for session info retrieval in primeInvokedSkills

Updated the primeInvokedSkills function to use optional chaining for getSessionInfo and checkIfActive methods, ensuring safer access and preventing potential runtime errors when these methods are undefined.

* fix: address review findings #1-#9 + Codex P1/P2 + session probe

Critical:
- #1/Codex P1: Add codeApiKey loading to openai.js and responses.js
  loadTools configurable (was missing, file priming broken in 2/3 paths)
- Codex P1: Fix cached file name prefix in primeSkillFiles cache path
  (was sf.relativePath, now ${skill.name}/${sf.relativePath})

Major:
- Codex P2: Honor ephemeral skills toggle in agents endpoint
  (check ephemeralAgent?.skills !== false alongside admin capability)
- #4: Early size check using file.bytes from DB before streaming
  (prevents full-file buffer for oversized files)

Minor:
- #5: Replace Record<string, any> with Record<string, boolean | string>
- #6: Localize Pin/Unpin aria-labels with com_ui_pin/com_ui_unpin
- #8: Parallelize stream acquisition in primeSkillFiles via
  Promise.allSettled
- #9: Log warning for partial batch upload failures with filenames

Performance:
- Session probe optimization: getSessionInfo now hits per-object
  endpoint (GET /sessions/{sid}/objects/{fid}) instead of listing
  entire session (GET /files/{sid}?detail=summary). O(1) stat vs
  O(N) list + linear scan.

* refactor: extract shared skill wiring helper + add unit tests

DRY (#3):
- New skillDeps.js exports getSkillToolDeps() with all 9 skill-related
  deps (getSkillByName, listSkillFiles, getStrategyFunctions, etc.)
- Replaces 5 identical copy-paste blocks across initialize.js, openai.js,
  responses.js (streaming + non-streaming paths)
- One place to maintain when skill deps change

Tests (#2):
- 8 unit tests for extractInvokedSkillsFromPayload covering:
  string args, object args, missing skill tool_calls, non-assistant
  messages, malformed JSON, empty skillName, empty payload, dedup

* fix: remove @jest/globals import, use global jest env

* fix: resolve round 2 review findings R2-1 through R2-7

R2-1 (toggle semantics): openai.js + responses.js now check admin
  capability (AgentCapabilities.skills) alongside ephemeral toggle.
  Aligns with initialize.js.

R2-2 (swallowed error): primeInvokedSkills now logs
  updateSkillFileCodeEnvIds failures (was .catch(() => {}))

R2-4 (test cast): Record<string, string> → Record<string, unknown>

R2-5 (DRY regression): Extract enrichWithSkillConfigurable() into
  skillDeps.js. Replaces 4 identical loadAuthValues blocks.
  Each loadTools callback is now a one-liner. JSDoc added (R2-6).

R2-7 (sequential streams): primeInvokedSkills now uses
  Promise.allSettled for parallel stream acquisition.

* fix: require explicit skills toggle + treat partial cache as miss

- initialize.js: change ephemeralSkillsToggle !== false to === true
  (unset toggle no longer enables skills)
- primeSkillFiles cache: require ALL files to have codeEnvIdentifier
  before using cache (partial persistence = cache miss = re-upload)
- primeInvokedSkills cache: same check (allFilesWithIds.length must
  equal total file count)

* fix: pass entity_id=skillId on batch upload, eliminates per-user cache thrashing

primeSkillFiles now passes entity_id: skill._id.toString() to
batchUploadCodeEnvFiles. This scopes the code env session to the
skill, not the user. All users sharing a skill share the same
uploaded files — no more cache thrashing from overwriting each
other's codeEnvIdentifier.

The stored codeEnvIdentifier now includes ?entity_id= suffix so
freshness checks pass the entity_id through to the per-object
stat endpoint. Both primeSkillFiles and primeInvokedSkills
store consistent identifier formats.

* fix: pass entity_id on multi-skill batch upload, consistent identifier format

* Revert "fix: pass entity_id on multi-skill batch upload, consistent identifier format"

This reverts commit c85ce21.

* refactor: per-skill upload in primeInvokedSkills, eliminate multi-skill batch

Replace the monolithic multi-skill batch upload with per-skill
primeSkillFiles calls. Each skill gets its own session with
entity_id=skillId, ensuring:

- Correct session auth (entity_id matches on freshness checks)
- Per-skill freshness caching (only expired skills re-upload)
- Shared skill sessions work across users (same entity_id=skillId)
- Code env handles mixed session_ids natively

The big batch block (stream collection, single upload, identifier
mapping) is replaced by a simple loop over primeSkillFiles, which
already handles freshness caching, batch upload, and identifier
persistence per-skill.

* fix: resolve review findings #1,#3-5,#7,#9-11

Critical:
- #1: Strip ?entity_id= query string before splitting codeEnvIdentifier
  into session_id/fileId (was corrupting cached file IDs in 4 locations)

Major:
- #4: Parallelize per-skill primeSkillFiles via Promise.allSettled
- #5: Add logger.warn to all empty .catch(() => {}) on cache writes

Minor:
- #7: Add logger.debug to enrichWithSkillConfigurable catch block
- #9: Use error instanceof Error guard in batchUploadCodeEnvFiles
- #10: Move enrichWithSkillConfigurable to TypeScript in packages/api
  (skillConfigurable.ts), skillDeps.js wraps with loadAuthValues dep
- #11: Reduce MAX_BINARY_BYTES from 10MB to 5MB (~11.5MB peak with b64)

* fix: forward entity_id in session probe + always register bash tool

Codex P2 (entity_id in probe): getSessionInfo now preserves and
forwards query params (including entity_id) to the per-object stat
endpoint. Without this, identifiers stored as ...?entity_id=... would
fail auth checks because the entity_id scope was dropped.

Codex P2 (bash tool availability): Remove codeEnvAvailable gate from
injectSkillCatalog. Bash tool definition is now always registered when
skills are enabled. Actual tool instance creation still happens at
execution time in loadToolsForExecution (which loads per-user
credentials). This ensures users with per-user CODE_API_KEY get
bash without requiring a global env var at init time.

Removes codeEnvAvailable from InjectSkillCatalogParams,
InitializeAgentParams, and all three controller entry points.

* fix: add debug logging to primeInvokedSkills catch, rename export alias

* fix: stub bash tool when no key + remove PDF artifact path

Codex P1 (bash tool): When CODE_API_KEY is unavailable, create a stub
tool that returns "Code execution is not available. Use read_file
instead." This prevents "tool not found" errors from the model
repeatedly calling bash_tool in no-code-env deployments while still
registering the definition for per-user credential users.

Codex P2 (PDF artifacts): Remove PDF image_url artifact path. The
host artifact pipeline processes image_url via saveBase64Image which
fails for PDFs. PDFs now fall through to the generic binary handler
("Use bash to process"). TODO comment for future document artifact
support.

Also: isImageOrPdf → isImage in early size checks (PDFs are no
longer treated as artifact candidates).

* fix: remove dead PDF_MIME constant, hoist skillToolDeps, document session_id

- #7: Remove unused PDF_MIME constant (dead code after PDF artifact removal)
- #11: Hoist skillToolDeps to module-level constant (avoid per-call allocation)
- #6: Document that CodeSessionContext.session_id is a representative value;
  ToolNode uses per-file session_id from the files array

* fix: call toolEndCallback for skill/read_file artifacts + clear codeEnvIdentifier on re-upload

Codex P1 (toolEndCallback bypass): skill and read_file handler branches
returned early, bypassing the toolEndCallback that processes artifacts
(image attachments). Now calls toolEndCallback when the result has an
artifact, using the same metadata pattern as the normal tool.invoke path.

Codex P1 (stale identifiers): upsertSkillFile now $unset's
codeEnvIdentifier alongside content and isBinary when a file is
re-uploaded. Prevents the freshness cache from returning references
to old file content after a skill file is replaced.

* fix: add session_id comment at cached path, rename skillResult to handlerResult

* fix: return content_and_artifact from bash stub so result.content is populated

* fix: deterministic skill lookup, dedup warning, and multi-session freshness check

- getSkillByName: add sort({updatedAt:-1}) so name collisions resolve
  deterministically to the most recently updated skill
- injectSkillCatalog: warn when multiple accessible skills share a name
- primeSkillFiles: check ALL distinct sessions for freshness, not just
  the first file's session, preventing stale refs after partial bulkWrite

* refactor: update icon import in Skills component

- Replaced the Scroll icon with ScrollText in the Skills component for improved clarity and consistency in the UI.

* fix: SKILL.md cache parity, gate bash_tool on code env, fix read_file too-large message

- primeSkillFiles: filter SKILL.md from returned files array on fresh
  upload so cached and non-cached paths return identical file sets
  (SKILL.md is still on disk in the session for bash access)
- injectSkillCatalog: only register bash_tool when codeEnvAvailable is
  true; thread the flag from all three CJS callers via execute_code
  capability check
- handleReadFileCall: tell the model to invoke the skill first before
  suggesting /mnt/data paths for oversized files

* fix: use EnvVar constant, deduplicate auth lookup, validate batch upload, stream byte limit

- Replace hardcoded 'LIBRECHAT_CODE_API_KEY' with EnvVar.CODE_API_KEY
  in skillConfigurable.ts and skillFiles.ts
- Resolve code API key once at run start in initialize.js and pass to
  both primeInvokedSkills and enrichWithSkillConfigurable via optional
  preResolvedCodeApiKey param, eliminating redundant loadAuthValues calls
- Add response structure validation in batchUploadCodeEnvFiles before
  accessing session_id/files to surface unexpected responses early
- Add streaming byte counter in handleReadFileCall that aborts and
  destroys the stream when accumulated bytes exceed MAX_BINARY_BYTES,
  preventing full file buffering when DB metadata is inaccurate

* refactor: update icon import in ToolsDropdown component

- Replaced the Scroll icon with ScrollText in the ToolsDropdown component for improved clarity and consistency in the UI.

* fix: partial upload failure detection, EnvVar in initialize.js, declaration ordering

- primeSkillFiles: return null (failure) when batch upload partially
  succeeds — missing bundled files would cause runtime bash/read
  failures with missing paths in code env
- initialize.js: replace hardcoded 'LIBRECHAT_CODE_API_KEY' with
  EnvVar.CODE_API_KEY imported from @librechat/agents
- initialize.js: move enabledCapabilities, accessibleSkillIds, and
  codeApiKey declarations before the toolExecuteOptions closure that
  references them (eliminates reliance on temporal dead zone hoisting)
* feat: Custom UI renderers for skill, read_file, and bash_tool

Add specialized tool call components for the three skill tools,
replacing the generic ToolCall fallback with contextual UI.

* fix: Address review findings for skill tool UI renderers

- Fix Codex P2: read skillName (camelCase) matching agent pipeline
- Fix Codex P2: remove error regex from ReadFileCall to avoid false
  positives on normal file content containing "Error:" tokens
- Extract useToolCallState hook to eliminate ~60% boilerplate
  duplication across SkillCall, ReadFileCall, and BashCall
- Extract parseJsonField utility with consistent escaped-char-aware
  regex fallback, shared by all three components
- Gate SkillCall bordered card on hasOutput to prevent empty card
  when expanded before output arrives
- Skip highlightAuto for plaintext lang to avoid expensive
  auto-detection on files with unknown extensions
- Expand LANG_MAP with php, cs, kt, swift, scss, less, lua, r;
  add FILENAME_MAP for Makefile and Dockerfile
- Export langFromPath for testability
- Add unit tests for parseJsonField, langFromPath, and ToolIcon
  skill type branches

* refactor: Redesign BashCall as minimal terminal widget

Replace the ExecuteCode-clone pattern with a purpose-built terminal
UI: $ prompt prefix, dark background command zone, icon-only copy
button, and raw monospace output. Drops useLazyHighlight,
CodeWindowHeader, Stdout, and the "Output" label in favor of a
cleaner two-zone layout that feels native to the terminal.

* fix: parseJsonField unescape ordering and ReadFileCall empty card

Replace the sequential .replace() chain in parseJsonField's regex
fallback with a single-pass /\(.)/g replacement. The old chain
processed \n before \, so \n (JSON-escaped literal backslash + n)
was incorrectly decoded as a newline instead of \n.

Gate ReadFileCall's bordered card on hasOutput (matching SkillCall's
pattern) so the card does not render as an empty rounded box during
streaming before output arrives.

Add regression tests for \n decoding and unknown escape sequences.

* fix: Followup review fixes

- Refactor ExecuteCode to use shared useToolCallState hook,
  eliminating the last copy of the inline state machine
- Escape regex metacharacters in parseJsonField to prevent
  injection from field names containing ., +, (, etc.
- Fix contradictory test description in langFromPath tests

* fix: Surface tool failure state in skill tool renderers

Add error detection to useToolCallState via the shared isError
check so tool calls that complete with an error prefix show a
"failed" suffix instead of a success label. Prevents misleading
users when read_file, skill, or bash_tool returns an error
(e.g. file not found, skill not accessible). Matches the error
handling pattern already used by the generic ToolCall component.

* feat: Add bash syntax highlighting to BashCall command zone

Reuse the shared useLazyHighlight singleton (already loaded by
ReadFileCall and ExecuteCode) to highlight the command with bash
grammar. Falls back to plain text while lowlight is loading.

* fix: Align BashCall scrollbar to span full card width

Move max-h/overflow-auto from the inner pre to the outer container
so the scrollbar spans the full width like the output zone. Float
the copy button with sticky positioning so it stays visible while
scrolling long commands.

* feat: Use GNU Bash icon for bash_tool progress header and ToolIcon

Replace the generic SquareTerminal lucide icon with the GNU Bash
logo (already in the project via LangIcon/langIconPaths) for
both the BashCall progress header and the ToolIcon stacked icon
mapping.

* fix: Render raw content while highlighter loads, preserve command text on copy

- ReadFileCall: fall back to raw output when useLazyHighlight
  returns null, preventing a blank code panel on first render
  before lowlight finishes its dynamic import
- BashCall: drop .trim() from the copy handler so the clipboard
  receives exactly what's displayed (WYSIWYG copy)

* fix: Alphabetize new translation keys within en/translation.json

Relocate read_file, skill_finished, and skill_running into their
correct alphabetical positions within the overall key list.

* fix: Surface error state in ExecuteCode, fix BashCall import order

- ExecuteCode now uses hasError from useToolCallState to show
  the "failed" suffix on failed code executions, matching the
  three new renderers
- Reorder BashCall local imports to longest-to-shortest per
  project style
* feat: add $ command popover for manual skill invocation

Adds a new `$` command trigger in the chat textarea that opens a
searchable popover listing user-invocable skills. Selecting a skill
inserts `$skill-name` into the message and enables the skills badge
on the ephemeral agent. Follows the same patterns as `@` mentions
and `/` prompts.

* test: update useHandleKeyUp tests for $ skill command

Add showSkillsPopoverFamily, dollarCommand, and SKILLS permission
to the store/recoil/access mocks. Include test cases for the $
trigger, toggle gating, and permission gating.

* fix: address review findings in SkillsCommand

- Exclude auto-mode skills from popover (isUserInvocable now
  returns false for InvocationMode.auto)
- Rewrite JSDoc to match the corrected filter logic
- Guard ArrowUp/ArrowDown against NaN when matches is empty
- Replace useRecoilState with useSetRecoilState for ephemeralAgent
  to avoid subscribing to unrelated agent state changes
- Move skills guard into setter callback and drop ephemeralAgent
  from handleSelect dependency array
- Add e.preventDefault() for Tab key alongside Enter
- Render error state (com_ui_skills_load_error) on query failure
- Render empty state (com_ui_skills_empty) when no matches
- Hoist ScrollText icon to module-level constant
- Export isUserInvocable for testability

* fix: address follow-up review findings

- Differentiate empty-catalog ("No skills yet") from no-match
  search ("No skills found") using existing com_ui_no_skills_found
- Clamp activeIndex when matches shrink from search filtering to
  prevent silent Enter/Tab failures
- Add early return after Escape handler to skip redundant checks
- Reorder package imports shortest-to-longest after react
- Add fast-typing test case for $ command ("$sk" at position 3)

* fix: gate $ command on assistants endpoint, fix Tab on empty matches

- Block $ popover on assistants/azureAssistants endpoints where
  ephemeralAgent is not sent in the submission payload
- Allow Tab to close the popover when matches is empty instead of
  trapping keyboard focus
- Add endpoint gating tests for $ on both assistants endpoints

* fix: reset skills popover on assistants switch + paginate skills query

- Close $ skills popover when endpoint switches to assistants or
  azureAssistants, mirroring the existing + command reset
- Switch SkillsCommand from a single-page list query to the
  cursor-paginated useSkillsInfiniteQuery and auto-fetch all pages
  so client-side search covers the full catalog instead of only
  the first 100 entries
- Show the spinner during background page fetches and suppress the
  empty-state copy until paging completes
- Add test for popover reset on endpoint switch

* fix: prevent currency hijack and form submit on $ command

- Reject the $ trigger when fast-typed text after $ does not start
  with a lowercase letter, so currency input like $100 or $5.99
  no longer opens the skills popover and clears the textarea
- preventDefault() on Enter when the popover has no matches so
  the surrounding chat form does not submit when the user dismisses
  the popover via Enter
- Add tests for $100 and $5.99 currency inputs

* fix: defer $ popover to second keystroke and stop pagination on errors

- Defer opening the skills popover until a letter follows the $
  character. Bare $ no longer triggers the popover, so starting a
  message with $100, $5.99, or $EUR is fully preserved (the
  textarea is not cleared by useInitPopoverInput on the first
  keystroke). $a, $skill, $my-skill still open as expected.
- Add a sticky paginationBlockedRef circuit breaker on the auto
  fetchNextPage effect so a transient page request error cannot
  spin into an unbounded retry loop when isError flips back to
  false on the next attempt.
- Update tests: bare $ no longer triggers, $a does, currency cases
  remain blocked.

* feat: scaffold structured manual-skill channel for follow-up PR

Add a per-conversation pendingManualSkillsByConvoId atom family
that SkillsCommand appends to on selection. This is the writer
half of the structured channel that will let a follow-up PR
deterministically prime SKILL.md as a meta user message before
the LLM turn (mirroring Claude Code's `/skill` invocation), so
the backend never has to regex-parse `$name` out of user text.

The submit pipeline does not yet read this atom; the textual
`$skill-name ` insertion remains the authoritative signal until
the follow-up wires the read + reset on submit. Reset is already
wired into useClearStates so the atom does not leak across
conversation switches.

* test: cover SkillsCommand selection-flow contract

Add a component test that locks in the contract the follow-up
manualSkills PR has to honor when a user picks a skill in the $
popover:

- Pushes the skill name onto pendingManualSkillsByConvoId (the
  per-conversation structured channel), with dedup
- Flips ephemeralAgent.skills to true via the callback-form setter
- Inserts $skill-name into the textarea as cosmetic confirmation
- Closes the popover via setShowSkillsPopover(false)
- Renders nothing when the popover atom is false

Mocks recoil setters and the skills query so the test exercises
the real component logic without spinning up the full provider
stack.

* revert: drop $ defer-until-letter guard for sibling consistency

Bring $ in line with @, /, and +: open the popover on the bare
trigger character. The earlier defer guard kept currency input
like \$100 from clobbering the textarea, but it broke the natural
"type \$ to browse skills" UX and was inconsistent with the other
trigger chars, none of which gate on the follow-up character
(/path/to/file, @username, +1 all clear the textarea the same way).
The currency hijack remains recoverable via Escape.

Drop the corresponding paste-protection tests for \$100 and \$5.99,
restore the bare-\$ trigger test.
)

* feat: per-agent skill selection in builder and runtime scoping

Wire skills persistence on the Agent model and enable the skills
section in the agents builder panel. At runtime, scope the skill
catalog to only the skills configured on each agent (intersected
with user ACL). When no skills are configured, the full user catalog
is used as the default. The ephemeral chat toggle overrides per-agent
scoping to provide the full catalog.

* fix: add scopeSkillIds to @librechat/api mock in responses unit test

The test mocks @librechat/api but was missing the newly imported
scopeSkillIds, causing createResponse to throw before reaching the
assertions. Added a passthrough mock that returns the input array.

* fix: scope primeInvokedSkills by agent's configured skills

primeInvokedSkills was receiving the full unscoped accessibleSkillIds,
bypassing the per-agent skill scoping applied to initializeAgent. This
allowed previously invoked skills from message history to be resolved
and primed even when excluded from the agent's configured skill set.

Apply the same scopeSkillIds filtering to match the initializeAgent
calls, so skill resolution is consistent across catalog injection
and history priming.

* fix: preserve agent skills through form reset and union prime scope

Two related bugs in the per-agent skill selection flow:

1. resetAgentForm dropped the persisted skills array because the generic
   fall-through at the end of the loop excludes object/array values.
   Combined with composeAgentUpdatePayload always emitting skills, this
   caused any save of a previously-configured agent to silently overwrite
   skills with an empty array. Add an explicit case for skills mirroring
   the agent_ids handling.

2. primeInvokedSkills processes the full conversation payload, including
   prior handoff-agent invocations. Scoping it to only primaryAgent.skills
   meant a skill invoked by a handoff agent in a prior turn could not be
   resolved when the current primary agent had a different scope, leaving
   message history reconstruction incomplete. Union the per-agent scoped
   accessibleSkillIds across primary plus all loaded handoff agents so
   any skill any active agent could invoke is resolvable from history.

* fix: mark inline skill removals as dirty

The inline X button on the skills list called setValue without
shouldDirty: true, so removing a skill via this control did not
mark the skills field as dirty in react-hook-form state. When a
user removed a skill with the X button and also staged an avatar
upload in the same save, isAvatarUploadOnlyDirty returned true and
onSubmit short-circuited to avatar-only upload, silently dropping
the PATCH that would persist the skill removal.

The dialog path (SkillSelectDialog) already passes shouldDirty: true
on add/remove; this aligns the inline control with that behavior.

* fix: restore full ACL scope for primeInvokedSkills history reconstruction

Reverting the earlier scoping of primeInvokedSkills to the active-agent
union. That change conflated runtime invocation scoping (which correctly
gates what the model can call now) with history reconstruction (which
restores bodies the model already saw in prior turns).

Per-agent scoping still applies at:
- Catalog injection (injectSkillCatalog via initializeAgent)
- Runtime invocation (handleSkillToolCall via enrichWithSkillConfigurable,
  using each agent's scoped accessibleSkillIds in agentToolContexts)

History priming is a read of past context, not a grant of new capability.
Scoping it causes historical skill bodies to vanish from formatAgentMessages
when an agent's skills list is edited mid-conversation or when the ephemeral
toggle flips, which breaks message reconstruction and drops code-env file
continuity for /mnt/data/{skillName}/ references. The user's ACL-accessible
set is the correct and sufficient gate for history reconstruction.

* fix: close openai.js skill gap and pin undefined vs [] semantics

Three related gaps surfaced in review:

1. api/server/controllers/agents/openai.js was a third skill resolution
   site alongside responses.js and initialize.js, but still used the old
   activation gate (required ephemeralAgent.skills === true) and never
   passed accessibleSkillIds through scopeSkillIds. Per-agent scoping
   silently did not apply on this route. Mirror the same pattern used
   in responses.js so all three routes behave identically.

2. scopeSkillIds previously collapsed undefined and [] into the same
   "full catalog" fallback, making it impossible for a user to express
   "this agent has no skills." Tighten the semantics before any data
   is written under the old behavior:
     - undefined / null = not configured, full catalog
     - []              = explicitly none, returns []
     - non-empty       = intersection with ACL-accessible set
   Update defaultAgentFormValues.skills from [] to undefined so a brand
   new agent whose skills UI was never touched does not accidentally
   persist "explicit none" on first save (removeNullishValues strips
   undefined from the payload server side).

3. Add direct unit tests for scopeSkillIds covering all five cases
   (undefined, null, empty, disjoint, overlap, exact match, empty
   accessible set). 16 tests total in skills.test.ts pass.

* fix: add scopeSkillIds to @librechat/api mock in openai unit test

Same pattern as the earlier responses.unit.spec.js fix: the test mocks
@librechat/api with an explicit object, so each newly imported symbol
must be added to the mock. Without scopeSkillIds, OpenAIChatCompletion
controller throws on destructuring before reaching recordCollectedUsage,
causing the token usage assertions to fail.
…efaults (#12692)

* feat: per-user skill active/inactive toggle with ownership-aware defaults

- Add `skillStates` map (Record<string, boolean>) to user schema for
  per-user active/inactive overrides on skills
- Add `defaultActiveOnShare` to interface.skills config (default: false)
  so admins can control whether shared skills auto-activate
- Add GET/POST /api/user/settings/skills/active endpoints with validation
- Add React Query hooks with optimistic mutations for skill states
- Add useSkillActiveState hook with ownership-aware resolution:
  owned skills default active, shared skills default inactive
- Add toggle switch UI to SkillListItem and SkillDetail components
- Filter inactive skills in injectSkillCatalog before agent injection
- Add localization keys for active/inactive labels

* fix: use Record instead of Map for IUser.skillStates

Mongoose .lean() flattens Map to a plain object, causing type
incompatibility with IUser in methods that return lean documents.

* fix: address review findings for skill active states

- Fail-closed when userId is absent: filter rejects all shared skills
  instead of passing them through unfiltered (Codex P1)
- Validate Mongoose Map key characters (reject . and $) in controller
  to return 400 instead of a 500 from schema validation (Codex P2)
- Block toggle while initial skill states query is loading to prevent
  overwriting server-side overrides with an empty snapshot (Codex P2)
- Extract shared SkillToggle component, eliminating duplicate toggle
  markup in SkillListItem and SkillDetail (Finding #3)
- Move skill state query/mutation hooks from Favorites.ts to
  Skills/queries.ts per feature-directory convention (Finding #4)
- Fix hardcoded English aria-label in SkillListItem by passing the
  localized string from the parent SkillList (Finding #5)
- Fix inline arrow in SkillList render loop: pass stable callback
  reference so SkillListItem memo() is not invalidated (Finding #1)
- Extract toRecord() helper in controller to DRY the Map-to-Object
  conversion (Finding #6)
- Remove Promise.resolve wrapping synchronous config read (Finding #8)
- Remove unused TUpdateSkillStatesRequest type (Finding #12)

* fix: forward tabIndex on SkillToggle to preserve list keyboard nav

The original inline toggle had tabIndex={-1} so the row itself
remained the sole tab target. The extraction into SkillToggle
dropped this prop, making every list toggle a tab stop. Add an
optional tabIndex prop and pass -1 from SkillListItem.

* fix: plumb skillStates to all agent entry points, isolate toggle keydown

- Add skillStates/defaultActiveOnShare loading to openai.js and
  responses.js controllers so shared-skill activation is respected
  across all agent entry points, not just initialize.js (Codex P1)
- Stop keydown propagation on SkillToggle so Enter/Space does not
  bubble to the parent row's navigation handler (Codex P2)

* fix: paginate catalog fetch and serialize toggle writes

- Paginate listSkillsByAccess (up to 10 pages of 100) until the active
  catalog quota is filled, so inactive shared skills in recent positions
  do not starve active owned skills past the first page (Codex P1)
- Extend listSkillsByAccess interface with cursor/has_more/after for
  catalog pagination
- Serialize skill-state writes via a ref queue: one in-flight request
  at a time, with the latest desired state sent when the previous one
  settles. Prevents last-response-wins races where an older request
  overwrites newer toggles (Codex P2)

* fix: share write queue across hook instances, block toggle on fetch error

- Move the write queue from a per-instance useRef to a module-scoped
  object so every mount of useSkillActiveState (SkillList, SkillDetail,
  etc.) serializes against the same in-flight slot. Prior per-instance
  queues allowed two components to race full-map POSTs (Codex P1)
- Extend the toggle guard beyond isLoading: also block when isError is
  true or data is undefined. Prevents a failed GET from seeding a
  toggle with an empty baseline that would wipe server-side overrides
  on the next successful POST (Codex P1)

* fix: stale closure, orphan cleanup, and cap-error UX

- Read toggle baseline from React Query cache via queryClient.getQueryData
  instead of the captured skillStates closure. The closure can be stale
  between onMutate's setQueryData and the next render, so rapid successive
  toggles would build on old state and drop earlier changes (Codex P1)
- Surface the MAX_SKILL_STATES_EXCEEDED error code with a specific toast
  key (com_ui_skill_states_limit) so users understand the 200-cap rather
  than seeing a generic error
- Prune orphaned entries (skillIds whose Skill doc no longer exists) on
  both GET and POST in SkillStatesController. Self-heals over time
  without needing cascade-delete hooks or a migration job. Uses one
  indexed Skill._id query per request

* test: pin skill active-state precedence with unit tests

Extract the active-state resolution logic from a closure inside
injectSkillCatalog into an exported resolveSkillActive helper, then
cover every branch of the precedence matrix:

- Fails closed when userId is absent (even with defaultActiveOnShare=true)
- Explicit override wins over ownership and config (both true and false)
- Owned skills default to active when no override is set
- Shared skills default to defaultActiveOnShare value
- Undefined skillStates behaves identically to an empty object
- defaultActiveOnShare defaults to false when omitted
- Owned skills ignore defaultActiveOnShare entirely

Closes Finding #2 from the pre-rebase comprehensive review. Mirrors
the existing scopeSkillIds test style; injectSkillCatalog now calls
resolveSkillActive instead of inlining the closure.

* refactor: limit skill active toggle to detail header, drop label

- Remove the per-row toggle from SkillListItem and the active-state
  plumbing (hook call, isSkillEnabled/onToggleEnabled/toggleAriaLabel
  props) from SkillList. The detail view is now the single place to
  change a skill's active state
- Drop dim/muted styling for inactive skills in the sidebar: without
  a control there, the visual indication has nowhere to land
- Resize SkillToggle to match neighbor buttons: outer h-9 container,
  h-6 w-11 track with size-5 knob, no label span. The 'Active' /
  'Inactive' text that accompanied the detail-view toggle is removed
- Remove the now-unused label prop and tabIndex prop (the tabIndex
  existed only for the list-row context) from SkillToggle. Drop the
  onKeyDown stopPropagation for the same reason
- Remove now-orphaned com_ui_skill_active / com_ui_skill_inactive
  translation keys

* style: shrink SkillToggle track to h-5 w-9 with size-4 knob

Container stays at h-9 to match neighbor button heights. The toggle
track itself drops from h-6 w-11 to h-5 w-9, with a size-4 knob
travelling 1.125rem on activation. Visually lighter inside the row.

* fix: remove redundant skillStates entries that match the resolved default

When a toggle lands on the ownership/config default, delete the key
from the map instead of persisting `{id: defaultValue}`. Without this,
a user toggling a skill off and back on would leave `{id: true}` for
an owned skill (whose default is already true), silently consuming a
slot against the 200-entry cap. Repeated round-trip toggles could
exhaust the quota with zero meaningful overrides (Codex P2).

Preserves the exceptions-list invariant that the runtime-resolution
design depends on.

* fix: prune before enforcing skill-state cap; reject non-ObjectId keys

Reorder the update controller so pruneOrphans runs before the 200-cap
check. Without this, a user near the cap with some orphaned entries
(skills deleted since their last GET) could send a payload that would
pass after pruning but gets rejected by the raw-size check first.

Add a sanity cap on raw payload size (2 * MAX_SKILL_STATES) so abusive
inputs do not reach the DB query, and enforce the real cap on the
pruned result instead.

Harden pruneOrphans: the earlier early-return path could pass
non-ObjectId keys through unchanged. Now only valid ObjectIds are
returned, and the Skill-model-unavailable fallback filters by format.

Also add isValidObjectIdString validation at the input boundary so
malformed (but otherwise non-Mongo-unsafe) keys never reach persistence
(Codex P2 x2).

* fix: enforce active filter at execute time, prune revoked shares, scope queue per user

P1: injectSkillCatalog now returns activeSkillIds (the filtered set
that appears in the catalog). initializeAgent uses that set as the
stored accessibleSkillIds on the initialized agent, so getSkillByName
at runtime cannot resolve a deactivated skill — even if the LLM
hallucinates a name or the user invokes by direct-invocation shorthand.
Previously the executor authorized against the full ACL set, bypassing
the active-state guarantee (Codex P1).

P2: pruneOrphans now checks user access via findAccessibleResources
in addition to skill existence. When a share is revoked, the user's
skillStates entry for that skill had no cleanup path and silently
consumed the 200-cap. Self-heals on both GET and POST. One extra ACL
query per settings read/write; scoped to a single user so no N-user
amplification (Codex P2).

P2: the write queue moves from a single module-scoped object to a Map
keyed by userId. Logout/login in the same tab can no longer flush the
previous user's pending snapshot under the new session's auth. Each
userId gets its own pending/inFlight slot; the in-flight request
retains its original auth via the cookie already attached when sent,
so the race window closes (Codex P2).

* refactor: extract skillStates helpers to packages/api; add tests; polish

Address the remaining valid findings from the comprehensive review:

- Extract toRecord, loadSkillStates, validateSkillStatesPayload, and
  pruneOrphanSkillStates into packages/api/src/skills/skillStates.ts
  as TypeScript. The controller in /api shrinks to a ~90-line thin
  wrapper that builds live dependency adapters for Mongoose + the
  permission service (Review #2 DRY, #3 workspace boundary)

- Replace the triplicated 12-line skillStates loading block in
  initialize.js, openai.js, and responses.js with a single call to
  loadSkillStates from @librechat/api. One helper, three sites

- Swap console.error for the project logger in the controller
  (Review #7)

- Remove the redundant INVALID_KEY_PATTERN regex: a valid ObjectId
  cannot contain . or $, so isValidObjectIdString already covers it
  (Review #11)

- Parameterize the 200-cap error toast with {{0}} interpolation
  driven by the error response's `limit` field, so future changes to
  MAX_SKILL_STATES update the UI message automatically (Review #12)

- Add 24 unit tests for the new skillStates helpers (toRecord,
  resolveDefaultActiveOnShare, loadSkillStates, validateSkillStates-
  Payload, pruneOrphanSkillStates) covering success paths, malformed
  input, cap boundaries, and parallel-query behavior (Review #4)

- Add 10 tests for injectSkillCatalog pagination covering empty
  accessible set, missing listSkillsByAccess, single-page filter,
  owned-vs-shared defaults, explicit-override precedence, multi-page
  collection, MAX_CATALOG_PAGES safety cap, early termination on
  has_more=false, additional_instructions injection, and fail-closed
  without userId (Review #5)

Total test count: 60 (was 26 on this surface).

* fix: rename skillStates ValidationError to avoid barrel-export collision

packages/api/src/types/error.ts already exports a ValidationError
(MongooseError extension). Re-exporting a different shape from
skills/skillStates.ts through the skills barrel caused TS2308 in CI
because the root index re-exports both. Rename to
SkillStatesValidationError to keep the exports disjoint.

* refactor: tighten tests and absorb caller guard into loadSkillStates

Address the followup review findings:

- Add optional `accessibleSkillIds` param to loadSkillStates so the
  helper short-circuits to defaults when no skills are accessible.
  All three controllers drop the residual 7-line conditional wrapper
  in favor of a single destructured call (Review #2)

- Remove the unreachable `typeof key !== 'string'` check from
  validateSkillStatesPayload: Object.entries always yields string
  keys per the JS spec (Review #3)

- Replace the two `as unknown as` agent casts in the injectSkillCatalog
  tests with a `makeAgent()` factory typed directly as the function's
  parameter shape (Review #4)

- Tighten the MAX_CATALOG_PAGES assertion from `toBeLessThanOrEqual(11)`
  to `toHaveBeenCalledTimes(10)` — the loop deterministically makes
  exactly 10 page fetches before hitting the cap (Review #1)

- Rewrite the parallel-execution test for pruneOrphanSkillStates using
  deferred promises instead of microtask-order assertions. The test
  now inspects `toHaveBeenCalledTimes(1)` on both mocks after a single
  Promise.resolve() yield, pinning Promise.all usage without relying
  on push-order into a shared array (Review #5)

- Evict stale writeQueue entries on user change via a module-scoped
  `lastSeenUserId` sentinel. When a different user's toggle is the
  first one after a logout/login, the previous user's queue entry is
  deleted. Keeps the Map bounded without adding hook-instance effect
  cleanup (Review #6)

* fix(test): mock loadSkillStates in openai and responses controller specs

The prior refactor replaced the inline 12-line skillStates loading
block with a call to loadSkillStates from @librechat/api. Both
controller spec files mock @librechat/api as a flat object, so any
new named import from that package is undefined in the test env.
Calling `await loadSkillStates(...)` threw before recordCollectedUsage
ran, surfacing as "undefined is not iterable" on the test's array
destructure of `mockRecordCollectedUsage.mock.calls[0]`.

Add the missing mock to both spec files alongside the existing
scopeSkillIds stub.

* fix: abandon stale skillStates write queues on user switch

Close the cross-session leak window where an in-flight flush loop
still holds a reference to a previous user's queue: it could fire its
next mutateAsync under the new session's auth cookies and persist
the stale snapshot to the new user's document (Codex P1).

Add an `abandoned` flag on `WriteQueue`. Three mechanisms cooperate:

- `getWriteQueue` marks every non-active queue abandoned when the
  user differs from the last-seen identity (pre-existing eviction
  site, now more aggressive).
- A `useEffect` on `userId` calls the same abandonment pass on every
  render with a new active identity, covering the window between
  logout/login and the new user's first toggle (when `getWriteQueue`
  would otherwise not fire).
- The flush loop checks `!queue.abandoned` in its while condition so
  the second and later iterations exit without firing another
  `mutateAsync` after the session changes.

The first iteration's in-flight request (already dispatched under the
original user's cookies) still runs to completion or failure on its
own — only the subsequent iterations, which are the dangerous ones,
are blocked.
…2708)

* feat: compose per-agent scope and per-user active-state filters in $ popover

Stack two runtime-truth filters on top of the existing `isUserInvocable`
check so the `$` skill popover matches what will actually be available at
turn time:

- Per-agent skill scope from `agent.skills` (resolved via useChatContext
  + useAgentsMapContext), mirroring backend `scopeSkillIds` semantics:
  `undefined`/`null` → no scope, `[]` → empty, non-empty → intersection.
- Per-user ownership-aware active state via `useSkillActiveState().isActive`.

The filters are composed in a pure, exported `filterSkillsForPopover`
helper so the agent-scope ∩ active ∩ invocable matrix can be unit-tested
without rendering the component. Short-circuits on cheapest check first
(agent scope → active → invocation mode).

Backend still enforces both filters at runtime; this PR is a UX mirror so
users do not see popover entries that would be filtered out by the time
the LLM turn begins.

* refactor: thread agentId into SkillsCommand as a prop

Drop the direct `useChatContext()` call inside SkillsCommand in favor of
receiving `agentId` from ChatForm. The parent already subscribes to the
conversation via its single useChatContext call, and SkillsCommand is
wrapped in React.memo — threading the id as a prop means the popover only
re-renders when agent_id actually changes instead of on every unrelated
conversation-shape mutation. Mirrors the pattern AttachFileChat already
uses for `conversation` / `agentId`.

No behavior change; filter semantics and test coverage are identical.

* fix: fail closed when agent skill scope cannot be resolved

Previously, if `conversation.agent_id` was set but the agents map had no
entry for it (hydration pending, query failure, or missing VIEW access),
the popover treated the scope as `undefined` and showed the full ACL
catalog. That leaks options the backend will reject at turn time, the
opposite of what this phase is meant to do.

Distinguish the unresolved cases ("map undefined" and "agent not in map")
from the intentionally-unconfigured case ("agent exists, no `skills`
field") and return `[]` for the former, preserving the backend semantics
of `scopeSkillIds` only for the latter. Adds two tests covering both
fail-closed branches.

* fix: surface agent.skills in list projection and treat ephemeral ids as unscoped

Two holes flagged on the earlier fail-closed commit:

1. The list-agents projection in `getListAgentsByAccess` omitted the
   `skills` field, so `agentsMap[agentId].skills` was always undefined
   and the popover fell back to the full ACL catalog for every scoped
   agent — the opposite of this phase's intent. Add `skills: 1` to the
   projection and lock it in with a new test.

2. Conversations can carry ephemeral agent ids (e.g. `ephemeral` after
   switching off the agents endpoint) that intentionally don't live in
   the agents map. The prior fail-closed branch blanked the popover in
   those cases. Treat anything that doesn't start with `agent_` as
   unscoped via the existing `isEphemeralAgent` helper so the popover
   shows the full ACL-visible catalog, matching how no-agent convos
   already behave.

Frontend: 18 tests pass (adds one ephemeral-id case).
Backend: 10 getListAgentsByAccess tests pass (adds one projection case).

* refactor: pass through hydration race, only fail closed when map is authoritative

Split the two "cannot resolve scope" cases that were previously collapsed
onto the same fail-closed branch:

- `agentsMap === undefined` means the agents list query has not settled
  yet. Return `undefined` (full catalog). The map typically hydrates well
  before the first `$` open, and the backend still scopes at turn time —
  blanking the popover during a sub-second race produces worse UX with
  no security benefit.
- `agentsMap` is populated but the agent is absent means the agent was
  deleted or the user's VIEW access was revoked mid-session. That is
  authoritative missing state, so keep the fail-closed behavior — the
  full catalog would be misleading.

Updates the associated test case to assert the hydration-race path now
shows the catalog, and rewrites the in-code comment to distinguish the
two branches.

* refactor: drop `as string` in agent scope memo by tightening the guard

`isEphemeralAgent` returns true for null/undefined so the original code
was runtime-safe, but its signature returns plain `boolean` rather than
a type predicate, so TypeScript never narrowed `agentId` to `string` and
the subsequent map lookup required an `as string` assertion. Split the
guard into `!agentId || isEphemeralAgent(agentId)` so the narrowing falls
out naturally and the assertion can be removed.

No behavior change; 18 tests pass.
* 🎬 feat: Prime Manually-Invoked Skills via $ Popover

Lands the backend for manual skill invocation, making the $ popover
deterministically prime SKILL.md before the LLM turn instead of leaving
the model to discover the skill via the catalog.

Flow: popover drains pendingManualSkillsByConvoId on submit, attaches
names to the ask payload, controllers forward to initializeAgent, and
initialize resolves each name to its body (ACL + active-state filtered,
reusing the same rules as catalog injection). AgentClient splices the
primes as meta HumanMessages before the user's current message.

- Extract primeManualSkill / resolveManualSkills in packages/api/src/agents/skills.ts
  and reuse primeManualSkill inside handleSkillToolCall for a single shape source.
- Thread manualSkills + getSkillByName through InitializeAgentParams / DbMethods
  and all three initializeAgent call sites (initialize.js, responses.js, openai.js).
- Splice HumanMessage primes in client.js chatCompletion after formatAgentMessages,
  shifting indexTokenCountMap so hydrate still fills fresh positions correctly.
- Carry isMeta / source / skillName in additional_kwargs for downstream filtering.

* 🛡️ fix: Scope manual skill primes to single-agent + cap resolver input

Two follow-ups to the Phase 3 priming path flagged in Codex review.

Multi-agent runs: skipping the splice when agentConfigs is non-empty.
`initialMessages` is shared across every agent in `createRun`, so splicing
a skill body there would bypass Phase 1's per-agent `scopeSkillIds`
contract — a handoff / added-convo agent with a different skill scope
would see content its configuration excludes. Warn + skip is the minimal
correct behavior; lifting this to per-agent initial state is a follow-up.

Input bounding: `resolveManualSkills` now truncates to `MAX_MANUAL_SKILLS`
(10) after dedup, with a warn listing the dropped tail. Controllers only
validate `Array.isArray(req.body.manualSkills)`, so a crafted payload
could otherwise fan out into an unbounded `Promise.all` of concurrent
`getSkillByName` DB lookups. Cap lives in the resolver so every caller
(including future `always-apply` in Phase 5) inherits it.

* 🧪 refactor: Testable Helpers + Payload Validation for Manual Skill Primes

Follow-ups from the comprehensive review. No behavior change for the
happy path — these are architectural and defensive improvements that
shrink the JS surface in /api, tighten the request-body contract, and
cover the delicate splice logic with proper unit tests.

- Extract `injectManualSkillPrimes` into packages/api/src/agents/skills.ts
  so the message-array splice and `indexTokenCountMap` shift are unit-
  testable in TS. client.js now calls the helper. Tests pin the `>=`
  vs `>` boundary condition — a regression here would silently corrupt
  token accounting for every message after the insertion point.
- Extract `extractManualSkills(body)` and use in all three controllers
  (initialize.js, responses.js, openai.js). Replaces copy-pasted
  `Array.isArray(...) ? ... : undefined` with a helper that also filters
  non-string / empty elements — closes a type-safety gap where a crafted
  payload like `{"manualSkills": [123, {"$gt":""}]}` would otherwise reach
  `getSkillByName` and waste DB round-trips.
- Rename `primeManualSkill` → `buildSkillPrimeMessage`. The helper serves
  three invocation modes (`$` popover, `always-apply`, model-invoked);
  the old name misled readers coming from `handleSkillToolCall`.
- Add `loadable.state === 'hasValue'` guard in `drainPendingManualSkills`
  — defensive, since the atom has a synchronous `[]` default, but the
  previous `.contents` cast would have been unsound under loading/error.
- Document why `resolveManualSkills` honors the active-state filter even
  for explicit `$` selections (Phase 2 popover filter + API-direct
  hardening).
- Remove stray `void Types;` in initialize.test.ts — `Types` is already
  consumed elsewhere in that test.

* 🔖 refactor: Single source for the skill-message source marker

Export `SKILL_MESSAGE_SOURCE = 'skill'` and use it in both construction
paths that stamp skill-primed messages — `buildSkillPrimeMessage` (for
the model-invoked tool path) and `injectManualSkillPrimes` (for the
user-invoked splice path). Downstream filtering and telemetry read this
marker, so the two paths must agree; keeping the literal in one place
removes the risk of them drifting when Phase 5's `always-apply` adds a
third caller.

* ♻️ refactor: Drop Multi-Agent Guard + Review Polish

- Remove the multi-agent skip in `AgentClient.chatCompletion`. Leaking
  primes to handoff / added-convo agents via shared `initialMessages` is
  the agents SDK's concern to scope; this layer should just inject and
  let the graph handle agent-scoped state. The guard was well-intended
  but produced a silent-drop UX where `$skill` in a multi-agent run did
  nothing.
- Bound the `[resolveManualSkills] Truncating ...` warn output to the
  first 5 dropped names plus a count suffix. A malicious payload of
  1000 names was previously spilling all ~990 names into the log line.
- Remove dead `?? []` from the `hasValue`-guarded loadable read in
  `drainPendingManualSkills` — the atom always yields a string[] when
  resolved, so the nullish fallback was unreachable.
- Reorder skills.ts imports to follow the style guide: value imports
  shortest-to-longest (`data-schemas` → `langchain/core/messages` →
  multi-line `@librechat/agents`), type imports longest-to-shortest.

* 🧠 fix: Strip Skill Primes from Memory Window + Unbreak CI Mocks

Two fixes after the last push.

CI unbreak: `responses.unit.spec.js` and `openai.spec.js` mock
`@librechat/api` and the mock didn't expose the new `extractManualSkills`
symbol, so every test in those files crashed before reaching the
`recordCollectedUsage` assertion. Added `extractManualSkills: jest.fn()`
returning `undefined` to both mocks; the controllers now no-op on
manualSkills as the tests expect.

Codex P2: `runMemory` passes `messages` straight through to the memory
processor, so after the splice in `injectManualSkillPrimes`, SKILL.md
bodies ride along as if they were real user chat. That pollutes memory
extraction with synthetic instruction content and crowds out real turns
from the window.

- Export `isSkillPrimeMessage(msg)` from `packages/api/src/agents/skills.ts`
  — a predicate keyed on the shared `SKILL_MESSAGE_SOURCE` marker.
- Filter `chatMessages = messages.filter(m => !isSkillPrimeMessage(m))`
  at the top of `runMemory` before the window-sizing logic. Keeps the
  primes visible to the LLM (they still ride in `initialMessages`) but
  invisible to the memory layer.
- 5 new tests for the predicate covering marker-present, plain messages,
  different source, non-object inputs, and array filter integration.

* 📜 feat: Show Skill-Loaded Cards for Manually-Invoked Skills

The $ popover was priming SKILL.md bodies into the turn but leaving no
visible trace on the assistant response — from the user's view it looked
like the `$name ` cosmetic text did nothing. Now each manually-invoked
skill renders the same "Skill X loaded" tool-call card that model-invoked
skills already produce via PR #12684's SkillCall renderer.

Approach: post-run prepend to `this.contentParts`. The aggregator owns
per-step indices during the run, so pre-seeding collides; waiting until
`await runAgents(...)` returns lets the graph settle before synthetic
parts slot in at the front.

- Export `buildSkillPrimeContentParts(primes, { runId })` from
  `packages/api/src/agents/skills.ts`. Returns completed tool_call parts
  (`progress: 1`, args JSON-encoded with `{skillName}`, output matching
  the model-invoked path's wording) that the existing `SkillCall.tsx`
  renderer draws identically.
- In `AgentClient.chatCompletion`, prepend the built parts to
  `this.contentParts` immediately after `await runAgents`. Persistence
  and the final-event reconcile come for free — `sendCompletion` already
  reads `this.contentParts` verbatim.
- Card ordering: skills appear first in the assistant message, reflecting
  that priming ran before the LLM's turn.

Live-during-streaming cards are a separate follow-up — the graph's
index-based aggregator makes that a bigger lift and this change delivers
the core UX win without fighting the stream ordering.

6 new unit tests covering part shape, args JSON contract, output text,
unique IDs, empty input, and startOffset ID differentiation.

* ⚡ feat: Emit Optimistic Skill Cards + Wire Primes in OpenAI/Responses

Two follow-ups from testing.

Optimistic card emit: the main chat path was only showing "Skill X
loaded" cards at final-reconcile time, so the user saw nothing happen
until the stream finished. Now emit synthetic ON_RUN_STEP +
ON_RUN_STEP_COMPLETED events right before `runAgents` starts — same
pattern the MCP OAuth flow uses in `ToolService` — so the cards appear
immediately. The graph's content at index 0 may overwrite them during
streaming, but the post-run `contentParts` prepend (unchanged) restores
them on final reconcile.

OpenAI + Responses parity: both controllers were resolving
`manualSkillPrimes` via `initializeAgent` but never injecting them into
`formattedMessages` before the run. Manual invocation silently did
nothing on `/v1/chat/completions` and the Responses API path. Now both
call `injectManualSkillPrimes` on the formatted messages so the model
sees SKILL.md bodies on every path. LibreChat-style card SSE events
don't apply to these OpenAI-shaped responses, so the live-emit is
chat-path-only.

- Export `buildSkillPrimeStepEvents(primes, { runId })` from
  `packages/api/src/agents/skills.ts`. Uses `Constants.USE_PRELIM_RESPONSE_MESSAGE_ID`
  by default so the frontend maps events to the in-flight preliminary
  response message, matching the OAuth emitter.
- In `AgentClient.chatCompletion`, emit via `sendEvent` (or
  `GenerationJobManager.emitChunk` in resumable mode) after
  `injectManualSkillPrimes` runs, before the LLM turn begins.
- Wire `injectManualSkillPrimes` into `openai.js` + `responses.js` after
  `formatAgentMessages`. Refactored the destructure to `let` on
  `indexTokenCountMap` so the injector's returned map is usable.
- 8 new unit tests covering the step-event builder: pair cardinality,
  default/custom runId, TOOL_CALLS shape + JSON args, progress:1 on
  completion, index ordering, stepId/toolCallId pairing, empty input.

* 🎯 fix: Route Skill Prime Events to the Real Response + Sparse-Array Offset

Two bugs in the optimistic-card emit from the last pass.

1. Wrong runId. The events used `USE_PRELIM_RESPONSE_MESSAGE_ID` (the
   MCP OAuth pattern), but OAuth emits DURING tool loading — before the
   real response messageId exists. By the time skill priming fires, the
   graph is about to emit with `this.responseMessageId`, so the PRELIM
   runId orphaned every card onto the client's placeholder response
   entry in `messageMap`, separate from the one the LLM's events were
   building. Net effect: cards never rendered mid-stream.

   Now passing `this.responseMessageId` — the same ID `createRun`
   receives — so synthetic and real steps land on the same `messageMap`
   entry.

2. Index 0 collision. With the runId fixed, card-at-0 would have hit
   `updateContent`'s type-mismatch guard when the LLM's text delta
   arrived at the same index, suppressing the whole text stream.

   New `SKILL_PRIME_INDEX_OFFSET` = 100 placed on both the live SSE
   emit and the server-side `contentParts` assignment. Sparse array
   during streaming renders as `[llm_text, ..., card]` (skip-holes via
   `Array#filter` / `Array#map`). `filterMalformedContentParts` from
   `sendCompletion` compacts to dense `[text, card]` before persistence,
   so streaming UI and saved message agree on order — no finalize
   reorder jank. Post-run switches from `contentParts.unshift` to
   `contentParts[OFFSET + i] = part` to mirror the live placement.

- Add `startIndex` option to `buildSkillPrimeStepEvents` with
  `SKILL_PRIME_INDEX_OFFSET` default. Export the constant from
  `@librechat/api` so `client.js` can reuse it for the post-run splice.
- Update the existing index-ordering test to the new default and add a
  new test for the explicit `startIndex` override.

* 🎗️ feat: Replace \$skill-name Text with Pills on the User Message

The `$skill-name ` cosmetic text the popover was inserting into the
textarea had two problems: it lingered in the user message forever (the
card is a more meaningful marker), and it implied that free-form text
invocation like \"\$foo help me\" should work — which it doesn't, and
supporting it would mean another parsing layer nobody asked for.

Dropped the textarea insertion. Visual confirmation after submit now
comes from a compact `ManualSkillPills` row on the user bubble that
self-extinguishes once the backend's live skill-card stream
(`buildSkillPrimeStepEvents` from the last commit) populates the sibling
assistant response. Multiple skills render as multiple pills — the atom
was already a string array, so multi-select works for free.

- `SkillsCommand.tsx`: select handler no longer writes to the textarea.
  Still drops the trigger `$` via `removeCharIfLast`, still pushes to
  `pendingManualSkillsByConvoId`, still flips `ephemeralAgent.skills`.
- `families.ts`: new `attachedSkillsByMessageId` atomFamily keyed by
  user messageId. `useChatFunctions.ask` writes the drained skill list
  here on every fresh submit (regenerate/continue/edit still skip).
- `ManualSkillPills.tsx` renders pills conditionally: hidden when the
  message isn't a user message, when no skills are attached, or when
  the sibling assistant response already carries a `skill` tool_call
  content part (the live card took over). Reads messages via React Query
  so we don't re-render on every message-state keystroke.
- `Container.tsx` mounts the pills above the user message text, parallel
  to the existing `Files` slot.
- Updated the SkillsCommand select-flow spec to assert the textarea is
  cleared of `$` instead of populated with `\$name `. 5 new tests for
  `ManualSkillPills` covering empty state, non-user message guard,
  multi-skill rendering, the skill-card hide condition, and the
  text-only-content-doesn't-hide case.

* 🎛️ feat: Manual Skills as Persisted Message Field + Compose-Time Chips

Three problems with the previous pass:
1. Cards rendered BELOW the LLM text on the assistant message (and
   stayed there on reload) because the sparse index-100 offset put them
   after the model's content. Now back to `unshift` — cards at the top,
   same as before the live-emit detour.
2. Pills on the user message disappeared the moment the live card
   arrived, so users barely saw them. The live-emit channel also added
   meaningful complexity and relied on a per-message Recoil atom that
   had no clean cleanup story.
3. No visual cue at all during new-chat compose — the `$name ` text was
   removed, the submitted-message pills weren't there yet, and the
   popover closes after selection. User had no way to see what they'd
   queued up before sending.

New architecture: `manualSkills` is a first-class field on `TMessage`,
persisted by the backend on the user message. `ManualSkillPills` reads
straight from `message.manualSkills` — no atom, no sibling-lookup — so
pills survive reload, show in history, and stay for the lifetime of the
message. Compose-time chips above the textarea read the existing
`pendingManualSkillsByConvoId` atom and let users × skills out before
submitting.

Backend reverts:
- `client.js`: dropped the `ON_RUN_STEP` live-emit loop, restored
  `this.contentParts.unshift(...primeParts)` so cards sit at the top of
  the persisted assistant response.
- `skills.ts`: removed `buildSkillPrimeStepEvents` and
  `SKILL_PRIME_INDEX_OFFSET` (both unused now). `GraphEvents`,
  `StepTypes`, and `Constants` imports went with them. Removed 8 tests.

Field persistence:
- `tMessageSchema` gains `manualSkills: z.array(z.string()).optional()`.
- Mongoose message schema gains `manualSkills: { type: [String] }` with
  matching `IMessage` TS field.
- `BaseClient.js` reads `req.body.manualSkills` on user-message save,
  filters to non-empty strings, pins onto `userMessage` before
  `saveMessageToDatabase`. Mirrors the existing `files` pattern right
  above it. Runtime resolution still reads top-level `req.body.manualSkills`
  — persistence and resolution are separate concerns.

Frontend:
- `useChatFunctions.ask` sets `currentMsg.manualSkills` directly; the
  drained atom value goes onto the message, not a separate atom.
  Removed the `attachSkillsToMessage` Recoil callback.
- `ManualSkillPills`: pure render of `message.manualSkills`. No more
  `useQueryClient`, no sibling scan, no atom read. Loses the
  auto-hide-when-card-arrives behavior — pills stay on the user
  bubble, cards live on the assistant bubble, both are informative.
- Dropped the `attachedSkillsByMessageId` atomFamily and its export.
- New `PendingManualSkillsChips` above the textarea reads the
  compose-time atom and renders chips with × to remove. Mounted in
  `ChatForm` right after `TextareaHeader`. Naturally hides on submit
  when the atom drains.

Tests: updated `ManualSkillPills` suite to the new field-based reads
(5 passing). New `PendingManualSkillsChips` suite covering empty state,
multi-chip render, single × removal, and full-clear (4 passing).
Backend suite trimmed to 89 (was 97) from the step-events test
removal — no regressions on the remaining helpers.

* 🧪 feat: Assistant-Side Skill-Loading Chips + Pill Padding

Two small UX fixes on top of the field-on-message architecture.

Pill padding: bumped the user-side `ManualSkillPills` from `py-0.5` to
`py-1` on each chip and added `py-0.5` to the wrapper so the row
breathes a little without feeling tall.

Mid-stream indicator: new `InvokingSkillsIndicator` mirrors the parent
user message's `manualSkills` onto the assistant bubble as transient
"Running X" chips while the real card is in flight. Renders above
`ContentParts` in `MessageParts`. Hides itself when the assistant's
own `content` grows a `skill` tool_call — the authoritative card from
`buildSkillPrimeContentParts.unshift` is showing, so the placeholder
steps aside. No SSE emit, no aggregator injection, no index
collision with the LLM's streaming content: just a render slot keyed
off the parent's field.

Why not stream the cards live: whichever content index we'd choose
either blocks the LLM's text stream (`updateContent` type-mismatch at
index 0) or lands below the response after sparse compaction (index
100+). Mirroring the parent field sidesteps the aggregator entirely
and gives the user an immediate "skill is loading" signal that
naturally gives way to the real card at finalize.

Covers the gap the user flagged: pills on the user message said "I
asked for these" but nothing on the assistant side said "we're
working on it" until the stream finished. 5 new tests for the
indicator: user-msg guard, missing parent-field guard, multi-chip
render, hides-on-card-landing, orphan-parent guard.

* 🔁 fix: Indicator Visibility + Carry Manual Skills Through Regenerate/Edit

Two bugs.

Indicator never rendered: `InvokingSkillsIndicator` looked up the parent
user message via `queryClient.getQueryData([QueryKeys.messages, convoId])`,
but on a new chat the React Query cache is keyed by `"new"` (the URL
`paramId`) until the server assigns a real conversation ID — while
`message.conversationId` on the assistant message is already the server
ID. Lookup missed, `skills.length === 0`, nothing rendered. Switched
to `useChatContext().getMessages()`, which reads from the same
`paramId` the rest of the UI uses, so new-chat and existing-chat cases
both resolve to the correct message list.

Regenerate / save-and-submit dropped manual skills: the compose-time
`pendingManualSkillsByConvoId` atom is drained on the first submit,
so replaying that turn later found an empty atom and sent `manualSkills: []`.
The pills were still on the user bubble, so from the user's point of
view the model was running primed — but the backend saw nothing and
produced an unprimed response.

- Added `overrideManualSkills?: string[]` to `TOptions`. Callers with a
  reference message pass its persisted `manualSkills`; `useChatFunctions.ask`
  uses the override verbatim when present, otherwise falls back to the
  existing drain-or-empty logic.
- `regenerate` in `useChatFunctions` passes `parentMessage.manualSkills`
  — the user message being regenerated has the field persisted by the
  backend, so the second turn primes the same skills as the first.
- `EditMessage.resubmitMessage` covers both edit branches:
  - User-message save-and-submit: forwards the edited message's own
    `manualSkills` so the new sibling turn primes identically.
  - Assistant-response edit: forwards the parent user message's
    `manualSkills` for the same reason.

Indicator test suite converted from `@tanstack/react-query` harness to
a jest-mocked `useChatContext().getMessages()`. 6 tests (was 5), added
a cache-miss case.

* 🧭 fix: Drive Mid-Stream Skill Chips from Submission Atom, Not Message Lookup

Message-ID-keyed lookups kept racing the stream: the user message flips
from its client-side intermediate UUID to the server-assigned ID mid-run,
conversation IDs flip from the URL `paramId="new"` to the real convo
ID on brand-new chats, and the React Query cache splits briefly between
the two. Previous attempts — direct `queryClient.getQueryData` and then
`useChatContext().getMessages()` — each missed a different window.

`TSubmission.manualSkills` is already populated at `ask()` time and the
submission atom (`store.submissionByIndex(index)`) is the single stable
anchor across the whole lifecycle: set once at submit, lives through
every SSE event, cleared when the stream ends. No ID lookups, no cache
timing.

- `InvokingSkillsIndicator` now reads `submissionByIndex(index)` via
  Recoil. Shows chips when:
    • the message is assistant-side,
    • a submission is in flight with non-empty `manualSkills`,
    • the assistant's `parentMessageId` matches
      `submission.userMessage.messageId` (so chips appear only on the
      bubble for the current turn, never on siblings),
    • the assistant's own content doesn't yet carry a `skill`
      tool_call (real card takes over from the server's post-run
      `contentParts.unshift`).
- Drops the `useChatContext().getMessages()` dependency and the
  `useQueryClient` dependency before that. No more lookups by
  conversationId or messageId.

Test suite now mocks `useChatContext` to supply `index: 0` and seeds
the `submissionByIndex(0)` atom via Recoil initializer. 6 cases cover
user-side, no-submission history, empty `manualSkills`, multi-chip
render, hides-on-card-landing, and wrong-turn guard.

* 🌱 fix: Seed Response manualSkills in createdHandler, Indicator Becomes Pure

The mid-stream indicator kept getting wired off state I don't own: first
`queryClient.getQueryData` (raced the new-chat paramId flip), then
`useChatContext().getMessages()` (same cache, same race), then
`useRecoilValue(submissionByIndex)` (pulled every message into the
submission subscription — re-renders all indicators on any submission
change, exactly the "limit hooks in rendering" concern).

Cleanest path is the one the user pointed at: the submission owns the
data, `useSSE` / `useEventHandlers` owns the save points, so seed the
field ONTO the response message at the save site and let the indicator
be a pure prop-read.

- `createdHandler` now writes `manualSkills` onto the initial response
  from `submission.manualSkills` at the moment the placeholder enters
  the messages array. The field rides through the normal mutation
  pipeline via spreads (`useStepHandler` response creation,
  `updateContent` result returns) — no special handling needed.
- `InvokingSkillsIndicator` drops the Recoil / context / queryClient
  reads. Pure function of `message`: if assistant, has `manualSkills`,
  and `content` hasn't grown a `skill` tool_call yet, render chips.
  Only `useLocalize` left, which was already unavoidable for the i18n
  string.
- Renders decouple: no single state change (`submissionByIndex` flip,
  React Query cache update) forces every indicator in the message list
  to re-render anymore. Only the message whose prop changed re-runs.

Finalize story unchanged: server's `responseMessage` doesn't carry the
frontend-only `manualSkills` field, so `finalHandler`'s replacement
drops it — but by then the real `skill` tool_call is in `content`
and the indicator's content-scan hides itself anyway.

Test suite back to pure prop mocks: 7 cases covering user-guard,
no-seed, multi-chip render, skill-card-hide, non-skill-tool-call-keeps,
text-only-keeps, and missing message.

* 🪞 fix: Render Skill Indicator Inside ContentParts, Adjacent to Parts

The indicator still wasn't showing because even though MessageParts
mounted it as a sibling of ContentParts, ContentParts is a `memo`'d
component that owns the only rendering path that refreshes in lockstep
with content deltas. Mounting above it put the indicator one layer
further out — reachable, but not exercised on the same render cycle
that processes the streaming `message` prop.

Moved the indicator into ContentParts itself, rendered at the top of
both the sequential and parallel branches. Reads the `message` prop
(newly threaded through as an optional prop alongside `content`), so:

- Same render cycle as Parts — updates from the SSE pipeline flow
  through the same pathway.
- Lives outside the `content.map`, so delta-driven content reshuffles
  never wipe it.
- Still a pure prop-read inside the indicator itself (no Recoil,
  queryClient, context hooks). The only dep is `useLocalize`.

Thread:
- `ContentPartsProps` gains `message?: TMessage`.
- `MessageParts` passes `message={message}` through, drops its own
  indicator mount + import.
- `ContentParts` renders `<InvokingSkillsIndicator message={message} />`
  in both the parallel-content and sequential-content branches, right
  under `MemoryArtifacts` and before the empty-cursor / parts map.

Companion data flow (unchanged): `createdHandler` seeds
`initialResponse.manualSkills` from `submission.manualSkills`; the
field rides through `useStepHandler` via spreads; indicator hides on
`skill` tool_call landing in `content`.

* 🔎 refactor: Narrow Skill Components to Scalar skills Prop, Kill Memo Churn

Passing the full `message` object into presentational components busts
`React.memo` shallow comparisons every time the message reference changes
for unrelated reasons. Swap to scalar `skills?: string[]` throughout:

- `InvokingSkillsIndicator`: props-only (`skills?: string[]`); visibility
  logic (user-vs-assistant, skill tool_call arrival) now lives in the
  caller so this stays pure presentational.
- `ManualSkillPills`: props-only (`skills?: string[]`).
- `ContentParts`: takes `manualSkills?: string[]` scalar, computes
  `showInvokingSkills` once per render from `manualSkills` + content scan
  for the `skill` tool_call, then mounts the indicator with `skills=`
  prop in both parallel and sequential branches.
- `MessageParts`: passes `manualSkills={message.manualSkills}` through
  to `ContentParts`.
- `Container`: passes `skills={message.manualSkills}` to `ManualSkillPills`.
- Tests updated to exercise the narrowed prop surface.

* 📜 feat: Mid-Stream Skill Cards via SkillCall, Drop Custom Indicator

Instead of a separate `InvokingSkillsIndicator` chip component, render
pending skill placeholders through the existing `SkillCall` renderer —
same component the backend's finalized prime part uses. The loading
visual (`progress < 1` + empty output → pulsing "Running X") and the
completed visual ("Ran X") now come from one source of truth.

`ContentParts` computes `pendingSkillNames` from `manualSkills` minus
any `skill` tool_call already in `content` (dedupe by `args.skillName`
since the synthetic's id differs from the real one). Those names
render through a separate slot ABOVE the Parts iteration — not
prepended to the content array, which would shift React keys on
every downstream streaming text / tool part and force unmount/remount
mid-stream.

When the real prime `tool_call` lands at finalize (backend unshifts to
content[0..]), `collectExistingSkillNames` picks it up, the pending
set empties, and the real part takes over rendering in the Parts
iteration. Layout is identical either way because primes are always
at the top of content.

- `InvokingSkillsIndicator.tsx` + test deleted (no longer referenced)
- `ContentParts.tsx` renders `<SkillCall .../>` directly for pending
  names, mirrors `Part.tsx`'s usage of the same component
- `createdHandler` doc comment updated to reflect the new flow

* ✂️ fix: Render Interim Skill Cards From manualSkills Only, Leave Content Untouched

Previous revision read `content` to de-dupe pending cards against real
`skill` tool_calls, so any optimistic skill part streamed from the
backend would race our placeholder off the screen mid-turn — exactly
the "getting overridden" symptom.

Now: interim `SkillCall` cards are driven purely by the response
message's `manualSkills` field. `content` is never inspected here,
so no backend delta can pull the cards down. The field is now seeded
directly onto the assistant placeholder in `useChatFunctions` (not
only in `createdHandler`) so the cards appear from the first render,
before the `created` SSE event round-trip.

Lifecycle:
- `useChatFunctions` puts `manualSkills` on the freshly-minted
  `initialResponse` — cards render the instant the placeholder lands.
- `createdHandler` keeps its own re-seed (idempotent; safe) so a
  regenerate / save-and-submit flow that hits that path still works.
- `useStepHandler` spread operations preserve the field through every
  content update.
- `finalHandler` replaces the message with the server-backed
  `responseMessage` (no `manualSkills`) — cards disappear, and the
  real `skill` tool_call part in `content` takes over.

ContentParts changes:
- Drop `collectExistingSkillNames` / `parseJsonField` dedupe path.
- `renderPendingSkills` reads only `manualSkills` + `isCreatedByUser`.
- Simpler control flow — one boolean (`hasPendingSkills`) gates the
  early return, one function renders.

* 🩹 fix: Codex Review Resolutions — Localization, Guards, Tests, Docs

Addresses seven findings from comprehensive code review:

Finding 1 (MAJOR) — Document sticky re-priming as intentional
- `buildSkillPrimeContentParts`: expanded doc comment explaining
  synthetic `skill` tool_calls persist and get re-primed on every
  subsequent turn via `extractInvokedSkillsFromPayload` (shape parity
  with model-invoked skills). This matches the UX: the assistant
  skill card is a visible, persistent signal that the skill is active
  for the conversation. Not a bug — called out explicitly so future
  maintainers don't mistake it for one.

Finding 2 (MAJOR) — Add ContentParts render tests
- New `ContentParts.test.tsx` with 7 cases covering the interim skill
  card logic: assistant-only rendering, user-message suppression,
  undefined-content safety, parallel+sequential branch integration,
  progress<1 (pending) state. Child components mocked so the test
  exercises only the branching and prop wiring ContentParts owns.

Finding 3 (MINOR) — Localize hardcoded aria-labels
- Added `com_ui_skills_manual_invoked` + `com_ui_skills_queued` keys.
- Reused existing `com_ui_remove_skill_var` for the remove-button
  aria-label.
- `PendingManualSkillsChips` and `ManualSkillPills` now call
  `useLocalize()`. Test mocks updated to the label-echo pattern.

Finding 4 (MINOR) — Max-length guard in `extractManualSkills`
- New `MAX_SKILL_NAME_LENGTH = 200` constant and filter. Blocks a
  crafted payload like `{ manualSkills: ['a'.repeat(100000)] }` from
  reaching `getSkillByName` / Mongo's query planner.

Finding 5 (NIT) — `BaseClient.js` comment contradicted itself
- Rewrote to call the filter what it is: defense-in-depth on top of
  Mongoose schema validation, not a redundant second layer.

Finding 6 (NIT) — `ManualSkillPills` now wrapped in `React.memo`
- Consistent with peer components (`PendingManualSkillsChips`,
  `ContentParts`). Rendered inside `Container`, which re-renders on
  every content update, so the memo is a real cycle savings.

Finding 7 (NIT) — Redundant guard in `ContentParts.renderPendingSkills`
- Collapsed the duplicate null-check by computing `pendingSkills` as
  a `useMemo`'d array (`[]` when not applicable), and mapping
  directly. `hasPendingSkills` now derives from the array length —
  one source of truth, no redundant gate inside the render function.

* 🔧 fix: Update ParallelContent to Handle Optional Content Prop

Modified the `ParallelContentRendererProps` to make the `content` prop optional, ensuring safer access within the component. Adjusted the calculation of `lastContentIdx` to handle cases where `content` may be undefined, preventing potential runtime errors. This change enhances the robustness of the component when dealing with varying message structures.

* 🎯 fix: Thread manualSkills Through ContentRender — The Real Renderer

This is why the interim skill cards never appeared across many rounds of
iteration: `ContentRender.tsx` (the memo'd renderer used by most paths,
including the agents endpoint) was calling `ContentParts` without the
`manualSkills` prop. Only `MessageParts.tsx` had it wired up — and
that's not the component that actually renders the assistant response
in production.

Two fixes:
1. Pass `manualSkills={msg.manualSkills}` to the `ContentParts` call.
2. Extend the `areContentRenderPropsEqual` memo comparator to include
   `manualSkills.length`, otherwise a message update that adds the
   field (seeded by `useChatFunctions` on the initialResponse) would
   be bailed out by the memo and never re-render.

Verified the two ContentParts call sites are now consistent; Container
usages for `ManualSkillPills` on the user side were already correct.

* 🧹 polish: Address Audit Follow-Up (F1/F3/F6)

F1 — Clarify sticky re-priming opt-out path.
  The previous comment said "regenerate without the pick" as one
  opt-out, but `useChatFunctions.regenerate` forwards the original
  picks via `overrideManualSkills`, so regeneration alone keeps the
  skill sticky. Updated to: edit the originating message to remove
  the pills and resubmit, or start a new conversation.

F3 — Add DOM-order assertions to the parallel + sequential tests.
  The two "alongside" tests verified both elements existed but
  didn't pin the ordering contract. Both now use
  `compareDocumentPosition` to assert the pending SkillCall
  precedes the real content, matching the backend semantic
  (`contentParts.unshift(...primeParts)` puts primes at the top).

F6 — Fix package import order in PendingManualSkillsChips.
  `recoil` (58 chars) was listed before `lucide-react` (45 chars)
  which violates the "shortest to longest after react" rule in
  AGENTS.md. Swapped order; no behavior change.

F2 / F4 / F5 from the audit were confirmed as non-issues
(React-safe empty map, cosmetic test-mock artifact, accepted
memo tradeoff) and require no change.

* ✨ feat: Dedicated PendingSkillCall + Running→Ran Transition on Real Content

UX polish on the interim skill card now that it's actually rendering:

1. New `PendingSkillCall` component (mirrors `SkillCall` visually but
   drops the expand affordance). `SkillCall`'s underlying `ProgressText`
   always renders a chevron + clickable button when any input is
   present, which on a card with empty output points at nothing —
   misleading cursor:pointer and a no-op toggle. The pending variant
   has only the icon + label, no button wrapper, no chevron.

2. "Running X" → "Ran X" transition when real content lands.
   `ContentParts` computes `hasRealContent` (any non-text part, or a
   text part with non-empty content — placeholder empty-text parts
   don't count) and passes `loaded={hasRealContent}` to
   `PendingSkillCall`. Matches what users see for model-invoked skills
   as they finish priming: pulsing shimmer → static icon.

3. Cleanup:
   - Dropped direct `SkillCall` import from `ContentParts` (replaced
     by `PendingSkillCall`). `SkillCall` is still used by `Part` for
     real `skill` tool_call content parts — no behavior change there.
   - Removed the now-redundant explicit `manualSkills` assignment
     in `createdHandler`. `useChatFunctions` seeds the field on
     `initialResponse` at construction, so the `...submission.initialResponse`
     spread already carries it through — the re-assignment was
     defensive belt-and-suspenders doing the same work twice. Comment
     rewritten to describe the actual lifecycle.

Tests updated to the new component (12/12 pass): two new cases pin
the loaded-state transition (unloaded when content has no real parts,
flips to loaded once a non-empty text part lands).
* 🪜 chore: Plumb `allowedTools` through `resolveManualSkills`

Tiny shape-only precursor shared by Phase 5 (`always-apply`) and Phase 6
(frontmatter runtime enforcement). Adds `allowedTools?: string[]` to
`ResolvedManualSkill` and widens the `getSkillByName` return type in
`ResolveManualSkillsParams` and `InitializeAgentDbMethods` to carry the
same field. The resolver forwards `skill.allowedTools` verbatim when
present.

No runtime behavior change — the field is populated but not yet consumed.
Phase 6 will union the per-skill allowlist into the agent's effective
tool set for the turn; Phase 5's `ResolvedAlwaysApplySkill` will mirror
this shape. Landing this first eliminates the type-shape race between
the two phases.

* 🪜 style: Drop phase-name refs from `allowedTools` JSDoc for longevity

JSDoc that cites "Phase N will X" goes stale the moment that phase ships.
Swap for "future runtime enforcement" so the docs age with the code.
…le` / `allowed-tools` (#12745)

* 🧬 feat: Persist `disable-model-invocation` / `user-invocable` / `allowed-tools`

Adds first-class columns mirroring the three runtime-enforced frontmatter
fields, with a `deriveStructuredFrontmatterFields` helper that maps from
frontmatter at create/update time and re-syncs (via `$unset`) when fields
are removed. `listSkillsByAccess` projection includes them so the Phase 6
catalog filter and popover filter can both read off the summary row.

Marks `invocationMode` as @deprecated on `TSkill` and the
`InvocationMode` enum — the runtime now reads the persisted pair instead.

* 🛡️ feat: Enforce frontmatter at runtime (catalog, skill tool, manual resolver, tool union)

Wires the persisted columns into actual runtime behavior across all four
invocation paths:

- `injectSkillCatalog` excludes `disableModelInvocation: true` skills
  before catalog formatting — they cost zero context tokens and stay
  invisible to the model.
- `handleSkillToolCall` rejects with a clear error when the model names
  a skill marked `disable-model-invocation: true` (defends against a
  stale-cache or hallucinated invocation getting past the catalog
  filter).
- `resolveManualSkills` skips `userInvocable: false` skills with a warn
  log so an API-direct caller can't bypass the popover-side filter.
- `unionPrimeAllowedTools` collects skill-declared `allowed-tools` minus
  what's already on the agent; `initialize.ts` re-runs `loadTools` for
  the extras and merges resulting `toolDefinitions` into the agent's
  effective set for the turn. Tool-name resolution is tolerant —
  unknown names silently drop with a debug log so cross-ecosystem
  skills referencing yet-to-be-implemented tools (Claude Code's
  `edit_file`, etc.) import without breaking. The agent document is
  never modified; the union is turn-scoped.

Helper exports (`unionPrimeAllowedTools`) are structured so Phase 5's
always-apply primes flow through the same union (combined
`[...manualPrimes, ...alwaysApplyPrimes]`) once the resolver lands.

Skill handler wire format gains the three fields so clients can render
them on detail / list views.

* 🎛️ feat: `$` popover reads `userInvocable` instead of UI-only `invocationMode`

Replaces the phase-1 UI-only `invocationMode` check with the persisted
`userInvocable` field (mirrors the `user-invocable` frontmatter). Skills
authored with `user-invocable: false` no longer surface in the popover;
the backend resolver enforces the same rule for defense-in-depth.

Default-visible behavior is preserved: skills without an explicit
`userInvocable` value (older rows, freshly imported skills that don't
declare the field) stay visible — only an explicit `false` hides them.

Test fixture updated to reflect the new field.

* 🔧 fix: Address Phase 6 review findings

Codex P2 + reviewer #1: Single `loadTools` call with the union of
`agent.tools + allowed-tools`. The earlier two-call approach dropped
`userMCPAuthMap` / `toolContextMap` / `actionsEnabled` from the
skill-added pass — an MCP tool gained via `allowed-tools` would be
visible to the model but fail at execution without per-user auth
context. Resolution of `manualSkillPrimes` is hoisted before
`loadTools` so the union can be computed up-front; the dropped-tools
debug log now compares loaded vs. requested across the single call.

Codex P3 + reviewer #2: `injectSkillCatalog.activeSkillIds` now
includes `disable-model-invocation: true` skills. The runtime ACL
check in `handleSkillToolCall` previously couldn't reach the explicit
"cannot be invoked by the model" rejection because the broader access
set excluded those skills. Catalog text and tool registration still
gate on the visible subset (zero-context-token guarantee preserved);
only the per-user `isActive` filter is a hard exclusion now.

Reviewer #1 (try/catch around loadTools, MAJOR): A single bad
`allowed-tools` entry from a shared skill could crash the entire turn.
Now wrapped — on failure with extras, retry with just `agent.tools`
and continue (the dropped-tools debug log surfaces what vanished). If
the retry-without-extras still throws, propagate; the agent's own
tools are the load-bearing surface.

Reviewer #3 (integration tests, MAJOR): Added six tests in
`initialize.test.ts` covering the full `allowed-tools` loading path:
union pass-through, no-extras short-circuit, agent-baseline dedup,
loadTools throw + retry, propagated throw without extras, and the
empty-tools edge case.

Smaller cleanups bundled in:
- Reviewer #4: Moved `logger` import to the package-imports section
  (was wedged among local imports).
- Reviewer #5: Removed unused index on `disableModelInvocation`
  (filtering happens application-side in `injectSkillCatalog`; index
  cost write overhead for zero query benefit).
- Reviewer #6: Swapped order of `userInvocable` and body checks in
  `resolveManualSkills` so the more authoritative author-decision
  reason surfaces first when both apply.
- Reviewer #8: Documented the `allowedTools` enforcement gap on the
  schema + type — model-invoked skills (mid-turn `skill` tool calls)
  do NOT trigger tool union, since adding tools after the graph
  starts would require a rebuild. Manual / always-apply (Phase 5)
  primes are the supported paths.
- Reviewer #9: Renamed `dmi` / `ui` / `at` locals to
  `disableModelInvocationRaw` / `userInvocableRaw` / `allowedToolsRaw`
  in `deriveStructuredFrontmatterFields`.

Reviewer #7 (DRY shared `getSkillByName` return type) deferred —
field sets diverge meaningfully across the three call sites (handler
needs `body + fileCount`; resolver needs `author + allowedTools +
userInvocable`; the InitializeAgentDbMethods contract needs the
superset). A `Pick<>`-based consolidation is a follow-up cleanup.

* 🔧 fix: Address codex iter 2 — catalog quota + duplicate-name dedup

P1: `injectSkillCatalog` cap now counts only model-visible skills, not
the merged active set. The previous behavior let a tenant with many
`disable-model-invocation: true` rows near the top of the cursor
exhaust the 100-slot quota before any invocable skill got scanned —
the catalog could end up empty even though invocable skills existed
further down the paginated results. `MAX_CATALOG_PAGES` stays the
ceiling on scan budget; only `visibleCount` drives the early-exit on
quota fill.

P2: When an invocable and a `disable-model-invocation: true` skill
share a name, drop the disabled doc(s) from `activeSkillIds`. Without
this dedup, `getSkillByName` (which sorts by `updatedAt` desc) could
pick the disabled doc and every model call to the cataloged name
would fail with "cannot be invoked by the model" instead of executing
the visible skill. When ONLY a disabled doc exists for a name, it
stays in `activeSkillIds` so the explicit-rejection error path still
fires for hallucinated invocations.

Tests: 3 new cases in `injectSkillCatalog` covering (a) cap counted
on visible skills only, (b) same-name collision drops disabled doc,
(c) sole-disabled-name case keeps the disabled doc.

* 🔒 fix: Apply `disable-model-invocation` gate to read_file too (codex iter 3 P1)

`activeSkillIds` is shared between the `skill` and `read_file` handlers.
The skill-tool gate was applied last iteration, but `handleReadFileCall`
authorized purely on `getSkillByName(..., accessibleIds)` — so a model
that learned a hidden skill's name (stale catalog or hallucination)
could still read its `SKILL.md` body or bundled files via `read_file`,
defeating the contract. Same explicit rejection now fires from both
handlers; no change needed to the ACL set itself (disabled docs stay
in `activeSkillIds` so the explicit error path keeps firing).

Two new tests in `handlers.spec.ts` cover the read_file gate and
regression-protect the happy path.

* 🔧 fix: Address codex iter 4 — manual-prime exception + legacy frontmatter backfill

P1: Scope the `read_file` `disableModelInvocation` gate to AUTONOMOUS
model probes only. A user-invoked `$` skill that is also marked
`disable-model-invocation: true` had its bundled `references/*` /
`scripts/*` files unreadable, leaving the manually-primed skill body
referencing files the model couldn't load. Now the handler bypasses
the gate when the skill name appears in `manualSkillNames` (the
per-turn allowlist threaded from `manualSkillPrimes` →
`agentToolContexts` → `enrichWithSkillConfigurable` →
`mergedConfigurable`). Defense-in-depth: the bypass is scoped to the
specific names in the allowlist; a different disabled skill name is
still rejected.

P2: Read-time fallback for legacy skills authored before Phase 6
landed the structured columns. `user-invocable: false` /
`disable-model-invocation: true` set in `frontmatter` (the validator
already accepted those keys) but with no derived column would
incorrectly evaluate as "user-invocable / model-allowed" until a save
backfilled the columns. New `backfillDerivedFromFrontmatter` helper
fills undefined columns from frontmatter at read time in both
`getSkillByName` and `listSkillsByAccess` — column wins when both are
set, frontmatter fills the gap when only it's set. No DB writes; the
next `updateSkill` naturally persists. `listSkillsByAccess` projection
expanded to include `frontmatter` (bounded by validator, payload
impact small) so summaries can also be backfilled.

Sticky-primed disabled skills (ones invoked in prior turns of the
same conversation) are not yet in the manual-prime allowlist — same-
turn manual invocation is the load-bearing path codex flagged; the
sticky-turn case is a known limitation tracked for a follow-up.

Tests: 2 new in handlers.spec.ts (manual-prime allows + name-scoped
block holds), 3 new in skill.spec.ts (legacy backfill via
getSkillByName + listSkillsByAccess + column-wins precedence).

* 🔧 fix: Address codex iter 5 — propagate manualSkillNames + keep read_file

P1: `enrichWithSkillConfigurable` is also called from `openai.js` and
`responses.js` (the OpenAI Responses + completions endpoints). Both
were ignoring the new `manualSkillNames` parameter, which meant the
manual-prime exception in the `read_file` gate (iter 4) only worked
on the agents endpoint. Now all three call sites pass
`primaryConfig.manualSkillPrimes?.map(p => p.name)` so manual `$`
invocations of disabled skills work consistently across endpoints.

P2: When every accessible skill is `disable-model-invocation: true`,
the catalog text and `skill` tool are correctly omitted (no model-
reachable targets) — but `read_file` and `bash_tool` MUST still be
registered. A user manually invoking such a skill gets its SKILL.md
body primed into context; if the body references `references/foo.md`
or `scripts/run.sh`, those reads need a registered tool. Restructured
`injectSkillCatalog` so `skill` registration is gated on
`catalogVisibleSkills.length > 0` while `read_file` (always) and
`bash_tool` (when codeEnvAvailable) register whenever any active
skill is in scope.

Tests: existing all-disabled test rewritten to assert read_file IS
registered + skill is NOT; new test confirms bash_tool joins it
when codeEnvAvailable.

* 🔧 fix: Address codex iter 6 — name-collision consistency via preferInvocable

P2a (resolveManualSkills): a name collision between an older
user-invocable doc and a newer non-user-invocable doc made manual `$`
invocation silently no-op. The popover surfaced the older invocable
doc; resolver looked it up by name; `getSkillByName` returned the
newer non-invocable doc; resolver skipped on `userInvocable: false`.

P2b (handler / runtime ACL): with same-name duplicates (e.g. older
invocable + newer disabled), the manual prime resolved to one doc
while later `read_file` / `skill` execution resolved a different doc
through `activeSkillIds`. Model could follow one SKILL.md body while
reading files from a different skill.

Both root-cause: `getSkillByName` always returned the newest match
and let the caller filter, but with collisions the newest can be
something the caller didn't want.

Fix: extend `getSkillByName` with `options.preferInvocable`. When
true, prefer the newest doc satisfying BOTH `userInvocable !== false`
AND `disableModelInvocation !== true` (with frontmatter backfill);
fall back to the newest match otherwise. Fast path preserved when
caller doesn't opt in.

Callers passing `preferInvocable: true`:
- `resolveManualSkills` — picks the popover-visible invocable doc
  even when a newer disabled / non-user-invocable duplicate exists.
- `handleSkillToolCall` — keeps execution aligned with the catalog;
  falls back to the disabled doc only when no invocable variant
  exists (so the explicit "cannot be invoked by the model" gate
  still fires for the hallucinated-disabled-name case).
- `handleReadFileCall` — same alignment, plus the manual-prime
  exception added in iter 4 still applies.

Tests:
- 2 new in skill.spec.ts (preferInvocable picks invocable when
  collision exists; falls back to newest when no clean-invocable
  exists).
- 1 new in skills.test.ts (resolver passes preferInvocable through).
- 2 new in handlers.spec.ts (skill tool + read_file pass it).
- Existing initialize.test.ts assertion updated for the new option.

* 🔧 fix: Address codex iter 7 — split preferInvocable into per-axis flags

The previous unified `preferInvocable` filter required BOTH
`userInvocable !== false` AND `disableModelInvocation !== true`. That
was wrong for the model paths: `userInvocable: false` skills are
model-only and remain valid `skill` / `read_file` invocation targets.
A duplicate-name scenario where the newer cataloged doc was model-
only would let the older user-invocable variant shadow it on every
model call.

Split the option into two independent axes:
- `preferUserInvocable` — for manual paths (`$` popover). Skips docs
  with `userInvocable: false`. Disable-model-invocation status is
  irrelevant; iter 4 explicitly supports manual prime of disabled
  skills.
- `preferModelInvocable` — for model paths (`skill` / `read_file`
  handlers). Skips docs with `disableModelInvocation: true`. User-
  invocable status is irrelevant; model-only skills are valid here.

Both flags fall back to the newest match when no preferred doc
exists, so the explicit-rejection error paths still fire correctly
in the sole-disabled-name case.

Callers updated:
- `resolveManualSkills` → `preferUserInvocable: true`
- `handleSkillToolCall` / `handleReadFileCall` → `preferModelInvocable: true`

Tests:
- New spec test for preferModelInvocable not filtering on userInvocable.
- Existing preferInvocable test renamed/split to cover the new axes.
- New test asserts preferUserInvocable still returns disabled docs
  (preserves iter 4 manual-disabled support).
- Caller tests assert each path passes the right single flag and
  does NOT pass the wrong one.

* 🔧 fix: TypeScript type-check failure in handlers.spec.ts (CI green)

`jest.fn(async () => ...)` without explicit args infers an empty tuple
for the call signature, so `mock.calls[0][2]` flagged as "Tuple type
'[]' has no element at index '2'." Cast to `unknown[]` then narrow to
the expected option shape. Behavior unchanged.

Caught by the `Type check @librechat/api` CI step
(.github/workflows/backend-review.yml).

* 🔧 fix: Address codex iter 8 — undefined-result fallback + read_file alignment

P1 (loadTools returning undefined): Production loaders
(`createToolLoader` in `initialize.js` / `openai.js` /
`responses.js`) wrap `loadAgentTools` in try/catch and return
`undefined` on failure rather than throwing. Without explicit
handling, my iter-1 try/catch only fired for thrown errors — a
silent-failure on a skill-added tool would fall through to the
empty fallback and silently DROP the agent's baseline tools for
the turn (much worse than just losing the extras). Added an
`undefined`-result branch that retries with just `agent.tools`,
mirroring the throw branch. Test pins both behaviors.

P2 (read_file alignment with manual prime): When a skill is in
this turn's `manualSkillNames`, the `read_file` handler now uses
`preferUserInvocable` instead of `preferModelInvocable`. Same
name-collision rule as `resolveManualSkills`, so the doc whose
files get read is the same doc whose body got primed. For
autonomous probes (skill not in `manualSkillNames`), the handler
keeps `preferModelInvocable` to align with the catalog the model
saw. Two new tests cover both branches and regression-protect that
the wrong flag isn't passed.

* 🔧 fix: Address codex iter 9 — pin read_file lookup to primed skill _id

P1 (manually-primed disabled IDs were dropped from activeSkillIds):
The `executableSkills` dedup in `injectSkillCatalog` correctly drops
`disable-model-invocation: true` duplicates when an invocable doc
shares the name — but `resolveManualSkills` legitimately primes
disabled docs (iter 4 supports manual `$` invocation of disabled
skills). When the resolver primed a disabled doc, the read_file
handler couldn't find it in the (deduped) `activeSkillIds` and
either resolved a different same-name skill or returned not-found.

Fix: `ResolvedManualSkill` now carries `_id`; the legacy `initialize.js`
/ `openai.js` / `responses.js` controllers build a
`manualSkillPrimedIdsByName` map and `enrichWithSkillConfigurable`
passes it into `mergedConfigurable`. `handleReadFileCall` now pins
its lookup's `accessibleIds` to `[primedId]` whenever the requested
skill is in the map. The constrained set guarantees the lookup
returns the EXACT doc the resolver primed — body/files come from the
same source even when same-name duplicates exist or the dedup
removed the prime's id from `activeSkillIds`.

Autonomous read_file probes (skill not in the manual-primed map)
keep the full ACL set + `preferModelInvocable` so they align with
the catalog the model saw and the disabled-only case still fires
the explicit-rejection gate.

Test fixture changes flow from `_id` becoming required on
`ResolvedManualSkill`. `buildSkillPrimeContentParts` /
`injectManualSkillPrimes` widen their param types to `Pick<...>`
because they only read `name` / `body` and shouldn't force test
literals to invent placeholder ids.

* 🧹 fix: Address independent reviewer findings (DRY + types + tests + docs)

Sanity-pass review surfaced 7 findings; addressed 6 (the 7th — DRY
on inline `getSkillByName` return types — is acknowledged tech debt
deferred to a follow-up).

#1 [MAJOR, DRY]: The 4-line `manualSkillPrimedIdsByName` map
construction was duplicated across 4 CJS call sites (openai.js,
responses.js x2, initialize.js). Extracted `buildManualSkillPrimedIdsByName`
helper in `skillDeps.js`; all four sites now call the helper. If
`ResolvedManualSkill` ever renames `_id` or gains identifying fields,
only the helper changes.

#2 [MINOR, type safety]: `handleReadFileCall` was casting a hex string
to `Types.ObjectId[]` via `as unknown as`, relying on mongoose's
auto-cast in `$in` queries. Replaced with `new Types.ObjectId(...)`
so any future consumer comparing with `.equals()` / `===` gets the
correct value type. Imported `Types` as a value (was type-only).

#5 [MINOR, test gap]: Added a test for the worst-case silent-failure
path — both the union and base-only `loadTools` calls return undefined.
The agent gets no tools but the turn doesn't crash hard; pinning
that contract.

#4 [MINOR, performance]: Added a TODO on the `listSkillsByAccess`
projection noting the `frontmatter` field can be dropped once a
write migration backfills all pre-Phase-6 skills' columns. ~2KB/skill
× 100/page is wasted bandwidth post-backfill.

#6 [NIT, docs]: `backfillDerivedFromFrontmatter` JSDoc said "Pure"
right before "mutates its undefined fields in place". Replaced with
"Side-effect-free w.r.t. the DB (no writes), but mutates its argument
in place" which describes both halves accurately.

#7 [NIT, test determinism]: Replaced `await new Promise(r => setTimeout(r, 5))`
in two same-name collision tests with explicit `updateOne` setting
`updatedAt: new Date(Date.now() - 1000)` on the older doc. Removes
the wall-clock race on fast CI runners. The pagination test (line
480) still uses setTimeout — that test is pre-existing and order
is incidental, not load-bearing.

Existing test fixtures updated to use valid 24-char hex ObjectIds
(required by the iter-9 test that constructs a real `ObjectId`).

#3 [MINOR, deferred]: Inline `getSkillByName` return type duplicated
across `handlers.ts`, `initialize.ts`, `skills.ts`. Reviewer
acknowledged this as deferred; field sets diverge across call sites
(handler needs `fileCount`, resolver needs `author`/`allowedTools`).
A `Pick<>`-based consolidation is a clean follow-up.
)

* 🔁 refactor: Rebase always-apply work onto merged structured-frontmatter columns

Phase 6 (disable-model-invocation / user-invocable / allowed-tools)
landed first on feat/agent-skills. Reconcile this branch with the new
mainline:

- Thread alwaysApplySkillPrimes through unionPrimeAllowedTools alongside
  manualSkillPrimes, applying the combined MAX_PRIMED_SKILLS_PER_TURN
  ceiling before loading tools.
- Add `_id` to ResolvedAlwaysApplySkill to match Phase 6's
  ResolvedManualSkill shape (read_file name-collision protection).
- Register 'always-apply' in ALLOWED_FRONTMATTER_KEYS / FRONTMATTER_KIND
  so Phase 6's validator recognizes it.
- Drop frontmatter from the listSkillsByAccess projection; the backfill
  helper remains as defensive code but its read path is no longer
  exercised on summary rows (no legacy rows exist — the branch never
  shipped), saving ~200KB per page.
- Retire the corresponding "backfills legacy on summaries" test.
- Plumb listAlwaysApplySkills through the JS controllers + endpoint
  initializer so the always-apply resolver sees a real DB method.

* 🧹 fix: Dedupe manual/always-apply overlap, share YAML util, tidy comments

Addresses review findings:

- Cross-list dedup: when a user $-invokes a skill that is also marked
  always-apply, the always-apply copy is now dropped so the same
  SKILL.md body never primes twice in one turn. Manual wins (explicit
  intent, closer to the user message). Dedup runs in both
  initializeAgent (so persisted user-bubble pills stay in sync) and
  injectSkillPrimes (defense-in-depth at splice time). New test cases
  cover single-overlap, partial-overlap, and dedup-before-cap.
- DRY: extract stripYamlTrailingComment to
  packages/data-schemas/src/utils/yaml.ts; packages/api/src/skills/import.ts
  now imports the shared helper. Also drop the redundant inner
  stripYamlTrailingComment call inside parseBooleanScalar — the call
  site already strips.
- Mark injectManualSkillPrimes as @deprecated in favor of
  injectSkillPrimes (kept for external consumers of @librechat/api).
- Document SKILL_TRIGGER_MODEL as forward-looking plumbing for the
  model-invoked path rather than leaving it as a bare unused export.
- Replace the stale "frontmatter is included" comment on
  listSkillsByAccess with an accurate explanation of why it was
  intentionally excluded.

* 🔒 fix: Include always-apply primes in skillPrimedIdsByName + clear alwaysApply on body opt-out

Two bugs flagged by Codex review:

P1 (read_file): `manualSkillPrimedIdsByName` only carried manual-invocation
primes, so an always-apply skill with `disable-model-invocation: true`
was blocked from reading its own bundled files, and same-name collisions
could resolve to a different doc than the one whose body got primed.
- Rename `buildManualSkillPrimedIdsByName` → `buildSkillPrimedIdsByName`
  (accepts both manual + always-apply prime arrays).
- Rename the configurable field `manualSkillPrimedIdsByName` →
  `skillPrimedIdsByName` throughout the plumbing (skillConfigurable.ts,
  handlers.ts, CJS callers, tests).
- Overlap resolution: manual wins on the rare edge case where the same
  name appears in both arrays (upstream dedup should prevent this, but
  defensive merging treats manual as authoritative).
- New tests: (1) gate-relaxation fires for always-apply primes, (2) `_id`
  pinning works for always-apply same-name collisions.

P2 (updateSkill): when a body update had no `always-apply:` key,
`extractAlwaysApplyFromBody` returned `absent` and the column was left
untouched. A skill that was once `alwaysApply: true` would keep
auto-priming even after its SKILL.md no longer declared the flag.
- Treat `absent` as a positive "not always-apply" declaration when the
  body is explicitly submitted; flip the column to `false`.
- Explicit top-level `alwaysApply` still wins (three-source precedence
  unchanged).
- New tests: body removes key → false, body has no frontmatter at all →
  false, explicit + body-without-key → explicit wins.

* 🧵 refactor: Collapse duplicate prime types + tighten parse + test hygiene

Sanity-check review follow-ups:

- Collapse `ResolvedManualSkill` / `ResolvedAlwaysApplySkill` into a
  single `ResolvedSkillPrime` canonical interface with two backward-
  compatible type aliases. Both resolvers feed the same pipeline stages
  (injectSkillPrimes, unionPrimeAllowedTools, buildSkillPrimedIdsByName);
  the per-source distinction lives on `additional_kwargs.trigger`, not
  on the resolver output.
- Move the `always-apply` branch in `parseFrontmatter` to operate on the
  raw post-colon text. The outer `unquoteYaml` was fine today because
  it's idempotent on non-quoted strings, but running it twice (once per
  line, once after stripping the inline comment) would be fragile if the
  unquoter ever grows richer YAML-escape handling.
- Add the missing `alwaysApplyDedupedFromManual: 0` field to the
  `injectSkillPrimes` mocks in `openai.spec.js` and `responses.unit.spec.js`
  so they match the full `InjectSkillPrimesResult` contract.
- Insert the blank line between the `unionPrimeAllowedTools` and
  `resolveAlwaysApplySkills` describe blocks.

* 🔧 fix(tsc): Cast mock.calls via `unknown` for strict tuple destructure

`getSkillByName.mock.calls[0]` is typed as `[]` by jest's generic default;
a direct cast to `[string, ..., ...]` fails TS2352 under `--noEmit` even
though the runtime shape matches. Go through `as unknown as [...]` like
the earlier test in the same file so CI's type-check step stays green.

* 🪢 fix: Propagate skillPrimedIdsByName into handoff agent tool context

Handoff agents go through the same `initializeAgent` flow as the primary
(with `listAlwaysApplySkills` now plumbed), so they resolve their own
`manualSkillPrimes` and `alwaysApplySkillPrimes` — but the
`agentToolContexts.set(...)` for handoff agents didn't carry
`skillPrimedIdsByName` into the per-agent context.

That meant `handleReadFileCall` fell back to the full ACL set + a
`prefer*` flag for handoff agents: same-name collisions could resolve to
a different doc than the one whose body got primed, and a
`disable-model-invocation: true` skill primed via manual `$` or
always-apply inside the handoff flow would be blocked from reading its
own bundled files.

Build the map via `buildSkillPrimedIdsByName(config.manualSkillPrimes,
config.alwaysApplySkillPrimes)` for every handoff tool context so
`read_file` behaves identically across primary and handoff agents.
responses.js referenced `appConfig` on lines 381 / 396 without ever
declaring it, so `createResponse` threw `ReferenceError: appConfig is
not defined` the moment it entered the skills-capability block. The
existing `recordCollectedUsage` unit tests silently stopped running
(try/catch swallowed the error into `logger.error`), so CI showed
6 assertions failing with "Expected calls: 1, Received: 0" — the
function never reached the recorder.

Mirror initialize.js: seed `appConfig = req.config` at the top of the
try block, before the `enabledCapabilities` Set it feeds into. The two
later `appConfig: req.config` call-sites keep the direct reference —
only the lexical reads needed a binding.

This failure already exists on origin/feat/agent-skills (the same 6
tests fail there with the same stack) but blocks our branch too since
we're rebased on top, so fix it here and cherry-pick back if needed.
* 🔌 refactor: Decouple bash_tool from Per-User CODE_API_KEY

Phase 4 of Agent Skills umbrella (#12625): gate bash_tool and skill
file priming on the `execute_code` capability only. Thread a boolean
`codeEnvAvailable` through `enrichWithSkillConfigurable` and
`primeInvokedSkills` in place of the old per-user `codeApiKey` +
`loadAuthValues` plumbing. The sandbox API key is the LibreChat-
hosted service key — system-level, not a user secret — so the
per-user lookup was legacy; when needed, it's read directly from
`process.env[EnvVar.CODE_API_KEY]` inside the capability gate.

`handleSkillToolCall` and `primeInvokedSkills` gate sandbox uploads
on `codeEnvAvailable` first, preventing skill-file uploads to the
sandbox when an agent has `execute_code` disabled even if the env
var happens to be set. The agents library resolves the env key
itself for `bash_tool`, so `ToolService.js` drops the
`loadAuthValues` lookup and the "Code execution is not available"
placeholder tool in favor of a plain `createBashExecutionTool({})`
with a loud error log if the env var is missing.

Also fixes a pre-existing `appConfig`-undefined lint error in
`responses.js`/`createResponse` that surfaced when this file was
touched (declares `const appConfig = req.config` at function top,
matching the existing pattern in other controllers).

Preserves the `skillPrimedIdsByName` threading added by Phase 3/5/6
and all Phase 3/5/6 call-site signatures. Adds
`skillConfigurable.spec.ts` (5 cases pinning the new surface) and
`skillFiles.spec.ts` (4-way matrix of capability × env key for
`primeInvokedSkills`).

* 🧪 refactor: Address Codex Review Feedback

Resolves findings from the second codex review on #12712:

- MAJOR: `handlers.spec.ts` now covers the `codeEnvAvailable` gate in
  `handleSkillToolCall` across three cases (gate off, gate on + env
  set, gate on + env unset). The gate is the critical regression
  prevention — a future edit that drops it would silently re-enable
  sandbox uploads for agents with `execute_code` disabled.

- MINOR: Hoist `codeEnvAvailable` and `skillPrimedIdsByName` out of
  `loadTools` closures in `openai.js` and `responses.js`. Both values
  are fixed once `initializeAgent` resolves, so recomputing them on
  every tool execution was wasted work. `responses.js` shares a single
  pair between its streaming and non-streaming branches.

- MINOR: `skillFiles.spec.ts` now has a test that exercises the full
  upload path end-to-end with real file records, asserting
  `batchUploadCodeEnvFiles` is called with the env-sourced apiKey and
  the correct file set (including the synthetic `SKILL.md`).

- NIT: Finish the `appConfig` extraction in `responses.js/createResponse`
  — replaces the remaining `req.config` references with `appConfig` for
  consistency with the pattern in other controllers.

No behavioral changes beyond what was already in place; this is
coverage and readability polish.

* 🧷 test: Tighten Spec Hygiene Per Codex Nit Feedback

Round-3 codex review flagged two NITs on the test code added in the
previous commit:

- Replace `_id: 'skill-id' as unknown as never` in the new
  `makeSkillHandlerWithFiles` helper with a real `Types.ObjectId`,
  matching the pattern used by the primed-skill tests further up in
  the same file (and by `skillFiles.spec.ts`). The `never` cast
  hides the fact that `_id` really is a string / ObjectId at runtime.

- Replace the ad-hoc `{ on, pipe, read }` stub with a real
  `Readable.from(Buffer.from(''))` in the upload-path test. The stub
  worked only because `batchUploadCodeEnvFiles` is mocked and never
  iterates the stream; `Readable.from` satisfies the same contract
  and is robust to any future partial-real replacement of the upload
  function.

Pure test-hygiene improvements; no runtime code touched.

* 🧹 chore: Remove Duplicate appConfig Declaration After Rebase

The upstream `2463b6acd` fix declared `const appConfig = req.config`
inside the try block (line 381) to patch the same `no-undef` error
I fixed in this PR at the top of `createResponse` (line 283). The
rebase kept both declarations side-by-side. Drops the inner one —
the outer binding covers every downstream reference already.
…er drop logs, SkillPills rename (#12760)

Post-merge sanity-review cleanup on top of #12746:

- `createSkill` / `updateSkill` now parse SKILL.md body's always-apply
  status once and reuse it for both validation and derivation (was
  parsing the same YAML block twice per call).
- Body-inline `always-apply:` validation becomes precedence-aware: a
  caller sending an explicit top-level `alwaysApply` or a structured
  `frontmatter['always-apply']` no longer gets rejected for a typo in
  the body — the body value is never consulted at derivation time when
  a higher-precedence source wins. New tests cover the three relevant
  interactions (explicit+body-typo, frontmatter+body-typo, body-only
  typo still rejects).
- OpenAI and Responses controllers now emit a `logger.warn` when
  `injectSkillPrimes` drops always-apply primes to stay under
  `MAX_PRIMED_SKILLS_PER_TURN`. `injectSkillPrimes` already logs
  internally; the controller-level warn adds endpoint context so
  operators can identify which path hit the cap at a glance. Mirrors
  AgentClient's existing log.
- Rename `ManualSkillPills` → `SkillPills` (component + type + file +
  test + all JSDoc references). The component handles both manual and
  always-apply pills now; the original name was carried over from the
  manual-only Phase 3 and misleads new readers.
- Drive-by fix: declare `appConfig = req.config` at the top of
  `createResponse` in `responses.js` — it was used unqualified on
  lines 381/396, which silently evaluated to `undefined` (via optional
  chaining) and disabled the skills-capability check on the Responses
  endpoint. Pre-existing, surfaced by lint on the touched file.
…faults Tests (#12766)

* 🔐 chore: Skills permissions housekeeping — reachable admin dialog + defaults tests

Phase 9 housekeeping pass. Skills was already gated on `PermissionTypes.SKILLS`
(seeded from `interface.skills`) and `AgentCapabilities.skills` everywhere it
matters, but two smaller parity gaps with Prompts/Memory/MCP remained:

- The skills admin settings dialog had no UI entry point. The only mount was
  inside an unused `FilterSkills` component, so admins had no way to reach the
  role-permissions editor for skills. Mounted it in `SkillsAccordion` gated on
  `SystemRoles.ADMIN`, matching the `PromptsAccordion` pattern.
- No regression lock on skill permission defaults. `roles.spec.ts` asserted
  structural completeness but not the specific shape — a future refactor
  could silently flip ADMIN's `USE/CREATE/SHARE/SHARE_PUBLIC` to false or
  drop SKILLS from USER defaults without failing. Added explicit Skills
  assertions for both roles.
- No lock on `AgentCapabilities.skills` being in `defaultAgentCapabilities`.
  Added an assertion in `endpoints.spec.ts`.

* 🩹 fix: Remove duplicate `const appConfig` in Responses createResponse

The Skills polish commit (#12760) added `const appConfig = req.config;` at
line 381 inside the try block of `createResponse`, without noticing that
the earlier drive-by fix (2463b6a) already declared it at the function
top (line 283). The second `const` creates a new block-scoped binding
inside the try, so earlier references within the same block (e.g.
line 348's `appConfig?.endpoints?.[EModelEndpoint.agents]?.allowedProviders`)
now hit the TDZ instead of the outer binding and throw
`ReferenceError: Cannot access 'appConfig' before initialization` —
which the outer try/catch then swallows into a generic 500.

This surfaced as all six token-usage tests in
`api/server/controllers/agents/__tests__/responses.unit.spec.js` failing
with `mockRecordCollectedUsage` never being called (because the throw
skips past the `recordCollectedUsage(...)` call).

Dropping the inner re-declaration restores the full control flow. All 11
tests in the file pass again.

* 🧹 refactor: Address review nits on Phase 9 housekeeping

- Move the `defaultAgentCapabilities` regression test out of the
  `createEndpointsConfigService` describe block and into its own
  top-level describe. It tests a module constant and has no relationship
  to the service factory; nesting was misleading and made it easier to
  accidentally drop if the service tests are later restructured.
- Re-order local imports in `SkillsAccordion.tsx` longest-to-shortest
  per AGENTS.md convention (`SkillsSidePanel` 48 chars before
  `useAuthContext` 41 chars).
* 🛠️ feat: Add registerCodeExecutionTools helper

Idempotently registers `bash_tool` + `read_file` in the run's tool
registry and tool-definition list via a registry `.has()` dedupe. Sets
up the single code-execution tool path shared by:

- `initializeAgent` (when an agent has `execute_code` in its tools and
  the capability is enabled for the run)
- `injectSkillCatalog` (when skills are active; unconditional read_file,
  bash_tool follows `codeEnvAvailable`)

Both callers reach the helper in the same initialization sequence, so
the second call becomes a no-op and exactly one copy of each tool
reaches the LLM — no more double registration for agents that combine
`execute_code` capability with active skills.

Unit-tested on a fresh run, idempotence (second call, overlap with
prior tooldefs, partial overlap), and the no-registry variant.

* 🔀 refactor: Route injectSkillCatalog bash_tool + read_file through registerCodeExecutionTools

The `skill` tool is still registered inline (it's skill-path-specific),
but `bash_tool` + `read_file` now flow through the shared idempotent
helper so a prior registration from the execute_code path doesn't
produce a duplicate copy later in the same run. Behavior preserved:

- `read_file` always registers when any active skill is in scope —
  manually-primed `disable-model-invocation: true` skills still need it
  to load `references/*` from storage.
- `bash_tool` follows `codeEnvAvailable` exactly as before.

Adds a test pinning the cross-call dedupe: when `injectSkillCatalog`
runs AFTER `registerCodeExecutionTools` has already seeded the registry
+ tool definitions with bash_tool/read_file, the resulting
`toolDefinitions` still contains exactly one copy of each.

* 🪄 feat: Expand `execute_code` tool name into bash_tool + read_file at initialize-time

When an agent's `tools` include `execute_code` and the `execute_code`
capability is enabled for the run, `initializeAgent` now registers
`bash_tool` + `read_file` via `registerCodeExecutionTools` before
`injectSkillCatalog`. The legacy `execute_code` tool definition is no
longer handed to the LLM — `execute_code` remains on the agent
document as a capability-trigger marker, but the runtime expands it
into the skill-flavored tool pair.

Call ordering matters: the `execute_code` registration runs BEFORE
`injectSkillCatalog`, so the skill path's own `registerCodeExecutionTools`
call inside `injectSkillCatalog` becomes a no-op via the registry's
`.has()` check. Exactly one copy of each tool reaches the LLM whether
the agent has:

- only `execute_code` (legacy path)
- only skills
- both

No data migration needed — `agent.tools: ['execute_code']` stays in
the DB unchanged; the expansion is a runtime operation.

Three tests cover the matrix: execute_code + capability on →
bash_tool + read_file registered; execute_code + capability off →
neither registered; no execute_code + capability on → neither
registered.

* 🗑️ refactor: Drop CodeExecutionToolDefinition from the builtin registry

Removes the legacy `execute_code` entry from `agentToolDefinitions` and
the corresponding import. With the initialize-time expansion in place,
nothing consults `getToolDefinition('execute_code')` for a tool schema
any more — the capability gate still filters on the string
`execute_code`, but the actual tool definitions the LLM sees come from
`registerCodeExecutionTools` (i.e. `bash_tool` + `read_file`).

`loadToolDefinitions` in `packages/api/src/tools/definitions.ts`
silently drops `execute_code` when it no longer resolves in the
registry — that's the expected path and is now covered by an updated
test. No caller of `getToolDefinition('execute_code')` expects a
non-undefined result after this change.

* 🔌 refactor: Read CODE_API_KEY from env for primeCodeFiles + PTC

Finishes the Phase 4 server-env-keyed rollout on the two remaining
`loadAuthValues({ authFields: [EnvVar.CODE_API_KEY] })` sites in
`ToolService.js`:

- `primeCodeFiles` (user-attached file priming on execute_code agents)
- Programmatic Tool Calling (`createProgrammaticToolCallingTool`)

Both now read `process.env[EnvVar.CODE_API_KEY]` directly, matching
`bash_tool`'s pattern. The per-user plugin-auth path is no longer
consulted for code-env credentials anywhere in the hot path — the
agents library owns the actual tool-call execution and also reads the
env var internally.

Priming still fires for existing user-file workflows so the legacy
`toolContextMap[execute_code]` hint ("files available at /mnt/data/...")
stays in the prompt; only the key lookup changed.

* 🔧 fix: Type the pre-seeded dedupe-test tools as LCTool

CI TypeScript type checks caught `{ parameters: {} }` in the new
cross-call dedupe test: `LCTool.parameters` is a `JsonSchemaType`,
not `{}`. Use `{ type: 'object', properties: {} }` and type the
local registry Map through the parameter-derived shape so the
pre-seeded values match what `toolRegistry.set` expects.

* 🛡️ fix: Run execute_code expansion before GOOGLE_TOOL_CONFLICT gate

Codex review caught a latent regression: the original Phase 8 placement
ran `registerCodeExecutionTools` after `hasAgentTools` was computed,
so an execute-code-only agent on Google/Vertex with provider-specific
`options.tools` populated would no longer trip `GOOGLE_TOOL_CONFLICT`
— the legacy `CodeExecutionToolDefinition` used to populate
`toolDefinitions` before the guard, but after dropping it from the
registry, `toolDefinitions` stayed empty until my expansion ran
downstream of the guard. Mixed provider + agent tools would silently
flow through to the LLM.

Fix moves the `execute_code` expansion to BEFORE `hasAgentTools`
computation. `bash_tool` + `read_file` now contribute to the check
the same way the legacy `execute_code` def did. Covered by a new
test that pins the Google+execute_code+provider-tools scenario —
the `rejects.toThrow(/google_tool_conflict/)` path would have
silently passed on the prior placement.

* 🔗 fix: Thread codeEnvAvailable through handoff sub-agents

Round-2 codex review caught the other half of the execute_code
expansion gap: `discoverConnectedAgents` omitted `codeEnvAvailable`
from its forwarded `initializeAgent` params, so handoff sub-agents
with `agent.tools: ['execute_code']` lost the `bash_tool` + `read_file`
registration (pre-Phase 8 the legacy `CodeExecutionToolDefinition`
would have landed in their `toolDefinitions` via the registry).

- Add `codeEnvAvailable?` to `DiscoverConnectedAgentsParams` and
  forward it verbatim on every sub-agent `initializeAgent` call.
- Update the three JS call sites that construct the primary's
  `codeEnvAvailable` (`services/Endpoints/agents/initialize.js`,
  `controllers/agents/openai.js`, `controllers/agents/responses.js`)
  to pass the same flag into `discoverConnectedAgents` — one
  authoritative source per request.
- Two regression tests in `discovery.spec.ts` pin the true/false
  passthrough so a future refactor that drops the param-forwarding
  surfaces immediately.

Left intentionally unchanged: `packages/api/src/agents/openai/service.ts`
(public API helper with no in-repo caller). External consumers of
`createAgentChatCompletion` who want code execution should pass a
`codeEnvAvailable`-aware `initializeAgent` via `deps` — documenting
the full public-API surface is out of scope for this Phase 8 PR.

* 🔗 fix: Thread codeEnvAvailable through addedConvo + memory-agent paths

Round-3 codex review caught the last two production `initializeAgent`
callers missing the Phase-8 capability flag:

- `api/server/services/Endpoints/agents/addedConvo.js` (multi-convo
  parallel agent execution). Added `codeEnvAvailable` to
  `processAddedConvo`'s destructured params and forwarded it into
  the per-added-agent `initializeAgent` call. Caller in
  `api/server/services/Endpoints/agents/initialize.js` passes the
  same `codeEnvAvailable` it computed for the primary.
- `api/server/controllers/agents/client.js` (`useMemory` — memory
  extraction agent). Computes its own `codeEnvAvailable` from
  `appConfig?.endpoints?.[EModelEndpoint.agents]?.capabilities` and
  forwards into `initializeAgent`. Memory agents rarely list
  `execute_code`, but if one does, pre-Phase 8 they got the legacy
  `execute_code` tool registered unconditionally — the passthrough
  restores parity.

With this, every production caller of `initializeAgent` explicitly
resolves the capability: main chat flow (primary + handoff), OpenAI
chat completions (primary + handoff), Responses API (primary + handoff),
added convo parallel agents, and memory agents. The one remaining
caller, `packages/api/src/agents/openai/service.ts::createAgentChatCompletion`,
is a public API helper with no in-repo consumer (external callers
must pass a capability-aware `initializeAgent` via `deps`).

* 🪤 fix: Remove duplicate appConfig declaration causing TDZ ReferenceError

The Responses API controller had TWO `const appConfig = req.config;`
bindings inside `createResponse`: one at the top of the function
(added by the Phase 4 `bash_tool` decouple) and one inside the try
block (added by the polish PR #12760). Because `const` is block-scoped
with a temporal dead zone, the inner redeclaration put `appConfig` in
TDZ for the entire try block, so any earlier reference inside the
try — notably `appConfig?.endpoints?.[EModelEndpoint.agents]?.allowedProviders`
at line 348 — threw `ReferenceError: Cannot access 'appConfig'
before initialization`. The error was silently swallowed by the
outer try/catch, leaving `recordCollectedUsage` unreached and the
six `responses.unit.spec.js` token-usage tests failing.

Removing the inner redeclaration fixes the six failing tests
(verified: 11/11 pass locally post-fix, 0 regressions elsewhere).
The outer function-scoped binding already provides `appConfig` to
every downstream reference.

* 🔗 fix: Thread codeEnvAvailable through the OpenAI chat-completion public API

Round-4 codex review (legitimate on the type-safety angle, even though the
runtime concern was already covered): the `createAgentChatCompletion`
helper defines its own narrower `InitializeAgentParams` interface locally,
and the type was missing `codeEnvAvailable`. External consumers who
supply a capability-aware `deps.initializeAgent` couldn't route
`codeEnvAvailable` through without a type-cast workaround.

- Widen the local `InitializeAgentParams` interface to include
  `codeEnvAvailable?: boolean` (matches the real
  `packages/api/src/agents/initialize.ts` type).
- Derive `codeEnvAvailable` inside `createAgentChatCompletion` from
  `deps.appConfig?.endpoints?.agents?.capabilities` (the same source
  the in-repo controllers use) and forward to `deps.initializeAgent`.
  Uses a string literal `'execute_code'` lookup so this file stays free
  of a `librechat-data-provider` import — keeping the dependency surface
  of the public helper minimal.

With this, external consumers of `createAgentChatCompletion` who pass
`appConfig` with the agents capabilities get `bash_tool` + `read_file`
registration automatically; consumers who don't pass `appConfig` retain
the existing "explicit opt-in" semantics (the flag stays `undefined`,
expansion is skipped).

* 🧹 chore: Review-driven polish — observability log, JSDoc DRY, test gaps, no-op allocation

Addresses the comprehensive review of PR #12767:

- **Finding #1** (MINOR, observability): `initializeAgent` now emits a
  debug log when an agent lists `execute_code` in its tools but the
  runtime gate is off (`params.codeEnvAvailable` !== true). The
  event-driven `loadToolDefinitionsWrapper` path doesn't log
  capability-disabled warnings, so without this the tool silently
  vanishes from the LLM's definitions with zero trace. Operators
  debugging "why isn't code interpreter working?" now get a signal at
  the initialize layer.

- **Finding #5** (NIT, allocation): `registerCodeExecutionTools` now
  returns the input `toolDefinitions` array by reference on the no-op
  path (both tools already registered by a prior caller in the same
  run) instead of allocating a fresh spread array every time. The
  common dual-call scenario — `initializeAgent` then
  `injectSkillCatalog` — saves one O(n) copy per request.

- **Finding #4** (NIT, DRY): Collapsed the duplicated 6-line JSDoc
  comment in `openai.js`, `responses.js`, and `addedConvo.js` into
  either a one-line `@see DiscoverConnectedAgentsParams.codeEnvAvailable`
  pointer (the two JS call sites) or a compact 3-line block referring
  back to the canonical source (addedConvo's @param).

- **Finding #2** (MINOR, test gap): Added
  `api/server/services/Endpoints/agents/addedConvo.spec.js` with three
  cases covering `codeEnvAvailable=true`, `codeEnvAvailable=false`,
  and omitted (undefined) passthrough. A future refactor that drops
  the param from destructuring now surfaces here instead of silently
  regressing multi-convo parallel agents with `execute_code`.

- **Finding #3** (MINOR, test gap): Added
  `api/server/controllers/agents/__tests__/client.memory.spec.js`
  pinning the capability-flag derivation that `AgentClient::useMemory`
  uses — six cases covering present/absent/null/undefined config shapes
  plus an enum-literal pin (`'execute_code'` / `'agents'`). Catches
  enum renames or config-path shifts that would otherwise silently
  strip `bash_tool` + `read_file` from memory agents.

Finding #7 (jest.mock scoping, confidence 40) left as-is: the
reviewer's own risk assessment noted `buildToolSet` doesn't touch
the mocked exports, and restructuring a file-level `jest.mock` to
`jest.doMock` + dynamic `import()` introduces more complexity than
the speculative risk justifies. The existing mock is scoped to the
test file and contains the same stubs the adjacent
`skills.test.ts` already uses.

Finding #6 (PR description commit count) addressed out-of-band via
PR description update.

All existing tests pass, typecheck clean, lint clean across touched
files. New tests: 9 cases across 2 new spec files.

* 🧽 refactor: Replace hardcoded 'execute_code' string with AgentCapabilities enum in service.ts

Follow-up review (conf 55) caught that `openai/service.ts`'s Phase 8
`codeEnvAvailable` derivation used the literal `'execute_code'` while
every in-repo controller uses `AgentCapabilities.execute_code` from
`librechat-data-provider`. The file deliberately uses local type
interfaces to keep the public API helper's type surface small, but
that pattern was never a ban on single-value imports from the data
provider — `packages/api` already depends on it. Importing the enum
value means a future rename of `AgentCapabilities.execute_code`
propagates to this file automatically, matching the in-repo
controllers' behavior.

Other follow-up findings left as-is per the reviewer's own verdict:

- #2 (memory spec mirrors the production expression rather than
  calling `AgentClient::useMemory` directly): reviewer flagged as
  "not blocking" / "design-philosophy observation." The test file's
  JSDoc already explicitly documents the tradeoff and pins the enum
  literals to catch the most likely drift vector. Standing up
  `AgentClient` + all its mocks for a one-line regression guard is
  disproportionate.
- #3 (`addedConvo.spec.js` mock signature vs. underlying
  `loadAddedAgent` arity): reviewer's own confidence 25 noted the
  mock matches the wrapper's actual call pattern in the production
  file. Not a real gap.
- #4 was self-retracted as a false alarm.

* 🗑️ refactor: Fully deprecate CODE_API_KEY — remove all LibreChat-side references

The code-execution sandbox no longer authenticates via a per-run
`CODE_API_KEY` (frontend or backend). Auth moved server-side into the
agents library / sandbox service, so LibreChat drops every reference:

**Backend plumbing:**
- `api/server/services/Files/Code/crud.js`: `getCodeOutputDownloadStream`,
  `uploadCodeEnvFile`, `batchUploadCodeEnvFiles` no longer accept
  `apiKey` or send the `X-API-Key` header.
- `api/server/services/Files/Code/process.js`: `processCodeOutput`,
  `getSessionInfo`, `primeFiles` drop the `apiKey` param throughout.
- `api/server/services/ToolService.js`: stop reading
  `process.env[EnvVar.CODE_API_KEY]` for `primeCodeFiles` and PTC; the
  agents library handles auth internally. Remove the now-dead
  `loadAuthValues` + `EnvVar` imports. Drop the misleading
  "LIBRECHAT_CODE_API_KEY" hint from the bash_tool error log.
- `api/server/services/Files/process.js`: remove the `loadAuthValues`
  call around `uploadCodeEnvFile`.
- `api/server/routes/files/files.js`: code-env file download no longer
  fetches a per-user key.
- `api/server/controllers/tools.js`: `execute_code` is no longer a
  tool that needs verifyToolAuth with `[EnvVar.CODE_API_KEY]` — the
  endpoint always reports system-authenticated so the client skips
  the key-entry dialog. `processCodeOutput` called without `apiKey`.
- `api/server/controllers/agents/callbacks.js`: `processCodeOutput`
  invoked without the loadAuthValues round trip, for both LegacyHandler
  and Responses-API handlers.
- `api/app/clients/tools/util/handleTools.js`: `createCodeExecutionTool`
  called with just `user_id` + files.

**packages/api:**
- `packages/api/src/agents/skillFiles.ts`: `PrimeSkillFilesParams`,
  `PrimeInvokedSkillsDeps`, `primeSkillFiles`, `primeInvokedSkills` all
  drop the `apiKey` param; the gate is purely `codeEnvAvailable`.
- `packages/api/src/agents/handlers.ts`: `handleSkillToolCall` drops
  the `process.env[EnvVar.CODE_API_KEY]` read; skill-file priming is
  now gated solely on `codeEnvAvailable`. `ToolExecuteOptions`
  signatures drop apiKey from `batchUploadCodeEnvFiles` and
  `getSessionInfo`.
- `packages/api/src/agents/skillConfigurable.ts`: JSDoc no longer
  references the env var.
- `packages/api/src/tools/classification.ts`: PTC creation no longer
  gated on `loadAuthValues`; `buildToolClassification` drops the
  `loadAuthValues` dep entirely (no LibreChat-side callers need it for
  this path anymore).
- `packages/api/src/tools/definitions.ts`: `LoadToolDefinitionsDeps`
  drops the `loadAuthValues` field.

**Frontend:**
- Delete `client/src/hooks/Plugins/useAuthCodeTool.ts`,
  `useCodeApiKeyForm.ts`, and
  `client/src/components/SidePanel/Agents/Code/ApiKeyDialog.tsx` —
  the install/revoke dialogs for CODE_API_KEY are fully dead.
- `BadgeRowContext.tsx`: drop `codeApiKeyForm` from the context type and
  provider. `codeInterpreter` toggle treated as always authenticated
  (sandbox auth is server-side).
- `ToolsDropdown.tsx`, `ToolDialogs.tsx`, `CodeInterpreter.tsx`,
  `RunCode.tsx`, `SidePanel/Agents/Code/Action.tsx` +`Form.tsx`: all
  API-key dialog trigger refs, "Configure code interpreter" gear
  buttons, and auth-verification plumbing removed. The
  "Code Interpreter" toggle is now a plain `AgentCapabilities.execute_code`
  checkbox — no key-entry gate.
- `client/src/locales/en/translation.json`: drop the three
  `com_ui_librechat_code_api*` keys and `com_ui_add_code_interpreter_api_key`.
  Other locales are externally automated per CLAUDE.md.

**Config:**
- `.env.example`: remove the `# LIBRECHAT_CODE_API_KEY=your-key` section
  and its header.

**Tests:**
- `crud.spec.js`: assertions flipped to pin "no X-API-Key header" and
  "no apiKey param".
- `skillFiles.spec.ts`: removed env-var save/restore; tests now pin
  that the batch-upload path is gated solely on `codeEnvAvailable` and
  that no apiKey is threaded through.
- `handlers.spec.ts`: same — just the `codeEnvAvailable` gate pins
  remain.
- `classification.spec.ts`: remove the two tests that asserted
  `loadAuthValues` was (not) called for PTC.
- `definitions.spec.ts`: drop every `loadAuthValues: mockLoadAuthValues`
  entry from the deps shape.
- `process.spec.js`: strip the mock of `EnvVar.CODE_API_KEY`.

**Comment hygiene:**
- `tools.ts`, `initialize.ts`, `registry/definitions.ts`: shortened
  stale comment references to "legacy `execute_code` tool" without
  naming the retired env var.

Tests verified: 678 packages/api tests pass, 836 backend api tests
pass. Typecheck clean, lint clean. Only remaining CODE_API_KEY
mentions in the code are two regression-guard assertions:
- `crud.spec.js`: pins "no X-API-Key header" stays absent.
- `skillConfigurable.spec.ts`: pins `configurable` never grows a
  `codeApiKey` field.

* 🧹 chore: Remove the last two CODE_API_KEY name mentions in LibreChat

Follow-up to the prior full deprecation commit: two tests still named
the retired identifier in their regression-guard assertions.

- `packages/api/src/agents/skillConfigurable.spec.ts`: drop the
  "does not inject a codeApiKey key" test. The `codeApiKey` field is
  gone from the production configurable shape, so an absence-assertion
  naming it re-introduces the retired identifier in code.
- `api/server/services/Files/Code/crud.spec.js`: rename the
  "without an X-API-Key header" case back to "should request stream
  response from the correct URL" and drop the
  `expect(headers).not.toHaveProperty('X-API-Key')` assertion. The
  surrounding request-shape checks (URL, timeout, responseType) still
  pin the behavior; the explicit header-absence line was named-after
  the deprecated contract.

Result: `grep -rn "CODE_API_KEY\|codeApiKey\|LIBRECHAT_CODE_API_KEY"`
against the LibreChat source tree returns zero hits. The only
remaining `X-API-Key` strings in this repo are on unrelated OpenAPI
Action + MCP server auth configurations, where the string is
user-facing config, not a LibreChat-owned identifier.

Tests: 677 packages/api pass (2 pre-existing summarization e2e failures
unrelated); 126 api-workspace controller/service tests pass.
Typecheck and lint clean.

* 🎯 fix: Narrow codeEnvAvailable to per-agent (admin cap AND agent.tools)

Before this commit, `codeEnvAvailable` was computed in the three JS
controllers as the admin-level capability flag only
(`enabledCapabilities.has(AgentCapabilities.execute_code)`) and passed
through `initializeAgent` → `injectSkillCatalog` / `primeInvokedSkills` /
`enrichWithSkillConfigurable` unchanged. A skills-only agent whose
`tools` array didn't include `execute_code` still got `bash_tool`
registered (via `injectSkillCatalog`) and skill files re-primed to the
sandbox on every turn — wrong, because the agent never opted in to
code execution.

**Fix:** `initializeAgent` now computes the per-agent effective value
once as `params.codeEnvAvailable === true && agent.tools.includes(Tools.execute_code)`,
reuses the same boolean for:

1. The `execute_code` → `bash_tool + read_file` expansion gate
   (previously already consulted `agent.tools`; now shares the single
   `effectiveCodeEnvAvailable` binding).
2. The `injectSkillCatalog` call (previously got the raw admin flag).
3. The returned `InitializedAgent.codeEnvAvailable` field (new, typed as
   required boolean).

**Controllers (initialize.js, openai.js, responses.js):** store
`primaryConfig.codeEnvAvailable` in `agentToolContexts.set(primaryId, ...)`,
capture `config.codeEnvAvailable` in every handoff `onAgentInitialized`
callback, and read it from the per-agent ctx inside the
`toolExecuteOptions.loadTools` runtime closure. The hoisted
`const codeEnvAvailable = enabledCapabilities.has(...)` locals in the
two OpenAI-compat controllers are gone — they were shadowing the
narrowed per-agent value.

**primeInvokedSkills:** `handlePrimeInvokedSkills` in
`services/Endpoints/agents/initialize.js` now uses
`primaryConfig.codeEnvAvailable` (per-agent, narrowed) instead of the
raw admin flag. A skills-only primary agent won't re-prime historical
skill files to the sandbox even when the admin enabled the capability
globally.

**Efficiency:** one extra `&&` in `initializeAgent`. No runtime hot-path
cost — the `includes()` scan on `agent.tools` was already happening for
the `execute_code` expansion gate; it's now just bound to a local. Tool
execution closures read `ctx.codeEnvAvailable === true` (property
access + strict equality, O(1)).

**Ephemeral-agent note:** per-agent narrowing is authoritative for both
persisted and ephemeral flows. The ephemeral toggle
(`ephemeralAgent.execute_code`) is reconciled into `agent.tools`
upstream in `packages/api/src/agents/added.ts`, so
`agent.tools.includes('execute_code')` is the single source of truth
by the time `initializeAgent` runs.

**Tests:** two new regression tests pin the narrowing contract:

- `initialize.test.ts` — four-quadrant matrix on
  `InitializedAgent.codeEnvAvailable` (cap on × agent asks, cap on ×
  doesn't ask, cap off × asks, neither). Catches future refactors that
  drop either half of the AND.
- `skills.test.ts` — `injectSkillCatalog` with `codeEnvAvailable: false`
  against an active skill catalog must NOT register `bash_tool` even
  though it still registers `read_file` + `skill`. This is the state
  a skills-only agent gets post-narrowing.

All 191 affected packages/api tests pass + 836 backend api tests pass.
Typecheck clean, lint clean.

* 🧽 refactor: Comprehensive-review polish — hoist tool defs, pin verifyToolAuth contract, doc appConfig

Addresses the comprehensive review of Phase 8. Findings mapped:

**#1 (MINOR): `verifyToolAuth` unconditional auth for execute_code**
- Added doc comment explicitly stating the deployment contract
  (admin capability → reachable sandbox; no per-check health probe
  to keep UI-gate queries O(1)).
- New `api/server/controllers/__tests__/tools.verifyToolAuth.spec.js`
  with 4 regression tests pinning the contract:
  1. `authenticated: true` + `SYSTEM_DEFINED` for execute_code.
  2. 404 for unknown tool IDs.
  3. `loadAuthValues` is never consulted (catches a future revert
     that would resurface the per-user key-entry dialog).
  4. Response `message` is never `USER_PROVIDED`.

**#2 (MINOR): `openai/service.ts` undocumented `appConfig` dependency**
- Expanded the `ChatCompletionDependencies.appConfig` JSDoc to spell
  out that omitting it silently disables code execution for agents
  with `execute_code` in their tools. External consumers of
  `createAgentChatCompletion` now have the contract documented at
  the type boundary.

**#5 (NIT): `registerCodeExecutionTools` re-allocates tool defs**
- Hoisted `READ_FILE_DEF` and `BASH_TOOL_DEF` to module-level
  `Object.freeze`d constants. The shapes derive entirely from
  static `@librechat/agents` exports, so a single frozen object per
  tool is safe to share across every agent init. Eliminates the
  ~4-property allocations on every call (including the common
  second-call no-op path).

**#6 (NIT): Verbose history-priming comment in initialize.js**
- Trimmed the 16-line `handlePrimeInvokedSkills` block to a 5-line
  summary with `@see InitializedAgent.codeEnvAvailable` pointer.
  The canonical narrowing explanation lives on the type; the
  controller comment is just the ACL-vs-capability rationale.

**Skipped:**

- #3 (memory spec tests a mirror function): reviewer self-dismissed
  as a design tradeoff; the enum-literal pin already catches the
  highest-risk drift vector.
- #4 (cross-repo contract for `createCodeExecutionTool`): user will
  explicitly install the latest `@librechat/agents` dev version
  once the companion PR publishes, so the version pin will be
  authoritative.
- #7 (migration/deprecation note for self-hosters): out of scope
  per user direction — release notes handle this.

Tests verified: 679 packages/api + 840 backend api tests pass.
Typecheck + lint clean.

* 🔧 chore: Update @librechat/agents version to 3.1.68-dev.1 across package-lock and package.json files

This commit updates the version of the `@librechat/agents` package from `3.1.68-dev.0` to `3.1.68-dev.1` in the `package-lock.json` and relevant `package.json` files. This change ensures consistency across the project and incorporates any updates or fixes from the new version.
* 🪆 feat: Subagents configuration (isolated-context child agents)

Surfaces the new @librechat/agents `SubagentConfig` primitive in the Agent
Builder. Subagents let a supervisor delegate a focused subtask to a child
graph running in an isolated context window: verbose tool output stays in
the child, only a filtered summary returns to the parent.

Data model: new `subagents: { enabled, allowSelf, agent_ids }` on Agent,
wired through the Zod, Mongoose, and form schemas plus a new
`AgentCapabilities.subagents` capability (enabled by default).

Backend: `initialize.js` loads explicit subagent configs alongside handoff
agents, and drops subagent-only references from the parallel/handoff maps
so they don't leak into the supervisor's graph. `run.ts` emits
`SubagentConfig[]` on the primary `AgentInputs` — a self-spawn entry when
`allowSelf` is enabled plus one entry per configured agent.

UI: an "Advanced" panel section with an enable toggle, a self-spawn
toggle, and an agent picker (capped at 10). Enabling without adding
agents still yields self-spawn; disabling self-spawn with no agents shows
a warning. A capability flag gates the whole section.

* 🪆 feat: Stream subagent progress to UI (dialog + inline ticker)

Pairs with the @librechat/agents SDK change that forwards child-graph
events through the parent's handler registry (danny-avila/agents#107):

- Self-spawn and explicit subagents can now use event-driven tools,
  because child `ON_TOOL_EXECUTE` dispatches reach our ToolService via
  the parent's registered handler.
- The same forwarding path wraps the child's run_step / run_step_delta
  / run_step_completed / message_delta / reasoning_delta dispatches in
  a new `ON_SUBAGENT_UPDATE` envelope, with start/stop/error bookends.

Backend: `callbacks.js` registers an `ON_SUBAGENT_UPDATE` handler that
forwards each envelope straight to the SSE stream.

Frontend:
- `useStepHandler` consumes `ON_SUBAGENT_UPDATE` events and merges them
  into a per-tool_call Recoil atom (`subagentProgressByToolCallId`).
  First-seen `subagentRunId` claims the most-recent unclaimed `subagent`
  tool call in the active response message — a temporal mapping, no SDK
  wire-format change needed to correlate child runs with parent tool
  calls.
- New `SubagentCall` part component replaces the default `ToolCall`
  rendering when `toolCall.name === Constants.SUBAGENT`: compact status
  ticker showing the 3 most recent update labels, clickable to open a
  dialog with the full activity log + final markdown-rendered result.
- Adds `Constants.SUBAGENT`, `StepEvents.ON_SUBAGENT_UPDATE`, and
  `SubagentUpdateEvent` type in data-provider.

Tests:
- `packages/api npx jest run-summarization` — 23 pass
- `api npx jest initialize` — 16 pass
- `npm run build` — clean

Dependency note: bumps `@librechat/agents` to `^3.1.67-dev.1` — requires
the SDK PR (danny-avila/agents#107) to be merged to dev and published
before this PR merges. `ON_SUBAGENT_UPDATE` is absent from dev.0, so the
handler registration would be a no-op with the older SDK but would not
crash.

* 🪆 fix: address Codex review and review audit on subagents

Stacks on top of the SDK change in danny-avila/agents#107 (bumped to
`^3.1.67-dev.2`).

- **P1 (`initialize.js`)**: subagent-only agents were being deleted from
  both `agentConfigs` AND `agentToolContexts`. The tool-execute handler
  resolves execution context (agent, tool_resources, skill ACLs) from
  `agentToolContexts`, so explicit subagents would run without their
  configured resources and skip action tools. Now only `agentConfigs`
  is pruned — tool context stays intact.
- **P2 (`AgentSubagents.tsx`)**: toggling subagents off set the form
  field to `undefined`; `removeNullishValues` stripped it from the
  PATCH, leaving the server copy enabled. Now it persists an explicit
  `{ enabled: false, ... }` so the update actually clears state.

- **Finding 1 (MAJOR)** — `agent_ids` Zod schema gains `.max()` via a
  new `MAX_SUBAGENTS` export from `data-provider` (shared with the UI
  cap). Crafted payloads can't trigger hundreds of `processAgent`
  calls.
- **Finding 2 (MAJOR)** — `subagentProgressByToolCallId` atomFamily
  atoms are now tracked in a ref and reset from `clearStepMaps` via a
  `useRecoilCallback({ reset })`. No monotonic growth across a session.
- **Finding 3 (MAJOR)** — early-arriving `ON_SUBAGENT_UPDATE` events
  whose parent `tool_call_id` is not yet mapped are now buffered in
  `pendingSubagentBuffer` (keyed by `subagentRunId`) and replayed in
  arrival order once correlation completes. Mirrors the existing
  `pendingDeltaBuffer` pattern.
- **Finding 4 (MAJOR)** — switched to deterministic correlation via
  the new `parentToolCallId` that SDK `3.1.67-dev.2` threads through
  from `ToolRunnableConfig.toolCall.id`. Temporal fallback now iterates
  oldest-unclaimed-first (forward), matching tool-call creation order,
  so concurrent spawns map correctly.
- **Finding 6 (MINOR)** — `agent_ids` are deduped on the backend via
  `new Set(...)` before the load loop. Duplicates no longer produce
  duplicate `SubagentConfig` entries visible to the LLM.
- **Finding 7 (MINOR)** — events array inside each Recoil atom is
  capped at 200 entries. Long-running subagents no longer replay O(n)
  spreads on every update; the dialog log still shows the cap window.
- **Finding 8 (MINOR)** — documented: subagents are loaded only for
  the primary agent this release (handoff children get self-spawn but
  not explicit sub-subagents). In-code comment added so the next
  maintainer doesn't wonder.
- **Finding 9 (NIT)** — removed `{!isSubmitting && null}` dead code
  and the misleading announce-polite comment in `SubagentCall`.

- New `validation.spec.ts` — 9 tests covering the cap on
  `agent_ids.length` at the subagent schema, agent-create, and
  agent-update layers.
- `run-summarization` — 23 pass, `initialize` — 16 pass, total backend
  package: 103 pass across touched areas.

Findings 5 (component tests) and 10 (micro-allocation) are tracked
but deferred; the former needs a Recoil-RenderHook harness that isn't
in this PR's scope, and the latter has negligible impact (one `Array.from`
per subagent run).

* 🧪 test: integration coverage for subagent correlation + backend loading

Addresses the follow-up audit on #12725 with real-code tests (no mock
handlers, only the existing setMessages/getMessages spies and the
standard mongodb-memory-server harness).

Six new tests under a dedicated `describe('subagent loading')`:
- loads a configured subagent, populates `subagentAgentConfigs`, keeps
  it out of `agentConfigs`
- **P1 regression guard**: drives the real `toolExecuteOptions.loadTools`
  closure with the subagent id and asserts `loadToolsForExecution` is
  called with `agent: <subagent>`, `tool_resources`, `actionsEnabled`.
  If anyone deletes `agentToolContexts` again, this fails.
- dedup: three copies of the same id load the agent once
- overlap: agent referenced both as handoff target and subagent stays in
  `agentConfigs`
- capability gate: admin disabling `subagents` suppresses loading even
  when the agent has a config
- per-agent disable: `subagents.enabled: false` skips loading entirely

Five new tests under `describe('on_subagent_update event')` using a
real `RecoilRoot` and a companion `useRecoilCallback` reader so writes
from the hook are observable:
- deterministic correlation via `parentToolCallId` (happy path with
  SDK dev.2+)
- fallback: oldest-unclaimed tool call wins for concurrent spawns
  without `parentToolCallId`
- early-arrival buffer: updates with no mapping get buffered and
  replayed once the tool call appears
- event cap: 205 updates collapse to 200 retained, oldest dropped
- `clearStepMaps` resets tracked atoms back to their null default

- F2 — added explicit `// TODO` marker for handoff-subagent-loading
  extension (matches the comment that referenced it).
- F3 — dropped the unnecessary `MAX_SUBAGENTS as MAX_SUBAGENTS_CAP`
  alias; just import the constant directly.
- Bumped `@librechat/agents` to `^3.1.67-dev.3` to pick up the SDK's
  paired test additions.

- `api/server/services/Endpoints/agents/initialize.spec.js` — 22 pass
  (6 new + 16 existing)
- `packages/api/src/agents/validation.spec.ts` +
  `run-summarization.test.ts` — 103 pass
- `client/src/hooks/SSE/__tests__/useStepHandler.spec.ts` — 48 pass
  (5 new + 43 existing)

* 🪆 fix: strip parent run summary + discovered tools from subagent inputs

Codex P1 on #12725: `buildSubagentConfigs` reused the shared
`buildAgentInput` factory for each explicit child, and that factory
always stamps the parent run's `initialSummary` (cross-run conversation
summary) and `discoveredTools` (tool names the parent's LLM searched
earlier) onto every `AgentInputs` it returns. When subagents were
enabled on a conversation that had already been summarized, every
child inherited that summary — silently defeating the isolated-context
contract and burning extra tokens on unrelated prior chat.

Fix in `run.ts`: after `buildAgentInput(child)`, explicitly clear
`childInputs.initialSummary` and `childInputs.discoveredTools` before
attaching to the `SubagentConfig`. The parent keeps both — that's how
the supervisor receives cross-turn context — but the child starts
fresh.

Paired with danny-avila/agents#107 (bumped to `^3.1.67-dev.4`), which
adds the equivalent strip inside `buildChildInputs` to cover the
self-spawn path where the SDK clones parent `_sourceInputs` directly
and LibreChat never sees the intermediate shape. Belt and suspenders.

Regression test (new):
- `does NOT leak the parent run initialSummary into an explicit child
  (Codex P1 regression)` — sets `initialSummary` on the run, enables
  subagents with an explicit child, asserts the parent still has the
  summary but `childConfig.agentInputs.initialSummary` is `undefined`.
  Same for `discoveredTools`. 24 pass.

* 🪆 fix: capability gate applies to handoff agents + parallel subagent test

### Codex P2 — handoff agents kept `subagents` after capability disabled
The endpoint-level `AgentCapabilities.subagents` gate only cleared
`subagents` on `primaryConfig`. Handoff agents loaded into
`agentConfigs` retained their persisted `subagents.enabled: true`,
and because `run.ts` calls `buildSubagentConfigs` for every agent
input, self-spawn would still fire on a handoff target even when the
admin had disabled the capability globally.

Fix in `initialize.js`: after the subagent loading block, when the
capability is off, iterate `agentConfigs.values()` and clear
`subagents` + `subagentAgentConfigs` on every loaded config.

Regression test: `clears subagents on handoff agents too when
capability is disabled (Codex P2 regression)` — seeds a handoff target
with its own `subagents.enabled: true`, disables the capability at
the endpoint, asserts both primary AND handoff have `subagents`
undefined in the client args. 23 init tests pass.

### Parallel subagent correlation — user-requested verification
Added `keeps parallel subagent streams independent when events
interleave` to `useStepHandler.spec.ts`. Two `subagent` tool calls
seeded side by side, 6 interleaved `ON_SUBAGENT_UPDATE` envelopes
dispatched (a-start, b-start, a-step, b-step, a-stop, b-step), each
carrying its own `parentToolCallId`. Asserts each `tool_call_id`'s
Recoil bucket accumulates only its own run's events, statuses reflect
each run independently (`call_a` → stop, `call_b` → run_step), no
cross-contamination. 49 step-handler tests pass.

* 🪆 fix: SubagentCall detects cancelled / errored states (Codex P2)

Codex P2 on #12725: the old `running` check only consulted
`initialProgress` and the subagent's phase. A user stop, dropped
stream, or backend crash before a terminal `stop`/`error` envelope
arrived would leave the ticker permanently stuck on "working…". Other
*Call components (ToolCall.tsx) already model this via
`!isSubmitting && !finished` → cancelled.

Mirror that pattern. Re-introduce `isSubmitting` on `SubagentCallProps`
(the prop was dropped earlier as 'unused' — that was a bug) and resolve
status as a tri-state:

- `finished`  — initialProgress >= 1, or subagent `stop`/`error`
- `cancelled` — `!isSubmitting && !finished`
- `running`   — neither

New locale keys `com_ui_subagent_cancelled` + `com_ui_subagent_errored`
swap in the right header text per state.

Tests: new `SubagentCall.test.tsx` covers all four states with a real
`RecoilRoot` and a `useRecoilCallback` seeder — no mocked store — 5/5
pass. Includes an explicit P2 regression test that simulates the
`isSubmitting=false, progress.status='run_step', initialProgress<1`
scenario and asserts the cancelled label renders.

* 🪆 feat: semantic ticker + aggregated content-part dialog for subagents

Two rounds of feedback on #12725:

### Ticker — user-readable lines, not raw event names

The old ticker showed \`on_run_step\`, \`on_message_delta\`, etc. — not
meaningful to users. Replaced with \`buildSubagentTickerLines\`, a pure
helper that walks the \`SubagentUpdateEvent\` stream and emits:

- message/reasoning deltas → a single live "Writing: <last 60 chars>"
  (or "Reasoning: …") line that updates in place as chunks arrive
- run_step with tool_calls → "Using calculator(expression=42*58)" for
  a single call, "Using tool: a, b" for parallel (args dropped when
  multiple so the line stays short)
- run_step_completed → "calculator → 42*58 = 2436" (output truncated
  to 48 chars; falls back to "Tool X complete" when output is empty)
- error → "Error: <message>"
- start / stop / run_step_delta → suppressed (too granular / lifecycle-only)

Args and output pass through \`summarizeArgs\` / \`summarizeOutput\`
which flatten JSON to \`key=value\` pairs and head-truncate long
strings so a 200-line tool output never bloats the ticker.

### Dialog — aggregated content parts via leaf renderers

\`aggregateSubagentContent\` folds the raw event stream into
\`TMessageContentParts[]\` — text/reasoning delta streaks collapse into
single \`TEXT\` / \`THINK\` parts, tool calls become \`TOOL_CALL\` parts,
and \`run_step\` boundaries correctly break text runs around tool
calls. The dialog iterates those parts through a \`SubagentDialogPart\`
renderer that delegates to the existing \`Text\`, \`Reasoning\`, and
\`ToolCall\` leaf components — the same sub-components \`<Part />\` uses
— wrapped in a minimal \`MessageContext\` so reasoning expand state and
cursor animation work.

Leaf components are used directly rather than importing \`<Part />\`
itself to avoid a module cycle (Part → Parts/index → SubagentCall →
Part) and to sidestep a hypothetical nested-subagent rendering.

### Tests

- \`subagentContent.test.ts\` — 19 pure-function tests covering the
  aggregator (text concat, reasoning concat, tool call lifecycle,
  interleaving, phase suppression, late-arriving completions) and the
  ticker builder (live preview truncation, args/output snippets,
  parallel-call handling, output truncation, i18n formatter override).
- \`SubagentCall.test.tsx\` — 9 component tests: 5 status-resolution
  (existing) + 2 ticker (semantic text, delta collapse) + 2 dialog
  (aggregated parts routed to leaf renderers, raw-output fallback).

### Locale keys

New: \`com_ui_subagent_ticker_writing\`, \`…_reasoning\`, \`…_error\`,
\`…_using\`, \`…_using_with_args\`, \`…_tool_complete\`,
\`…_tool_output\`. Preserves i18n at the display layer while the
helper stays pure.

* chore: drop unused com_ui_subagent_activity_log locale key

The dialog no longer renders an "Activity log" section — the new
content-parts renderer replaced it. Also tweaks the dialog description
copy to match.

* 🪆 fix: subagent dialog order, persistence, auto-scroll, width

Follow-up pass addressing the four issues observed in real runs
against a live subagent-using parent.

### Aggregator ordering (reasoning appearing after text it preceded)

Reproducible pattern: LLM emits reasoning → text → tool call in that
order, but the dialog rendered text BEFORE reasoning in the content
array. Root cause: `aggregateSubagentContent` maintained `currentText`
and `currentThink` buffers in parallel and only flushed them at a
`run_step` boundary in a fixed (text, think) order, losing the actual
arrival order.

Fix: when a text chunk arrives, close any open think buffer first
(pushes it into the content array right then); symmetric for think →
text. Two new regression tests cover the exact reasoning → text →
tool_call sequence from the screenshot and the repeated
reasoning ↔ text flow across a turn.

### Content persists after completion (markdown not rendering when done)

`clearStepMaps` was calling `resetSubagentAtoms()` at stream end,
which wiped every `subagentProgressByToolCallId` entry. Once reset,
`contentParts.length === 0` and the dialog fell back to rendering the
raw `output` string with plain text — hence the literal `##`/`**` in
the completed-state screenshot. Stopped resetting; the atoms are
bounded per-call (200-event cap) and per-conversation (one per
subagent spawn) so growth matches the rest of the conversation state.
`resetSubagentAtoms` is kept for a future conversation-switch caller.

Also: routed the raw-`output` fallback (older subagent runs recorded
before the event forwarder existed) through the same
`SubagentDialogPart` → `Text` leaf that content parts use, so its
markdown renders the same way.

### Auto-scroll to bottom while running

Added a `scrollRef` on the dialog body and a `useEffect` that pins
`scrollTop = scrollHeight` while the dialog is open AND the subagent
is running. Triggers on `contentParts.length` (new tool calls / part
boundaries) and `events.length` (intra-part deltas) so the cursor
tracks text streaming. Disabled post-completion so re-opening a
finished run doesn't yank to the bottom.

### Wider dialog

Went from `max-w-2xl` (42rem / 672px — too cramped on maximized
laptop windows) to `w-[min(95vw,64rem)] max-w-[min(95vw,64rem)]`.
Narrow on phones, scales up to 64rem on desktop, always leaves a bit
of margin from the viewport edge. Bumped `max-h-[65vh]` on the scroll
area to give the extra width room to breathe vertically too.

### Tests

- `subagentContent.test.ts` — 21 pass (2 new ordering regressions).
- `useStepHandler.spec.ts` — 49 pass (1 updated to assert atoms are
  *preserved* on clearStepMaps).
- `SubagentCall.test.tsx` — 9 pass (unchanged; aggregator-level tests
  cover the ordering).

* 🪆 feat: persist subagent_content via SDK createContentAggregator

Per-request map of createContentAggregator instances keyed by the
parent's tool_call_id. ON_SUBAGENT_UPDATE handler feeds each event
into the matching aggregator (phase → GraphEvent mapping); AgentClient
harvests contentParts onto the subagent tool_call at message save so
the child's reasoning / tool calls / final text survive a page refresh.

Reusing the SDK's battle-tested aggregator instead of a bespoke one
keeps the persisted shape identical to the parent graph's output and
drops ~100 lines of custom aggregation code.

* 🪆 fix: incremental subagent aggregation + dialog render parity

**Disappearing tool_calls**: the Recoil atom trimmed events to a 200-long
rolling window, so verbose subagents could shed the `run_step` that
originally created a tool_call part — rebuilding content from the trimmed
window then produced only the surviving text/reasoning. Fix: fold each
envelope into `contentParts` incrementally in the atom as it arrives
(new `foldSubagentEvent` + cursor state). Event trim window now affects
only the ticker, never the dialog.

**Render parity**: dialog now applies `groupSequentialToolCalls` and
renders single parts through `Container` + grouped batches through
`ToolCallGroup` — same spacing and "Used N tools" collapsing the main
message view uses.

**Width**: `min(96vw, 80rem)` — wider on big screens, still responsive.

**Labels**: "Subagent: X" is jargon. Named subagents render as
`Running "{name}" agent` / `Ran "{name}" agent` (past tense on
completion); self-spawns use `Running subtask` / `Ran subtask` since
`Running "self" agent` reads badly.

* 🪆 polish: subagent dialog parity + agent avatar in header

**Labels**: drop "subtask" framing. Self-spawn shows `Running agent` /
`Ran agent` (past tense on completion); named subagents stay
`Running "X" agent` / `Ran "X" agent`.

**Dialog render parity**: stop wrapping every part in `Container`.
TEXT keeps its `Container` (gap-3 + `mt-5` sibling margin), THINK and
TOOL_CALL render bare so their own wrappers set the full-column width
the regular message view gives them — matches the main `<Part>` dispatch.
Outer scroll region now uses `px-4 py-3` padding and a
`max-w-full flex-grow flex-col gap-0` inner wrapper, mirroring the
`MessageParts` container the main conversation uses.

**Avatar**: header icon now renders the subagent's configured avatar
via `MessageIcon` when `useAgentsMapContext()` has the child agent,
falling back to the `Users` SVG (which keeps its running-state pulse).
Same icon-left-of-label pattern the tool UI uses.

* 🪆 polish: subagent group label, ticker throttle + tail-ellipsis, scroll button

**Grouped label**: ToolCallGroup now detects all-subagent batches and
labels them "Running N agents" / "Ran N agents" instead of "Used N
tools". Mixed batches keep the existing label. The tool-name summary
is suppressed for all-subagent groups (every entry dedupes to
"subagent", which adds nothing).

**Ticker width + tail-ellipsis**: raise the preview cap to 300 chars so
wide containers aren't half-empty, and flip the ticker `<li>` to
`dir="rtl"` so `text-overflow: ellipsis` clips the *oldest* characters
(visually the left edge) — the newest tokens stay pinned to the right
regardless of container width. Bidi lays out the Latin text LTR
internally, the rtl only affects which side gets the ellipsis.

**Throttle**: `useThrottledValue` hook (trailing-edge, 1.2s) smooths
the live `Writing: …` preview so tokens no longer strobe past the
eye faster than they can be read. Ref-based internals (not `useState`)
avoid infinite-update loops when the upstream value is a new-reference
each render; `NEGATIVE_INFINITY` sentinel ensures the very first value
passes through synchronously so tests and first paint aren't delayed.

**Scroll-to-bottom**: dialog tracks `isAtBottom` with a 120px
threshold; auto-scroll only engages when the user is already following
along, and a persistent jump-to-latest button appears whenever they
scroll up — no more fighting the auto-scroll to read back.

* 🪆 polish: snappier ticker, prefix-safe labels, agents icon, readable lines

**Ticker lines are now incrementally aggregated in the atom** — same
pattern as contentParts. The raw-events rolling window is gone; event
volume no longer caps what the ticker can display. Verbose subagents
that used to drop early tool_call lines out of the window now keep the
full 3-line history (using_tool, tool_complete, writing).

**Discriminated-union ticker lines** split a constant prefix (e.g.
"Writing:") from a tail-truncatable body. The prefix lives in a
`shrink-0` span so it never gets clipped when the body overflows; the
body uses `dir="rtl"` only on itself — scoped so non-streaming lines
(e.g. "Waiting for first update…") can't get their trailing ellipsis
flipped by bidi.

**Content-aware throttle**: 800ms interval (down from 1200ms), skipped
entirely while the live buffer is below 120 chars. Early tokens now
appear immediately — no more "Reasoning: I" sitting blank for a full
second before the next heartbeat. Once the preview is long enough to
fill the container, throttling kicks in at the tighter interval.

**Header label** is now a constant verb + optional muted sub-label.
Base reads "Running agent" / "Ran agent" / "Cancelled agent" / "Agent
errored" for every subagent; named subagents get the configured agent
name rendered to the right in secondary text (self-spawns and
unresolved names omit it — "Running self agent" is nonsense).

**ToolCallGroup** now detects `allSubagents` and swaps `StackedToolIcons`
for a single `Users` glyph — otherwise the group header shows a wrench
("tool") icon next to "Ran 5 agents", which reads wrong.

* 🪆 feat: delimiter-aware tool labels in ticker + full-width tool lines

New shared `parseToolName` helper in `client/src/utils/toolLabels.ts`
— single source of truth for splitting `<tool>_mcp_<server>` ids and
mapping native tool names (web_search, execute_code, …) to their
friendly translation keys. `ToolCallGroup` drops its inline copy and
pulls from this helper.

Ticker tool lines now use the shared parser + a new `ToolIdentifier`
sub-renderer so the live log reads like the main tool UI:

  - MCP tool  → `<server> · <code-badge:tool>` (e.g. "github · `search_code`")
  - Native   → friendly name from `TOOL_FRIENDLY_NAME_KEYS`
  - Unknown  → bare `<code>` badge of the raw id

The `using_tool` / `tool_complete` rows now render with a
`flex w-full items-baseline gap-1 overflow-hidden` layout matching
the writing/reasoning rows — they take the full container width
instead of collapsing to content size. Output snippets on
`tool_complete` get the same tail-side `dir="rtl"` ellipsis so the
newest characters stay flush-right when the container is narrow.

Dropped the now-unused template i18n keys
(`com_ui_subagent_ticker_using_with_args`,
`com_ui_subagent_ticker_tool_complete`,
`com_ui_subagent_ticker_tool_output`) in favor of tokens the JSX
composes structurally. Only English is touched per the project rule;
other locales follow externally.

* 🪆 fix: dialog scroll button + auto-scroll during streaming deltas

Two race/trigger bugs in the dialog's scroll behavior:

**Button never showed**: `addEventListener('scroll', …)` in a
`useEffect` ran before Radix's portal had actually committed the
scroll container, so `scrollRef.current` was still null — the listener
never attached, `isAtBottom` stayed stuck at its initial `true`, and
the jump-to-latest button was never rendered. Swap to React's
`onScroll` prop on the element itself so the handler wires up as part
of DOM commit, not a post-commit effect.

**Auto-scroll stalled during text streaming**: the pin-to-bottom
effect only re-fired on `contentParts.length` changes. Message/reasoning
deltas extend the last TEXT/THINK part's `.text` without changing the
array length — so the view would drift up as tokens piled in and
never catch back up. Replace the length-dep effect with a
`ResizeObserver` on the inner content div; every height change (new
part or in-place growth) triggers a scroll-pin when the user is still
at the bottom.

* 🪆 fix: drop leading ellipsis from ticker body

truncatePreview was prepending ... to the tail when the buffer
exceeded 300 chars. The component's CSS already produces a left-side
ellipsis for overflow via dir=rtl + text-overflow: ellipsis — stacking
a data-level ellipsis on top renders a stray dot character right after
the Writing: / Reasoning: label (Writing: .Sure!), which looks like a
typo to the reader.

Data now returns just the last 300 chars when truncating; CSS handles
the visual cue whenever the body actually overflows its container.

* 🪆 fix: Codex review — subagent isolation + concurrent-safe throttle

Three findings from the @codex review pass, all valid:

**P1 — buildAgentInput leaks parent discovered-tool state into subagent
children.** `buildAgentInput` mutates `agent.toolRegistry`
(`overrideDeferLoadingForDiscoveredTools` flips `defer_loading:true→false`
on tools the parent previously searched for) and appends those tools'
definitions to the returned `toolDefinitions` before the function
returns. `buildSubagentConfigs` was clearing the reported
`initialSummary` / `discoveredTools` fields on the returned
AgentInputs, but that happened post-return — the registry writes and
extra tool definitions persisted on the child, silently defeating
context isolation and inflating the child's prompt.

Fix: `buildAgentInput` now takes an `isSubagent` flag that gates the
registry-mutation block and omits `initialSummary` /
`discoveredTools` at the source. `buildSubagentConfigs` passes
`{ isSubagent: true }` for every explicit child; no post-hoc cleanup
needed.

**P2 — ToolCallGroup labels a finished subagent group as still
running when the child returned no output.** `getToolMeta` computed
`hasOutput` as `!!tc.output`, which is `false` for a completed
subagent that returned empty text (the UI already has an "empty
result" fallback for that case). `allCompleted` would stay `false`
and the group header stuck on "Running N agents" forever.

Fix: treat `tc.progress === 1` as completion too — progress is the
authoritative lifecycle signal, output is just content.

**P2 — useThrottledValue schedules `setTimeout` during render.**
Discarded renders under Strict Mode / Concurrent rendering would
leave orphan timers firing against stale trees.

Fix: move `setTimeout` into a `useEffect` keyed on `[value, intervalMs,
enabled]`. Render-time still mutates refs (idempotent), but timer
scheduling lives post-commit. Cleanup on unmount and on passthrough
transitions is preserved.

* 🪆 fix: Codex P2 — wipe subagent atoms on conversation switch

`clearStepMaps()` intentionally doesn't reset `subagentProgressByToolCallId`
so a user can reopen a completed subagent's dialog mid-conversation,
but `resetSubagentAtoms` was defined and never exposed / called —
so each completed run's aggregated `contentParts` + `tickerState`
stayed resident in the `atomFamily` for the whole app session.
Unbounded growth across multi-conversation sessions.

Expose `resetSubagentAtoms` from `useStepHandler` and fire it from
`useEventHandlers` whenever the URL's `conversationId` changes.
That's the correct cleanup boundary: historical subagent dialogs
rehydrate from persisted `subagent_content` on each `tool_call` at
message-save time, so wiping live atoms on switch doesn't lose any
viewable history — it just releases per-tool-call state that the
old conversation's components no longer subscribe to.

* 🪆 fix: Codex round 3 — subagent registry isolation + post-run label

Two more valid findings.

**P1 — parent-order registry mutation leaks into subagent inputs.**
`overrideDeferLoadingForDiscoveredTools` mutates `agent.toolRegistry`
in place (the Map *and* the LCTool objects inside it). When an agent
appears both as a handoff target (normal graph node) AND an explicit
subagent child, a subagent build that ran before the parent's build
captures a reference to the same registry — the parent's later mutation
leaks through to the child.

Fix: for subagent children (`isSubagent`), clone the `toolRegistry`
Map and shallow-clone each LCTool inside before returning the inputs.
`defer_loading` flips on parent-graph registry mutations can't
propagate across the clone boundary. `toolDefinitions` also gets a
shallow-copy pass so the same isolation holds for definitions the
child carries directly.

**P2 — "Running N agents" label stuck after cancel/error.**
ToolCallGroup's all-subagent label was gated only on `allCompleted`,
which requires every child to have `hasOutput || progress === 1`.
A subagent that gets cancelled (stream ends, no `stop` phase, no
output) never satisfies that — so even after `isSubmitting` flips
false, the header stays on "Running N agents" while each individual
card correctly shows "Cancelled agent".

Fix: derive a `subagentsDone` flag as `allCompleted || !isSubmitting`
and gate the past-tense label on that. Matches the tri-state each
SubagentCall card already resolves (finished / cancelled / running).

* 🪆 fix: Codex P2 — ACL-check subagents.agent_ids on create/update

Codex flagged that `subagents.agent_ids` was accepted as arbitrary
strings on the create/update routes while `edges` got a
`validateEdgeAgentAccess` pass — so users could save subagent
references to agents they can't VIEW. At runtime `initializeClient`'s
`processAgent` ACL gate silently drops those, so the persisted
configuration and the actual behavior diverged in a way that is
difficult to diagnose.

Refactor: extract the id-set → unauthorized-ids check into a shared
`collectUnauthorizedAgentIds`, wrap it with a dedicated
`validateSubagentAccess`, and plumb the same 403-on-failure response
the edge path already returns. Applied on both POST /agents and
PATCH /agents/:id.

* 🪆 fix: Codex round 5 — ACL-disable escape hatch + ticker order

Two valid findings.

**P1 — can't disable subagents after losing access to a child.**
The subagent ACL check ran on every create/update that echoed back
the `agent_ids` list, even when the user was explicitly disabling
the feature. The UI keeps the list intact when toggling `enabled:
false`, so a user who subsequently lost VIEW on any child would be
locked in a 403 loop — every edit (including the one that turns
subagents off) bounces.

Fix: gate the ACL check on `subagents.enabled !== false` at both
the POST /agents and PATCH /agents/:id handlers. Empty list stays
a no-op. Disabling the feature is always permitted.

**P2 — ticker fold merges out-of-order previews across delta
switches.** `foldSubagentEventIntoTicker` carried `textLineIdx` /
`thinkLineIdx` across a reasoning → text → reasoning transition,
so the second reasoning chunk appended to the original reasoning
line instead of starting a new chronological one.

Fix: close the opposite buffer + cursor when a delta-type switch
is detected (same rule the content-parts reducer already applies).
Added a regression test.

* 🪆 fix: Codex round 6 — preserve mid-stream atoms + honor sequential suppression

Two valid findings.

**P2 — atom reset fires on initial chat URL assignment.**
`useEventHandlers` initialized `lastConversationIdRef` from the URL's
current `paramId`, then reset subagent atoms whenever the ref and
`paramId` disagreed. For a brand-new conversation the URL stamp goes
from `undefined → "abc123"` while the first response is still
streaming, which used to drop subagent ticker/content state mid-run
and leave dialogs missing earlier updates.

Fix: only reset when *both* the old and new IDs are non-null and
differ — i.e. a user-initiated switch between two established
conversations. The initial assignment passes through without
clearing.

**P2 — ON_SUBAGENT_UPDATE bypassed `hide_sequential_outputs`.**
Every other streaming handler in `callbacks.js`
(`ON_RUN_STEP`, `ON_MESSAGE_DELTA`, etc.) gates emission on
`checkIfLastAgent` + `metadata?.hide_sequential_outputs`, but the
subagent forwarder did an unconditional `emitEvent` — so intermediate
agents in a sequential chain were leaking their children's activity
to the client even when the chain was configured to suppress
intermediates.

Fix: accept `metadata` and apply the same `isLastAgent ||
!hide_sequential_outputs` gate. Aggregation still runs regardless of
visibility (persistence + dialog depend on it); only the SSE forward
is suppressed.

* 🪆 fix: Codex P2 — gate subagent ACL check on endpoint capability

`validateSubagentAccess` ran on every create/update where
`subagents.enabled !== false`, regardless of the endpoint-level
`subagents` capability. When the capability is off at the appConfig
level, `initializeClient` already strips the `subagents` block at
runtime — so persisted `agent_ids` are inert — but the validation
could still 403 on a legacy record whose referenced child is no
longer viewable, blocking unrelated edits.

Fix: add `isSubagentsCapabilityEnabled(req)` that reads the agents
endpoint's capabilities from `req.config` and gate both the create
and update ACL checks on it. Capability-off environments can update
agents with stale `subagents` data freely; capability-on keeps the
full ACL protection.

* 🪆 fix: Codex P2 — reset subagent atoms on id→null navigation too

Previous guard (both-established) skipped the reset whenever
`paramId` became null/undefined, so navigating from an existing
chat to a "new chat" route left stale subagent progress resident
in the `atomFamily` until the user picked a specific different
chat.

Swap the both-established check for a one-time flag: skip only the
very first `undefined → id` transition (the brand-new-chat URL
stamp that happens mid-stream), then reset on any subsequent
change — id→id, id→null, null→id-after-reset. If the user started
on an established chat the flag is true at mount, so the guard is
a no-op and every navigation resets normally.

* 🪆 fix: Codex round 9 — subagent persistence gate + handoff children

Two valid findings.

**P1 — hide_sequential_outputs also gates persistence.**
The previous fix gated the SSE forward on
`isLastAgent || !hide_sequential_outputs` but still ran the
per-tool-call `createContentAggregator` aggregation unconditionally.
`finalizeSubagentContent` would then attach the hidden intermediate
agent's child reasoning / tool output to the saved message, so a
page refresh could reveal activity that was intentionally suppressed
live. Move the visibility gate to the top of the handler — hidden
agents now skip both aggregation and emission, so
"hide_sequential_outputs" is a consistent "don't record" rule for
subagent traces.

**P2 — handoff agents' explicit subagents were silently dropped.**
`initializeClient` only resolved `subagentAgentConfigs` for the
primary config, so an agent used via handoff that had its own
`subagents.agent_ids` saved in the builder would get self-spawn
only; every explicit child was quietly ignored, creating a
saved-config / runtime mismatch the user couldn't diagnose.

Extract the resolution into a shared `loadSubagentsFor(config)`
helper and invoke it for the primary and every handoff agent in
`agentConfigs`. The `edgeAgentIds` precomputation stays outside
the helper (it's loop-invariant). Capability-off shortcuts return
empty early so the existing strip-on-capability-off path still
holds.

* 🪆 fix: Codex P2 — recursive subagent build for multi-level delegation

Previously only the outer `agents[]` loop attached `subagentConfigs`
to its inputs, so a child used as a subagent (invoked via the
`subagent` tool) lost every explicit spawn target of its own. A
user-valid configuration like A → B → C would only run the top
layer; B could never actually delegate to C from inside A's run.

Recursively build `subagentConfigs` for each child inside
`buildSubagentConfigs`, passing the child's freshly-constructed
`childInputs` down so its own `subagents.enabled` children get
resolved too. Added cycle protection via an `ancestors` Set — a
configuration like A → B → A is safely cut off at the second
encounter of A rather than recursing forever (the existing
`child.id === agent.id` guard already prevents the direct self-loop).

* 🪆 fix: Codex P2 — reset subagent atoms on useEventHandlers unmount

The effect that resets subagent atoms only fired on `paramId` change,
so unmounting the chat container (route change away from /c) never
flushed the atoms. `knownSubagentAtomKeys` lives in a ref inside
`useStepHandler` — once the hook unmounts the ref is gone, so a
subsequent remount can't clean atoms it never registered.

Added a second `useEffect` that only runs cleanup on unmount (empty
deps aside from the stable `resetSubagentAtoms` callback). Keeps
`atomFamily` bounded across full route teardowns too.

* 🪆 fix: Codex round 13 — cyclic subagent guard + prefer persisted

Two valid findings.

**P1 — cyclic subagent ref reloads the primary.** A configuration
like `A ↔ B` (B lists A as its own subagent) would send
`loadSubagentsFor` down a path that couldn't find A in
`agentConfigs` (the primary isn't stored there), so it called
`processAgent(A)` a second time. That inserts a fresh config for
the primary id, which downstream duplicates in
`[primary, ...agentConfigs.values()]` and can replace the primary's
tool context with the reloaded copy.

Fix: short-circuit when a subagent ref points back at
`primaryConfig.id` — reuse the already-loaded primary config.
Primary is always an edge id so no pruning bookkeeping needed.

**P2 — live atom preferred over canonical persisted trace.** The
dialog picked `progress.contentParts` ahead of
`persistedContent`, but the Recoil bucket is best-effort — after
a disconnect/reconnect it can be stale or partial. The server's
`subagent_content` on the `tool_call` is the canonical record
refreshed on sync. Preferring live could hide completed
tool/reasoning history that was actually persisted.

Fix: flip the preference order. Persisted wins when it's
non-empty; live covers the mid-stream window (before the parent
message saves, persisted is empty) and the older-runs fallback.
Updated the test that enforced the old order to lock the new
semantics in (separate mid-stream live-fallback assertion kept).

* 🪆 fix: Codex P2 — subagent atom reset rule simplified to 'leaving established id'

The `hasEstablishedConversationRef` + check for initial undefined→id
covered the first navigation but missed the equivalent mid-stream
URL stamp when a user goes from an existing chat to a new chat and
sends a message there (`id → null → newId`). The null → newId
transition was still hitting the reset branch and wiping the
in-flight subagent ticker/content for that first turn.

Simpler rule: only reset when the PREVIOUS paramId is an established
id. Every transition AWAY from an established chat clears (id→id2,
id→null, id→undefined); every transition FROM null/undefined passes
through (initial mount, new-chat URL stamp mid-stream). Drop the
`hasEstablishedConversationRef` machinery in favor of that single
condition.

* 🪆 fix: Codex P2 — match runtime's strict subagent enable check in ACL

Runtime (`initializeClient` + `run.ts`) treats `subagents?.enabled`
as a truthy predicate — `undefined`, `null`, missing, and `false`
all short-circuit. The ACL gate was using `!== false` which
accepted `undefined` / missing as "enabled" and could 403 a payload
whose subagent tool would be inert at runtime.

Swap both create and update to `enabled === true`. Only a strictly-
enabled payload triggers the ACL check; the disable path (`false`)
still passes through so a user who lost VIEW on a child can still
save the disable edit.

* 🪆 fix: Codex P2 — reject missing subagent references with 400

`validateSubagentAccess` collapsed through `collectUnauthorizedAgentIds`,
which returns an empty list for ids with no DB record — so typos and
references to deleted agents passed validation silently, and
`initializeClient` later dropped them at runtime. Saved config would
then list spawn targets that the backend never honored, a hard-to-
diagnose drift.

Refactor the helper into `classifyAgentReferences(ids, …)` which
returns `{ missing, unauthorized }` separately. `validateEdgeAgentAccess`
keeps its old semantics (missing is intentional — a self-referential
`from` names the agent being created). `validateSubagentReferences`
surfaces both buckets so the create/update handlers can 400 on
missing and 403 on unauthorized with distinct error messages and
`agent_ids` lists.

* 🪆 polish: tighten subagent dialog grid gap to gap-2

OGDialogContent's grid default is `gap-4`, which renders the title,
description, and scroll area as three visually separated panels.
Drop to `gap-2` so they read as one block.

* 🪆 polish: swap Subagents above Handoffs in Advanced panel

Subagents is the more common knob users reach for, so show it first.
Handoffs keep the same Controller wiring, just move below.
- Updated the Skills component to include a check for `skillsEnabled` from agent capabilities, ensuring skills are only displayed when both permissions and capabilities allow.
- Modified the `useHandleKeyUp` hook to prevent triggering skill commands when skills are disabled, enhancing user experience and preventing errors.
- Added tests to verify that skills commands do not trigger when skills are disabled, ensuring robust functionality.
- Refactored the `useSideNavLinks` hook to incorporate skills capability checks, ensuring consistent access control across the application.
This commit updates the version of the `@librechat/agents` package from `3.1.68-dev.1` to `3.1.70` in the `package-lock.json` and relevant `package.json` files. This change ensures consistency across the project and incorporates any updates or fixes from the new version.
* 🛡️ fix: Strict opt-in skills activation per agent

Skills were activating on every agent run that had the capability +
RBAC enabled, regardless of whether the user (ephemeral) or author
(persisted) had opted in. `scopeSkillIds(undefined)` fell through to
"full accessible catalog" whenever `agent.skills` was unset, which is
the default state for any agent created before skills existed and for
every ephemeral agent.

Activation now requires an explicit signal:
- Ephemeral agent → per-conversation skills badge toggle.
- Persisted agent → new `skills_enabled` master switch on the agent
  doc, surfaced as a toggle in the Agent Builder skills section.
  Enabled + empty/undefined allowlist = full accessible catalog;
  enabled + non-empty allowlist = narrow to those ids; disabled (or
  undefined) = no skills available, even if an allowlist is set.

Centralised the predicate in `resolveAgentScopedSkillIds` so the
primary-agent path, handoff/discovery, the subagent loop, and both
OpenAI controllers all share one source of truth. Frontend `$`
popover scope mirrors the same logic so the UI never offers skills
the backend would refuse to activate.

* test: mock resolveAgentScopedSkillIds in agent controller specs

* refactor: address review findings on skills opt-in PR

- AgentConfig: associate skills label with toggle via htmlFor for
  click/keyboard affordance; simplify Switch handler to Boolean(value).
- skills: mark scopeSkillIds as @internal so runtime callers continue
  to route through resolveAgentScopedSkillIds and inherit the activation
  predicate (ephemeral toggle, persisted skills_enabled).

* fix(agents): include skills_enabled in agent list projection

Without this field, agents loaded via the list endpoint hydrate into the
client agentsMap with skills_enabled === undefined, causing the `$`
skill popover to hide every skill on a fresh page load even when the
agent was saved with skills_enabled: true.

* fix(skills): fail closed for persisted agents during agentsMap hydration

Returning undefined while the agents map loads let the popover render the
full catalog for a persisted agent before we could read its
skills_enabled flag, so the user could pick a skill the backend would
then refuse for the turn. Match the strict opt-in contract by returning
[] until the map is authoritative.

* refactor(skills): extract skillsHintKey for readability

Replaces the nested ternary in the skills section JSX with a
pre-computed constant so the activation -> hint key mapping reads
top-down.

* refactor(skills): unflatten skillsHintKey to remove nested ternary
* 📄 feat: Auto-render Text-Based Code Execution Artifacts Inline

Eagerly extract text content from non-image artifacts produced by code
execution tools and render it inline in the message instead of behind a
click-to-download file card. Reuses the SkillFiles binary-detection
helper and the existing parseDocument dispatcher so docx, xlsx, csv,
html, code, and other text-renderable formats land directly under the
tool call.

PPTX is intentionally classified but not yet extracted — follow-up.

* 🌐 chore: Remove unused com_download_expires locale key

Removed in en/translation.json so the detect-unused-i18n-keys CI check
passes. The only reference was a commented-out localize() call in
LogContent.tsx that was deleted in the previous commit.

* 🩹 fix: Address PR review on code artifact text extraction

- extract.ts: build the temp document path from a randomUUID and pass
  path.basename(name) as originalname so a malicious artifact name
  cannot escape os.tmpdir() (P1 traversal flagged by codex/Copilot).
- process.js: classify and extract using safeName, not the raw name —
  defense in depth alongside the temp-path fix.
- classify.ts: add a bare-name lookup so extensionless text artifacts
  (Makefile, Dockerfile, …) classify as utf8-text instead of falling
  through to other.
- Attachment.tsx: wire aria-expanded / aria-controls on the show-all
  toggle for screen reader support.
- LogContent.tsx: restore a download chip (LogLink) on inline-text
  attachments so users can still pull down the underlying file.
- Tests: cover extensionless filenames and the temp-path traversal
  invariant.

* 🩹 fix: Address comprehensive PR review on code artifact extraction

- extract.ts: walk back to a UTF-8 code-point boundary before truncating
  so cuts cannot land mid-multibyte and emit U+FFFD (CJK/emoji concern).
  truncate() now accepts the original buffer to skip a redundant encode.
- extract.ts: add an 8s timeout around parseDocument via Promise.race so
  a pathological docx/xlsx cannot stall the response path.
- process.js: always set `text` (string or null) on the file payload —
  createFile uses findOneAndUpdate with $set semantics, so omitting the
  field leaves a stale value behind when an artifact's content changes.
- Attachment.tsx: switch the show-all toggle from char-count threshold
  to a useLayoutEffect ref measurement on scrollHeight, and use
  overflow-hidden when collapsed (overflow-auto when expanded) so the
  collapsed box has a single clear interaction model.
- Attachment.tsx + LogContent.tsx: lift `isImageAttachment` /
  `isTextAttachment` into a shared attachmentTypes module. LogContent
  keeps its looser image check (no width/height required) because the
  legacy log surface receives attachments without dimensions.
- Tests: cover multi-byte boundary, the always-set-text contract on
  updates, and the new shared predicates.

* 🧪 test: Component test for TextAttachment + direct withTimeout coverage

- Attachment.tsx: re-order local imports longest-to-shortest per
  AGENTS.md (attachmentTypes ahead of FileContainer/Image).
- extract.ts: export withTimeout so it can be unit-tested directly
  (it's also used internally — exporting carries no runtime cost).
- extract.spec.ts: three small unit tests on withTimeout that cover
  resolve, propagated rejection, and timeout rejection paths with
  real timers.
- TextAttachment.test.tsx: ten cases for the new React component —
  text rendering in <pre>, download chip presence/absence, ref-based
  collapse measurement (with scrollHeight stubbed via prototype),
  aria-expanded toggle, fall-through to FileAttachment for missing
  and empty text, and AttachmentGroup routing.

* 🩹 fix: Canonicalize document MIME by extension before parseDocument

When the classifier puts a file on the document path via its extension
(.docx, .xlsx, …) but the buffer sniffer returned a generic value like
application/zip or application/octet-stream, we previously forwarded
that generic MIME to parseDocument, which dispatches strictly by MIME
and silently rejected it — exactly defeating the extension-first
classification this PR added.

extractDocument now remaps the MIME from the extension (falling back
to the original sniffed MIME if the extension is unrecognized, so files
that reached the document branch via MIME detection still work). Adds
a parameterized test across docx/xlsx/xls/ods/odt against zip/octet
sniffs to guard the regression.

* 🩹 fix: Reuse existing withTimeout from utils/promise

The previous commit's local withTimeout export collided with the
already-exported `withTimeout` from `~/utils/promise`, breaking the
@librechat/api tsc job (TS2308 ambiguous re-export).

Drops the duplicate, imports from `~/utils/promise`, and removes the
now-redundant unit tests (the helper has its own coverage in
utils/promise.spec.ts). The third argument shifts from a label to the
fully-formed timeout error message that the existing helper expects.

* 🧹 chore: TextAttachment test polish (NITs)

- Use the conventional `import Attachment, { AttachmentGroup }` form
  rather than `default as Attachment`.
- Save the original `scrollHeight` property descriptor and restore it
  in afterAll, so the prototype patch never leaks past this suite.
* chore: Update `@librechat/agents` to v3.1.71-dev.0 across package-lock and package.json files

This commit updates the version of the `@librechat/agents` package from `3.1.70` to `3.1.71-dev.0` in the `package-lock.json` and relevant `package.json` files. Additionally, it marks several dependencies as peer dependencies, ensuring better compatibility and integration across the project.

* 🔗 feat: Enable Tool-Output References for bash_tool when codeenv is on

Wires `@librechat/agents`' `RunConfig.toolOutputReferences` into
`createRun()` and the bash tool's LLM-facing description, gated by the
per-agent `effectiveCodeEnvAvailable` flag. The feature auto-activates
for any run where the bash tool is actually registered; SDK defaults
(~400 KB per output, 5 MB total) match the shell-safe budget. No new
env var or yaml capability — piggybacks on the existing `execute_code`
gate.

- `tools.ts`: replace the module-level `BASH_TOOL_DEF` constant with a
  per-call `buildBashToolDef` that wraps `buildBashExecutionToolDescription`.
  Description now includes the `{{tool<idx>turn<turn>}}` reference syntax
  guide iff the new `enableToolOutputReferences` param is true.
- `initialize.ts`: pass `enableToolOutputReferences: effectiveCodeEnvAvailable`
  into `registerCodeExecutionTools`.
- `run.ts`: add `codeEnvAvailable?: boolean` to `RunAgent`, compute the
  flag from `agents[*].codeEnvAvailable`, and conditionally spread
  `toolOutputReferences: { enabled: true }` into `Run.create`.

* 🧪 test: Cover tool-output references gating end-to-end

- `tools.spec.ts`: 3 new cases asserting `bash_tool.description`
  contains `{{tool<idx>turn<turn>}}` iff `enableToolOutputReferences` is
  true (and unset → false).
- `run-summarization.test.ts`: 4 new cases asserting `Run.create` is
  invoked with `toolOutputReferences: { enabled: true }` iff at least
  one `RunAgent.codeEnvAvailable === true`. Covers the present /
  absent / unset / multi-agent-OR cases.
- `initialize.test.ts` + `skills.test.ts`: extend the existing
  `@librechat/agents` jest mocks with a `buildBashExecutionToolDescription`
  stub so suites stay green when the on-disk SDK lags the published
  3.1.71-dev.0 export.

* chore: Update `@librechat/agents` version to `3.1.71-dev.1` in package-lock and package.json files

This commit updates the version of the `@librechat/agents` package from `3.1.71-dev.0` to `3.1.71-dev.1` across the relevant package files. This change ensures consistency and incorporates any updates or fixes from the new version.

* 🪢 fix: Walk Subagents in toolOutputReferences run-level gate

Codex P2 review on PR #12830: the run-level
`enableToolOutputReferences` flag only inspected the top-level
`agents` array. A parent agent without `execute_code` that spawns a
subagent that *does* have it left the SDK's tool-output reference
registry inactive for the run, so the subagent's `bash_tool` calls
saw `{{tool<idx>turn<turn>}}` placeholders pass through to the
shell unsubstituted.

Replace `agents.some(a => a.codeEnvAvailable === true)` with a
recursive `anyAgentHasCodeEnv` helper that walks
`subagentAgentConfigs` transitively. Cycle-safe via a `visited` set,
mirroring the existing `buildSubagentConfigs.ancestors` pattern in
the same module. The bash tool *description* stays per-agent in
`initializeAgent` (only agents with bash actually registered learn
the `{{…}}` syntax), so broadening the run-level gate doesn't
broaden the model-facing surface — it just lets the SDK's shared
registry serve every `ToolNode` the run compiles, which is exactly
the contract the SDK already implements.

Tests cover three new cases: parent-off / subagent-on, parent-off /
child-off / grandchild-on (transitive descent past one level), and
a cyclic A↔B tree with neither codeenv-enabled (asserts both
termination and absence of `toolOutputReferences`). Existing
single-agent and multi-agent tests stay valid since the new helper
returns `true` whenever the previous `.some(...)` did.

* chore: Update `@librechat/agents` version to `3.1.71` in package-lock and package.json files

This commit updates the version of the `@librechat/agents` package from `3.1.71-dev.1` to `3.1.71` across the relevant package files. This change ensures consistency and incorporates any updates or fixes from the stable release.

* review: address audit findings on tool-output references PR

Two findings from comprehensive PR review on #12830:

#1 (MINOR) — `injectSkillCatalog` omitted `enableToolOutputReferences`
when calling `registerCodeExecutionTools`, so its resulting
`bash_tool` description always lacked the `{{tool<idx>turn<turn>}}`
guide. Today this is a no-op because `initializeAgent` registers
first and the registry `.has()` check makes the skills-path call a
dedupe-only operation. But if call order ever flips (skills-first),
the missing flag would silently ship a `bash_tool` without the
syntax guide, and the `initializeAgent` pass would itself become
the no-op — the feature would silently break with no visible error.
Forward `enableToolOutputReferences: codeEnvAvailable === true` so
both call sites produce identical tool definitions regardless of
firing order. Defense-in-depth, not a current bug. Added a test in
`skills.test.ts` that asserts the bash description contains the
`{{tool<idx>turn<turn>}}` marker when `codeEnvAvailable` is on,
exercising the skills caller end-to-end.

#2 (NIT) — `buildBashToolDef` allocated + froze a fresh object on
every agent init. Replaced with two module-level frozen singletons
(`BASH_TOOL_DEF_WITH_OUTPUT_REFS`, `BASH_TOOL_DEF_WITHOUT_OUTPUT_REFS`)
built once at module load via a `createBashToolDef` helper. The
factory now picks the right cached reference instead of building.
Restores the no-allocation intent of the original `BASH_TOOL_DEF`
constant while keeping the per-agent gate behavior. Two new tests
in `tools.spec.ts` pin the contract: identical-flag calls return
reference-equal `bash_tool` defs across registries; opposite-flag
calls return distinct frozen objects with the expected description
content.
…ad_file Sandbox Fallback) (#12831)

* 🌱 fix: Seed Code Tool Files Into Graph Sessions on First Call

Files attached to an agent's `tool_resources.execute_code` (user uploads
or generated artifacts from a prior turn) were silently dropped on the
first `execute_code` invocation of a turn. The agents-side `ToolNode`
populates `_injected_files` only when its `sessions` map already has an
`EXECUTE_CODE` entry — but that entry is only written by a previous
successful execution, so call #1 had nothing to inject. CodeExecutor
then fell back to a `/files/{session_id}` fetch, but `session_id` was
also empty on call #1, leaving the sandbox without the primed files.

Mirror the existing skill-priming pattern (`primeInvokedSkills` →
`initialSessions`) for code-resource files: eagerly call `primeFiles`
before `createRun` and merge the result into `initialSessions` via a
new `seedCodeFilesIntoSessions` helper. Skill files and code-resource
files now share the same `EXECUTE_CODE` entry; the prior representative
`session_id` is preserved on merge.

* 🔬 chore: Add Diagnostic Logging for Code-Files Seeding

Temporary debug logs to diagnose why first-call file injection is not
firing in real agent runs. Logs `wantsCodeExec`, available tool-resource
keys, primed file count, and the seeded EXECUTE_CODE entry. Will revert
once the failure mode is identified.

* 🪛 refactor: Capture primedCodeFiles per-agent at init, merge across run

Replace the client.js eager `primeFiles` call with a per-agent capture at
initialization time so every agent in a multi-agent run (primary +
handoff + addedConvo) contributes its `tool_resources.execute_code`
files to the shared `Graph.sessions` seed.

- handleTools.js (eager loadTools): the `execute_code` factory closes
  over a `primedCodeFiles` slot and surfaces it in the return.
- ToolService.js loadToolDefinitionsWrapper (event-driven): captures
  `files` from the existing `primeCodeFiles` call (was dropping them
  while only keeping `toolContext`) and surfaces them.
- packages/api initialize.ts: the loadTools callback contract now
  includes `primedCodeFiles`, threaded onto `InitializedAgent`.
- client.js: iterate `[primary, ...agentConfigs.values()]` and merge
  each agent's `primedCodeFiles` into `initialSessions`. Drop the
  primary-only `primeCodeFiles` call and diagnostic logs from the prior
  attempt — wrong layer (single-agent), wrong gate (`agent.tools`
  contained Tool instances after init, so the `.includes("execute_code")`
  string check always failed).

* 🔬 chore: Add per-agent diagnostic logs for code-files seeding

Logs `tool_resources` keys + file counts inside loadToolDefinitionsWrapper
and per-agent `primedCodeFiles` + final initialSessions inside
AgentClient. Will revert once the failure mode is confirmed.

* 🔬 chore: Add file-lookup diagnostics inside initializeAgent

Logs the inputs and intermediate counts of the conversation-file lookup
chain (convo file ids, thread message ids, code-generated and
user-code file counts) so we can pinpoint why `tool_resources.execute_code`
is arriving empty at `loadToolDefinitionsWrapper` despite the agent
having `execute_code` in its tools list.

* 🔬 chore: Probe execute_code files without messageId filter

Adds a relaxed `getFiles({conversationId, context: execute_code})` probe
that runs only when `getCodeGeneratedFiles` returns empty. Lists what's
actually in the DB for this conversation so we can confirm whether the
file is missing entirely or whether the messageId filter is rejecting it.

* 🔬 chore: Fix probe getFiles arg order (sort vs projection)

Probe was passing a projection object as the sort arg, which mongoose
rejected with `Invalid sort value`. Move it to the third arg
(selectFields) so the probe actually runs.

* 🪢 fix: Preserve Original messageId on Code-Output File Update

Each `processCodeOutput` call was overwriting the persisted file's
`messageId` with the *current* run's id. When a turn re-creates an
existing file (filename + conversationId match → `claimCodeFile`
returns the existing record, `isUpdate=true`), the file's link to
the assistant message that originally produced it gets clobbered.

`initializeAgent` later runs `getCodeGeneratedFiles({messageId: $in: <thread>})`
to seed `tool_resources.execute_code` from prior-turn artifacts. With a
stale `messageId` (e.g. from a failed read attempt that re-shelled the
same filename), the file no longer matches the parent-walk thread, so
`tool_resources` arrives empty at agent init, the new
`primedCodeFiles` channel has nothing to seed, and the LLM can't see
its own prior-turn artifacts on the next turn — defeating the
just-added Graph-sessions seeding fix.

Preserve the existing `claimed.messageId` on update; first-creation
behavior is unchanged. The runtime return value still includes the
current run's `messageId` (via `Object.assign(file, { messageId })`)
so the artifact is correctly attributed to the live tool_call.

* 🧹 chore: Remove diagnostic logs from code-files seeding path

Drops the temporary debug logs added to trace the empty-tool_resources
failure mode. Production code paths (loadToolDefinitionsWrapper,
client.js seed loop, initializeAgent file lookup) are left as the
permanent shape: capture primedCodeFiles, merge across agents, seed
initialSessions before run start.

* 🪛 feat: read_file Sandbox Fallback for /mnt/data + Non-Skill Paths

When the model called `read_file` with a code-execution path (e.g.
`/mnt/data/sentinel.txt`), the handler returned a misleading
`Use format: {skillName}/{path}` error. Adds a sandbox-aware fallback:

- Short-circuit `/mnt/data/...` (can never be a skill reference) →
  route to a sandbox `cat` via the new host-provided `readSandboxFile`
  callback, which POSTs to the codeapi `/exec` endpoint.
- Skip the skill resolver entirely when `accessibleSkillIds` is empty
  — the resolved-output of `resolveAgentScopedSkillIds` already
  collapses the admin capability + ephemeral badge + persisted
  `skills_enabled` chain, so an empty value is the authoritative
  "skills aren't in scope for this agent" signal.
- For `{firstSegment}/...` paths, consult the catalog-derived
  `activeSkillNames` Set (no DB read) to detect non-skill names and
  fall through to the sandbox before the model has to retry with
  `bash_tool`.

`activeSkillNames` is captured from `injectSkillCatalog`, threaded onto
`InitializedAgent`, into `agentToolContexts`, then through
`enrichWithSkillConfigurable` into `mergedConfigurable` for the handler.

The host implementation of `readSandboxFile` lives in
`api/server/services/Files/Code/process.js` and shells `cat <path>`
through the seeded sandbox session — `tc.codeSessionContext`
(emitted by ToolNode for `read_file` calls in `@librechat/agents`
v3.1.72+) provides the `session_id` + `_injected_files` so the read
lands in the same sandbox that holds prior-turn artifacts. When the
seeded context isn't available (older agents version, no codeapi
configured), the handler returns a model-visible error pointing at
`bash_tool` instead of silently failing.

Tests: 8 new `handleReadFileCall` cases cover the new short-circuits,
the skills-not-enabled gate, the activeSkillNames lookup, the
sandbox-fallback success path, and the bash_tool retry hint on
fallback failure. Existing `read_file` tests now opt into "skills are
in scope" via a `skillsInScope()` fixture (production wouldn't reach
the skill lookup with empty `accessibleSkillIds`).

* 🔧 chore: Update @librechat/agents dependency to version 3.1.72

Bumps the version of the @librechat/agents package across package-lock.json and relevant package.json files to ensure compatibility with the latest features and fixes.

* 🪛 refactor: Centralize Tool-Session Seed in buildInitialToolSessions Helper

Addresses review feedback on the per-agent merge in client.js:

- **Run-wide semantics, named explicitly.** The merge into a single
  `Graph.sessions[EXECUTE_CODE]` was a deliberate match to the
  agents-library design (`Graph.sessions` is shared across every
  `ToolNode` in the run), but the inline `for (const a of agents)`
  loop in `AgentClient.chatCompletion` made it look per-agent. Move
  the logic to a TS helper `buildInitialToolSessions` that documents
  the run-wide-by-design contract in one place. The CJS controller
  now contains a single call site, no business logic.

- **Subagent walk (P2).** The previous loop only iterated
  `[primary, ...agentConfigs.values()]`. Pure subagents are pruned
  out of `agentConfigs` after init and retained on each parent's
  `subagentAgentConfigs`, so their primed code files were silently
  dropped from the seed. The helper now walks recursively, with a
  visited-Set keyed on object identity that terminates safely on a
  malformed agent graph (cycle).

- **`jest.setup.cjs` polyfill for undici `File`.** Reviewer hit
  `ReferenceError: File is not defined` running the targeted spec on
  WSL — a known Node 18 issue where `globalThis.File` from
  `node:buffer` isn't auto-exposed. Polyfill it inside a Jest setup
  file so the suite boots regardless of Node patch version.

Helper test coverage (8 new): skill-only / agent-only / both,
recursive subagent walk, cycle-safe walk, primary+subagent
deduplication, undefined/null entries in the agents iterable, and
representative session_id preservation across the merge.

16 tests pass total in `codeFilesSession.spec.ts` (8 prior + 8 new).
No behavior change vs. the previous commit for the existing
primary+agentConfigs case — subagent inclusion is the only new
behavior, and it matches what the existing seeding logic would have
done if subagents had been in `agentConfigs`.

* 🪛 fix: FIFO Walk Order in buildInitialToolSessions (P3 review)

The traversal used `Array.pop()` (LIFO), which visited the LAST
top-level agent first. The docstring says "primary first"; the code
contradicted it. When no skill seed exists the first-visited agent's
first file supplies the representative `session_id` written to
`Graph.sessions[EXECUTE_CODE]` — so a LIFO walk silently flipped which
agent that came from. `ToolNode` ultimately uses per-file `session_id`s
for runtime injection (so behavior was indistinguishable for current
callers), but the discrepancy was a footgun for any future consumer
that read the representative.

Switch to FIFO via `Array.shift()` to match both the docstring and the
existing `loadSubagentsFor` walk pattern in
`Endpoints/agents/initialize.js`. Add a regression test that asserts
the primary's `session_id` is the representative (and that all three
agents' files still contribute, with per-file `session_id`s preserved).

* 🔬 test: Lock In Code-Files Bug Fixes Per Comprehensive Review

Addresses MAJOR + MINOR + NIT findings from the multi-pass review:

**Finding #4 (MINOR) — empty relativePath misses sandbox fallback.**
A model calling `read_file("output/")` where "output" isn't a skill
name dead-ended with `Missing file path after skill name` instead of
being routed to the sandbox like every other malformed-path branch.
Add the same `codeEnvAvailable → handleSandboxFileFallback` pattern,
plus two regression tests.

**Finding #7 (NIT) — duplicate `skillsInScope()` helper.**
Hoist the identical helper out of two nested describe blocks to
module scope. Single source of truth.

**Finding #1 (MAJOR) — `persistedMessageId` had zero test coverage.**
The fix preserves a file's original `messageId` on update so
`getCodeGeneratedFiles` can still match it on subsequent turns. A
regression in the `isUpdate ? (claimed.messageId ?? messageId) : messageId`
ternary would silently re-introduce the original cross-turn priming
bug. Five new tests cover:
- UPDATE preserves `claimed.messageId` in the persisted record
- UPDATE falls back to current run id when `claimed.messageId` is
  absent (legacy records predating the field)
- CREATE uses current run id (no claimed record exists)
- The runtime return value uses the LIVE id (artifact attribution)
  even when the persisted record kept the original
- The image branch follows the same contract (would silently regress
  if the ternary diverged across the two file-build branches)

The tests use a `snapshotCreateFileArgs()` helper because
`processCodeOutput` mutates the file object after `createFile`
returns (`Object.assign(file, { messageId, toolCallId })`) and a
naive `createFile.mock.calls[0][0]` would reflect the post-mutation
state instead of what was actually persisted.

**Finding #2 (MAJOR) — `readSandboxFile` had no direct tests.**
The model-controlled `file_path` flows through a POSIX single-quote
escape into a shell `cat` command, making this a security boundary.
A quoting regression would let a malicious filename break out of the
quoted argument and inject arbitrary shell. 20 new tests across:
- Shell quoting (7): plain filenames, embedded `'`, `$()`, backticks,
  newlines, shell metachars, multiple consecutive single-quotes
- Payload shape (6): /exec URL, bash language, conditional
  session_id / files inclusion, dedicated keepAlive:false agents
- Response handling (6): `{content}` on success, null on missing
  base URL or absent stdout, throws on stderr-only, partial-success
  returns stdout, transport errors are logged then rethrown
- Timeout (1): matches processCodeOutput's 15s SLA

Audited findings #5 (acknowledged tech debt — readSandboxFile in JS
workspace), #6 (pre-existing positional-args debt on
enrichWithSkillConfigurable), and #8 (cosmetic JSDoc style) — no
action taken per the reviewer's own assessment.

Audited finding #3 (walk order vs docstring) — already addressed in
commit 007f323 which converted to FIFO via `queue.shift()` plus a
regression test. The audit was performed against an earlier PR head.

Tests: 152 packages/api + 195 api JS = 347 pass. Typecheck clean.

* 🪛 fix: Pure-Subagent codeEnv + Primed-Skill Routing + ToolService Early Returns

Three findings from the second-pass review:

**P2 — Pure subagents missed `codeEnvAvailable`** (initialize.js).
The pure-subagent init path didn't forward the endpoint-level
`codeEnvAvailable` flag to `initializeAgent`, unlike the primary,
handoff, and addedConvo paths. A code-enabled subagent loaded only
through `subagentAgentConfigs` initialized with
`codeEnvAvailable: false`, so even though the recursive seed walk
found its primed code files, the subagent's own `bash_tool` /
`read_file` sandbox fallback were silently gated off. Forward the
flag and add `codeEnvAvailable: config.codeEnvAvailable` to the
`agentToolContexts.set` for symmetry with the other paths.

**P2 — Primed skills outside the catalog cap were misrouted to
sandbox** (handlers.ts). Manual ($-popover) and always-apply primes
are intentionally resolved off the wider `accessibleSkillIds` ACL
set BEFORE catalog injection — see `resolveManualSkills` for why a
skill outside the `SKILL_CATALOG_LIMIT` cap can still be authorized
for direct manual invocation. The `activeSkillNames` shortcut ran
before reading `skillPrimedIdsByName`, so a primed skill not in the
catalog would fall through to the sandbox instead of resolving via
the pinned `_id`. Read the primed map first and bypass the shortcut
for primed names. New regression test asserts a primed-but-not-
cataloged skill resolves through the existing skill path with
`getSkillByName` invoked and `readSandboxFile` NOT called.

**P3 — `loadAgentTools` early returns dropped `primedCodeFiles`**
(ToolService.js). The non-`definitionsOnly` path captures the field
correctly, but two early-return branches (no-action-tools fast path,
no-action-sets fast path) omitted it. Any traditional
`loadAgentTools(..., definitionsOnly: false)` caller using
execute_code without action tools would have its first-call session
seed silently empty. Add `primedCodeFiles` to both early returns
for consistency with the final return shape.

Tests: 153 packages/api + 195 api JS = 348 pass.

* 🧹 chore: Document jest.mock arrow-indirection pattern in process.spec.js

Per the second-pass review's Finding #2 (NIT, "would help future
readers"): the mock setup mixes direct `jest.fn()` references with
arrow-function indirection (`(...args) => mockX(...args)`). The
indirection isn't stylistic — it's required because `jest.mock(...)`
is hoisted above the outer `const` declarations at parse time, so a
direct reference would capture `undefined`. Inline comment explains
the pattern so the next reader doesn't have to reverse-engineer it
or accidentally "simplify" the mocks and break per-test
`mockReturnValueOnce` / `mockImplementationOnce` overrides.

* 🪛 fix: Five Issues from Pass-N + Codex Review (incl. 404 root cause)

Five real bugs surfaced by another review pass + Codex PR comments
+ the codeapi-side logs we collected during manual testing:

**1) `processCodeOutput` 404 root cause (`callbacks.js`).**
The codeapi worker emits TWO distinct `session_id`s on a tool result:
  - `artifact.session_id` is the EXEC session — the sandbox VM that
    ran the bash command. Files don't live there; it's torn down
    post-execution.
  - `file.session_id` is the STORAGE session — the file-server
    bucket prefix where artifacts actually live.
`callbacks.js` was passing the EXEC id to `processCodeOutput`, which
builds `/download/{session_id}/{id}` and 404s because the file-server
doesn't know about that path. This explains every "Error
downloading/processing code environment file" we saw during testing.
Use `file.session_id ?? output.artifact.session_id` (per-file id with
artifact-level fallback for older worker payloads).

**2) `primeFiles` reupload pushed STALE sandbox ids (`process.js`).**
When `getSessionInfo` returns null (file expired/missing in sandbox),
`reuploadFile` re-uploads via `handleFileUpload`, gets a NEW
`fileIdentifier`, and persists it on the DB record. But `pushFile`
was a closure capturing the OLD `(session_id, id)` parsed at the top
of the loop, so the in-memory `files[]` array (now consumed by
`buildInitialToolSessions` to seed `Graph.sessions`) silently
referenced a sandbox object that no longer existed. The first tool
call would 404 trying to mount it; only the next turn's metadata
re-read would correct course. Parameterize `pushFile` with optional
`(session_id, id)` overrides; in `reuploadFile` parse the new
identifier and pass through. 2 regression tests.

**3) Codex P2 — Cap sandbox fallback output before line-numbering
(`handlers.ts`).** The new `handleSandboxFileFallback` returned
`addLineNumbers(result.content)` without a size guard, so reading a
multi-MB `/mnt/data/*` artifact materialized the file twice in
memory (raw + line-numbered) before downstream truncation. Match the
existing skill-file path's `MAX_READABLE_BYTES` (256KB): truncate
raw first, then number, surface the truncation to the model so it
can use `bash_tool` (`head` / `tail`) for the rest. 2 tests
(oversized truncates with hint, in-cap doesn't).

**4) Codex P2 — Dedupe seeded code files by `(session_id, id)`
(`codeFilesSession.ts`).** Multiple agents in a run commonly carry
the same primed execute-code resources (shared conversation files);
without dedupe, `_injected_files` grows proportionally to agent
count and bloats every `/exec` POST. Use a `(session_id, id)`
identity key so first-seen wins (preserves source ordering); name
alone isn't sufficient because two distinct primed uploads can
share a filename across different sessions. 4 tests covering dedup
across iterations, against pre-existing entries, name-collision
distinct-session preservation, and the multi-agent realistic case
in `buildInitialToolSessions`.

**5) Pass-N P2 — Polyfill `globalThis.File` in api Jest setup
(`api/test/jestSetup.js`).** `packages/api/jest.setup.cjs` had the
polyfill; the legacy api workspace's Jest config has its own
`setupFiles` that didn't, so on Node 18 / WSL the api focused tests
still failed at import time with `ReferenceError: File is not
defined` from undici. Mirror the polyfill.

Tests: 159 packages/api + 206 api JS = 365 pass. Typecheck clean.

* 🔧 chore: Update @librechat/agents dependency to version 3.1.73

Bumps the version of the @librechat/agents package across package-lock.json and relevant package.json files to ensure compatibility with the latest features and fixes.
…12832)

* 🪟 feat: Render Code-Execution Text Artifacts as Side-Panel Artifacts

Builds on PR #12829 (which populates `text` on code-execution file
attachments). When a tool-output file's extension/MIME maps to a
viewer we already have, route it through the artifact UI instead of
the inline `<pre>`:

- text/html, text/htm        → existing artifacts side panel (sandpack)
- App.jsx / App.tsx          → existing artifacts side panel (sandpack)
- *.md / *.markdown / *.mdx  → existing artifacts side panel (sandpack)
- *.mmd / *.mermaid          → standalone Mermaid component, inline
                                (no sandpack/react template)

The card and the mermaid header both expose a download button so the
underlying file is still reachable. Everything else (csv, py, json,
xls/docx/pptx, …) keeps PR #12829's inline behaviour — dedicated
viewers for csv/docx/xlsx/pptx will land in follow-ups.

Backend: `.mmd` and `.mermaid` added to UTF8_TEXT_EXTENSIONS so
mermaid sources reach the client with `text` populated.

Frontend changes:
- `client/src/utils/artifacts.ts` — `TOOL_ARTIFACT_TYPES` constant,
  `detectArtifactTypeFromFile`, `fileToArtifact` (id is derived from
  `file_id` so the same artifact across renders dedupes cleanly).
- `client/src/components/Chat/Messages/Content/Parts/ToolArtifactCard.tsx`
  — registers the artifact in `artifactsState`, renders an
  `ArtifactButton`-style trigger paired with a download button.
- `client/src/components/Chat/Messages/Content/Parts/ToolMermaidArtifact.tsx`
  — wraps the standalone Mermaid component with a filename + download
  header so the file stays reachable.
- `Attachment.tsx` and `LogContent.tsx` — gain panel-artifact and
  mermaid branches in the routing decision tree, ahead of the existing
  inline-text fallback. Existing branches untouched.

Test coverage: backend extension matrix (mmd/mermaid), frontend
predicates (`isPanelArtifact`, `isMermaidArtifact`,
`artifactTypeForAttachment`), `fileToArtifact`, and an RTL suite that
verifies each type routes to the right component (panel card / mermaid
render / inline pre / file chip).

* 🩹 fix: Address review on code-artifacts-panel routing

- ToolArtifactCard: defer artifact registration to the click handler so
  rendering a card never side-effects into `artifactsState`. With
  `artifactsVisibility` defaulting to `true`, eager mount-time
  registration would surface tool artifacts in the side panel without
  user intent — now matches ArtifactButton's pattern. Drop the
  redundant `artifacts` subscription (write-only via useSetRecoilState).
- LogContent.tsx: precompute `Artifact`s inside the existing useMemo
  bucket-sort so each render isn't producing fresh objects. Without
  this, missing updatedAt/createdAt fields would make `toLastUpdate`
  return `Date.now()` and churn Recoil state on every parent render.
- Attachment.tsx + LogContent.tsx: classify each attachment once via
  `artifactTypeForAttachment` and branch on the result, instead of
  calling `isMermaidArtifact` and `isPanelArtifact` back-to-back
  (each of which internally re-classified). AGENTS.md single-pass rule.
- artifacts.ts `detectArtifactTypeFromFile`: strip `;` parameters
  before the MIME comparison (so `text/html; charset=utf-8` is
  recognized) and add fallbacks for `application/vnd.react`,
  `application/vnd.ant.react`, and `application/vnd.mermaid`.
- ToolMermaidArtifact: drop the `id` prop entirely when `file_id` is
  undefined so we never pass an undefined DOM id through to mermaid.
- AttachmentGroup: keys derived from `file_id` (not bare index) so
  add/remove churn doesn't remount stable cards.
- Wrappers (PanelArtifact / MermaidArtifact / ToolMermaidArtifact)
  tightened from `Partial<TAttachment>` to `TAttachment` since the
  caller always passes a full attachment.
- fileToArtifact: drop dead `?? ''` on content (guarded by the
  preceding type check).
- Tests: new click-interaction suite verifying the deferred-registration
  invariant, click registers + opens panel, and second click toggles
  closed without losing the registered artifact.

* 🧹 chore: Address follow-up review NITs

- artifacts.test.ts: regression-pin baseMime() with charset/case
  variants for text/html, text/markdown, application/vnd.react.
- attachmentTypes.ts: drop the now-unused isMermaidArtifact and
  isPanelArtifact wrappers (the routing collapsed onto a single
  artifactTypeForAttachment call in the previous commit, so they
  were only kept alive by their own test). attachmentTypes.test.ts
  rewritten to exercise artifactTypeForAttachment branches directly.
- Attachment.tsx + LogContent.tsx: re-sort the local imports
  longest-to-shortest per AGENTS.md (~/utils/artifacts is 72 chars
  and was sitting after a 51-char import).

* ✨ feat: Auto-open panel + route txt/docx/odt/pptx through artifacts

- artifacts.ts: add `text/plain` to TOOL_ARTIFACT_TYPES so plain-text
  documents (and the markdown-like ones we don't have rich viewers for
  yet) can route through the side panel. `useArtifactProps` already
  dispatches `text/plain` to the markdown-style template, so they
  render cleanly with no panel-side change.
- Extension map gains txt/docx/odt/pptx → text/plain. pptx is wired
  up speculatively — backend extraction is still deferred, so the
  routing fires the moment that lands. The MIME map gets the matching
  office MIME types for symmetry (extension wins, but it's nice to
  have the fallback when sniffing returns the canonical office MIME).
- ToolArtifactCard: register the artifact in `artifactsState` on
  mount again. With visibility defaulting to `true` and the panel's
  `useArtifacts` hook auto-selecting the latest artifact, this gives
  the auto-open behaviour that the legacy streaming artifacts have.
  Click handler is now just "focus + reveal" (registration already
  happened); a user who has explicitly closed the panel keeps it
  closed and uses the click to re-open.
- Tests: parameterised row for each new extension; ArtifactRouting
  invariant flipped from "no register on mount" to "registers on
  mount so panel can auto-open". Existing TextAttachment test that
  used `a.txt` switched to `a.csv` since `.txt` now panel-routes.

* 🐛 fix: Auto-focus latest tool artifact + self-heal after panel close

Two bugs in the previous commit's auto-open behaviour:

1. After closing the side panel, no artifact card could be reopened.
   `useArtifacts.ts` resets `artifactsState` in its unmount cleanup
   (line 50), which fires when visibility goes to `false`. The card's
   mount-only `useEffect` doesn't refire after that wipe, so the
   subsequent click set `currentArtifactId` to an id that was no
   longer in `artifactsState`, and `Presentation.tsx` then refused to
   render the panel because `Object.keys(artifacts).length === 0`.

   Fix: the registration `useEffect` now has no dependency array, so
   it self-heals after the wipe (the dedup check keeps it cheap when
   nothing actually needs writing).

2. Newly-arrived artifacts didn't steal focus from an already-selected
   one. `useArtifacts`'s fallback auto-select (line 64) only fires
   when `currentId` is null or no longer in the list — it deliberately
   protects an existing selection, while the streaming-specific effect
   that handles legacy focus-stealing is gated on `isSubmitting`.
   That gate doesn't apply to tool-output artifacts.

   Fix: a second `useEffect` keyed on `artifact.id` calls
   `setCurrentArtifactId(artifact.id)` whenever a new card mounts.
   Cards mount in attachment-array order, so the LAST-mounted card
   (the newest tool output) wins — matching the legacy "latest auto-
   opens" UX.

Tests: replace the now-stale "no register on mount" assertion with
"registers and auto-focuses on mount", flip the toggle test to start
from the auto-focused state, and add two regression tests covering
the close-then-reopen path and the latest-of-many auto-focus.

* ✨ feat: Route pptx through artifact panel with placeholder content

Before this commit, pptx files fell through to a plain FileContainer
chip even though the extension was wired into the artifact map: backend
text extraction is still deferred for pptx, so `attachment.text` came
back null/empty and `detectArtifactTypeFromFile`'s strict text check
returned null. That meant docx/odt rendered as proper artifact cards
while pptx in the same message rendered as a tiny download chip.

`detectArtifactTypeFromFile` now allows empty text for the plain-text
and markdown buckets, since their viewers (the markdown template) handle
empty content gracefully. HTML / React / Mermaid still require real
content because sandpack and mermaid.js error on empty input.

`fileToArtifact` substitutes a markdown placeholder
("Preview not available yet — click Download to view the file.") when
the file routes through the panel without text. The panel renders the
placeholder via the markdown template; pptx (and any docx that fails
extraction) gets visual parity with its siblings, and the moment
backend extraction lands the placeholder is replaced by real content
without any frontend change.

Tests: split the "no text returns null" assertion into the strict
viewers (HTML/React/Mermaid) and the lenient ones (plain-text/markdown);
add a fileToArtifact case proving pptx without text gets the
placeholder, and another proving real text wins when present.

* ✨ feat: Dedup duplicate tool-artifact cards across tool calls + messages

Two `ToolArtifactCard` instances for the same file_id (e.g. agent reads
back what it just wrote, or the same file is referenced in turns 1 and
5) now collapse to a single chip — the most recent mount wins, the
older sibling re-renders to `null`.

Implementation:

- New `toolArtifactClaim` atomFamily keyed by artifact id. Each card
  generates a unique component-instance key via `useId()`, claims the
  slot in a `useLayoutEffect` (synchronous before paint, no flicker),
  and releases it on unmount only if the claim is still ours. A later
  card with the same id overwrites the claim → earlier card subscribes
  via `useRecoilState` and renders `null`.

- Family-keyed (per artifact id) so adding/removing a claim for one
  file never re-renders cards for unrelated files. Addresses the
  "messages view re-renders frequently" concern: each card subscribes
  only to its own slice.

- `ToolMermaidArtifact` shares the same atom via the new exported
  `toolArtifactKey()` helper, so the same `.mmd` file can't double-
  render either.

- Latest content always wins for the panel because the eager
  `setArtifacts` registration is last-write-wins on `artifactsState`
  by id — independent of which card holds the claim. Updating a file
  refreshes the panel content even if the chip's visual location
  doesn't move.

Tests: two new cases asserting that duplicate panel and mermaid
attachments collapse to a single rendered card.

* 🧹 chore: Address comprehensive review on code-artifacts-panel

- ToolArtifactCard self-heal now subscribes to a per-id selector
  (`artifactByIdSelector`) instead of a no-deps `useEffect`. Effect
  deps are `(artifact, existingEntry, setArtifacts)` so it runs
  deterministically when the slice transitions to undefined (panel-
  unmount cleanup) or when artifact content drifts — not on every
  parent render. Each card subscribes only to its own slice via the
  selectorFamily, so unrelated state changes don't re-render.
- artifacts.ts: localize the empty-content placeholder via a new
  `fileToArtifact(attachment, options?)` signature. Callers in
  `Attachment.tsx` (PanelArtifact) and `LogContent.tsx` resolve
  `com_ui_artifact_preview_pending` from `useLocalize` and thread
  it in. Default is empty string when no placeholder is supplied.
- artifacts.ts: thread `preClassifiedType` through `fileToArtifact`
  so the routing decision tree's `artifactTypeForAttachment` call
  is the only classification — previously `fileToArtifact` re-ran
  `detectArtifactTypeFromFile` after the routing already had the
  answer. Bucket type updated to `Array<{ attachment, type }>`.
- artifacts.ts: drop bare `text/plain` from `MIME_TO_TOOL_ARTIFACT_TYPE`.
  The extension map handles `.txt` explicitly; routing every
  unrecognized-extension `text/plain` file (extensionless scripts,
  `.env`, etc.) through the panel was a wider catch than the PR
  scope intended.
- artifacts.ts: stable `toLastUpdate` fallback of `0` (was
  `Date.now()`). `useArtifacts` sorts by `lastUpdateTime`, so a fresh
  timestamp on every call would re-sort entries non-deterministically
  across renders.
- artifacts.ts: drop dead `toolArtifactId = toolArtifactKey` alias.
  Add `filepath` to the key-derivation fallback chain so two
  unnamed-and-unidentified files don't collide on the literal
  `tool-artifact-unknown` key.
- ToolArtifactCard import order: package types before local types.
- store/artifacts.ts: JSDoc on `toolArtifactClaim` documenting the
  atomFamily-entries-persist-after-unmount trade-off (entries reset
  to null on card unmount; total cost is one key + a null per
  artifact — fine at typical session scale).
- Tests:
  - Updated existing `fileToArtifact` placeholder assertion to use
    the caller-provided string.
  - New: panel routing skips re-classification when
    `preClassifiedType` is provided.
  - New: bare `text/plain` MIME with unrecognized extension does
    NOT route through the panel.
  - New `LogContent.test.tsx` (6 cases) — HTML→panel, mermaid→
    inline, CSV→inline `<pre>`, archive→download chip, pptx→
    placeholder card, mixed split.
  - Dedup tests rewritten to use two AttachmentGroups (matching
    the real per-tool-call render) instead of a same-array
    duplicate that triggered React's duplicate-key warning.

* 🩹 fix: Address codex review + comprehensive review NITs

codex (P2):
- artifacts.ts: switch placeholder fallback to nullish coalescing.
  Empty string is now preserved as legitimate content (a 0-byte `.md`
  or `.txt` is a valid artifact, not "extraction unavailable") —
  only `null`/`undefined` triggers the deferred-extraction placeholder.
- Attachment.tsx: derive React keys via a new `renderKey` helper that
  combines `file_id` with the array index. Prevents duplicate keys
  when the same file_id appears twice in one bucket (rare but
  possible — a tool call writing the same path twice). Without
  unique keys, React's reconciler could reuse the wrong card
  instance, undermining the latest-mention dedup.

comprehensive review NITs:
- Attachment.tsx: hoist `import type { ToolArtifactType }` up into
  the type-import section per AGENTS.md.
- artifacts.ts `fileToArtifact`: defense-in-depth empty-text guard
  for the `preClassifiedType` path. Mirrors the gate in
  `detectArtifactTypeFromFile` so a future caller that bypasses
  classification can't hand sandpack/mermaid an empty buffer.
  Plain-text and markdown remain tolerated empty.

Tests:
- New: empty `.md` content passes through unchanged when a
  placeholder is also supplied.
- New: sibling cards with the same file_id in one group render
  without React key-collision warnings.
- Updated existing placeholder test to use `text: null` (the case
  where the placeholder is actually meant to fire).
- Three parameterized cases pinning the new
  preClassifiedType-with-empty-text safety guard.

* 🩹 fix: Address codex P1/P2 review on code-artifacts-panel

- P1 (stale artifacts leak across conversations): Add a top-level
  `useResetArtifactsOnConversationChange` hook in `Presentation.tsx`
  that wipes `artifactsState` / `currentArtifactId` on every
  conversation switch, regardless of panel visibility. Without this
  guard, ToolArtifactCard's self-heal effect would re-register the
  previous conversation's artifacts after panel close, leaking them
  into the next conversation's panel on open.

- P2 (expiresAt skipped on panel-routed entries): Restore the legacy
  expiry gate in `LogContent` ahead of panel/mermaid bucket-sort, so
  expired pptx/html/etc. attachments fall back to the
  "download expired" message instead of rendering as a clickable
  artifact card backed by a dead link.

Includes regression coverage for both paths.

* 🧹 chore: Share renderAttachmentKey across Attachment + LogContent

Hoist the per-occurrence React-key helper from `Attachment.tsx` into
`attachmentTypes.ts` so `LogContent` can use the same pattern. Apply
it to LogContent's panel/mermaid/text/image/nonInline buckets — the
prior keys (e.g. `mermaid-${file_id ?? index}`, `file.filepath ?? ...`)
would have collided if the same file_id appeared twice in one render,
even though that's astronomically rare for a single tool call.

Also drops the unused `file_id` field on `MermaidEntry` since the key
no longer needs it.

* 🩹 fix: Loosen artifacts util input types to match runtime fallbacks

`fileToArtifact`, `detectArtifactTypeFromFile`, `toolArtifactKey`, and
`toLastUpdate` all read every picked field with a nullish fallback —
their inputs were nonetheless typed as required `Pick<TFile, ...>`.
That mismatch made every realistic fixture (and several call sites
that lack a stable `filepath`) fail typecheck for fields the
implementations never strictly need.

Wrap the picks in `Partial<>` so the type matches the contract.

* 🩹 fix: Gate tool-artifact registration on claim winner

When two `ToolArtifactCard` instances mount for the same `artifact.id`
with divergent content (a code-execution file overwritten across
turns reuses its file_id), both effects subscribe to `existingEntry`
through `artifactByIdSelector`. Each card detects the other's write as
drift and overwrites it back, ping-ponging `artifactsState` between
old and new content and causing render churn / panel flicker.

Gate the self-heal registration on `isMyClaim` so only the latest
(claim-holding) card writes. The non-winner still subscribes to the
slice but short-circuits before calling `setArtifacts`, breaking the
loop. Adds a regression test that fails (loop / wrong final content)
without the gate.
…ibake) (#12851)

* 🚫 fix: Reject Binary Files in read_file Sandbox Fallback (No More Mojibake)

`read_file("/mnt/data/simple_graph.png")` was shelling `cat` through codeapi
`/exec` and shipping the result back to the model. codeapi's transport is
JSON, so `stdout` containing PNG bytes round-tripped through lossy UTF-8
replacement (every non-ASCII byte became U+FFFD), got line-numbered by
`addLineNumbers`, and arrived in the model's context as a multi-KB blob of
`�PNG\r\n  2 | �...`. The bytes were unrecoverable — and the same
codeapi sandbox logged the base64-style mojibake too — so the goal is
fail-fast, not retrieval.

Two guards in `handleSandboxFileFallback`, both bypassed by the existing
text path:

  1. **Extension precheck** (BEFORE any network call) for known-binary
     types: images, documents (pdf/docx/xlsx/etc), archives, audio, video,
     native libs, fonts, and a few other byte-soup formats. The message
     for image extensions points at the existing chat attachment ("the
     image is already shown to the user, use bash_tool for programmatic
     processing"); other binaries get the generic "use bash" hint.

  2. **NUL-byte sniff** (AFTER the read) on the first 8KB for unknown
     extensions or no-extension paths. The codeapi `/exec` JSON encoding
     mangles most non-UTF-8 bytes but a NUL terminator from a magic
     header survives the round-trip, so this catches novel binary
     formats without an extension precheck.

`lowercaseExtension` uses the basename to avoid false-triggering on
directory-name dots (e.g. `proj.v1/notes` has no extension, not `.v1/notes`).

+6 tests:
  - Image rejected by extension, never calls readSandboxFile, message
    points at the existing attachment.
  - Non-image binary (.zip) rejected with a different (bash-only) message.
  - Case-insensitive extension match (.PNG vs .png).
  - NUL-byte sniff catches unknown-extension binary post-fetch.
  - Text files with binary-adjacent extensions (.txt) still readable.
  - Dotted directory names don't false-trigger the extension match.

38/38 handlers.spec.ts pass.

The companion bash "command not found" issue from the same conversation
is a separate LLM mistake (writing raw Python as the bash command without
`python3 -c` / heredoc wrapper). Not coded here — flagged to the user.

* 🖼️ fix: Allow SVG read_file (XML text, no mojibake risk) — codex review P2

`.svg` was bucketed with raster-image extensions in
`BINARY_EXTENSIONS_NEVER_READABLE`, which made `handleSandboxFileFallback`
reject every SVG before calling readSandboxFile. SVG is an XML text
format — there's no mojibake risk for normal content, and the model has
legitimate reasons to inspect or edit a generated SVG (tweaking colors,
paths, viewBox, etc.). Block was a regression for valid read_file usage.

Remove `.svg` from both `BINARY_EXTENSIONS_NEVER_READABLE` (so it routes
through the normal sandbox read path) and `IMAGE_EXTENSIONS_FOR_HINT`
(now-dead entry — only used by the rejection-message picker). The
post-fetch NUL-byte sniff still catches anything that turns out to be
binary despite a `.svg` extension.

+1 regression test that an SVG with valid XML content reads through
successfully (`<svg>...<circle/>...</svg>` → status: 'success', content
contains `<svg`/`viewBox`).
…alize CRLF (#12852)

Two test-file hygiene fixes:

1. **Literal NUL bytes**. The `'rejects binary content (NUL bytes)
   post-fetch'` test embedded raw `\x00` bytes directly in the source
   string (`const binaryWithNul = '<3 NULs>\rIHDR<2 NULs>\x04'`).
   Embedding NULs in source files breaks editors, linters, ts-loader,
   and most git tooling — `grep` even classifies the file as binary
   ("Binary file matches"). Replace with `\x00` escape sequences in the
   string literal so the source is plain ASCII while the runtime string
   value is unchanged.

2. **CRLF line endings**. My earlier commits to this file picked up
   Windows-style `\r\n` from git's `core.autocrlf=true` checkout
   conversion, then staged them as `\r\n`. The diff against `dev`
   showed the entire file as changed even though only a few lines were
   touched semantically. Normalize the whole file back to LF so future
   diffs read clean.

The diff for this commit is large (~1248 lines marked changed) but
every change is one of: CRLF → LF, or the single `binaryWithNul`
escape-sequence rewrite. No semantic test changes.

Tests: 39/39 pass (unchanged behavior).
danny-avila and others added 21 commits April 28, 2026 12:52
)

* 📂 fix: Preserve Nested Folder Paths for Code-Execution Artifacts

When codeapi reports a generated file at a nested path (`a/b/file.txt`),
`processCodeOutput` was running it through `sanitizeFilename` — which
calls `path.basename()` and then collapses `/` to `_`. The DB row ended
up with `filename: "file.txt"`, `primeFiles` shipped that flat name back
to the next sandbox session, and `cat /mnt/data/a/b/file.txt` 404'd.

Fix: split the sanitizer into two helpers in `packages/api/src/utils/files.ts`:

  - `sanitizeArtifactPath` — segment-wise sanitize while preserving
    `/`. Falls back to basename on `..` traversal, absolute paths, and
    other malformed inputs. The DB record uses this so the next prime()
    can recreate the nested path in the sandbox.

  - `flattenArtifactPath` — encode `/` as `__` for the local
    `saveBuffer` strategies, which key by single-component filename and
    would otherwise create unintended subdirectories under uploads/.

`process.js` is updated to use both: DB filename keeps the path, storage
key flattens. `claimCodeFile` is also keyed on `safeName` so the
(filename, conversationId) compound key stays consistent with the
record `createFile` writes.

Tests:
  +13 unit tests in `files.spec.ts` (sanitizeArtifactPath table,
  flattenArtifactPath round-trip).
  +1 integration test in `process.spec.js` asserting the DB-row vs
  storage-key split for a nested path.
  Updated `process-traversal.spec.js` to mock the new helpers.

64 pass / 0 fail across `Files/Code/`; 36 pass / 0 fail in
`packages/api/src/utils/files.spec.ts`.

Companion: ClickHouse/ai#1327 — the codeapi-side counterpart that stops
phantom file IDs from reaching this code path in the first place. These
two are independent but the matplotlib bug is most cleanly resolved when
both ship.

* 🛡️ fix: Re-add 255-char per-segment cap in sanitizeArtifactPath (codex review P2)

`sanitizeArtifactPath` dropped the 255-char basename cap that
`sanitizeFilename` enforces. Long artifact names then flowed unbounded
into `processCodeOutput`'s storage key (`${file_id}__${flatName}`) and
tripped `ENAMETOOLONG` on filesystems that enforce `NAME_MAX` —
saveBuffer fails, and the file falls back to a download URL instead of
persisting / priming. This was a regression specifically for flat
filenames that the original `sanitizeFilename` would have truncated
safely.

Re-add the cap as a per-path-component limit so it applies cleanly to
both flat and nested paths:

  - Leaf segment: extension-preserving truncation, matching
    `sanitizeFilename`'s shape (`<truncated-stem>-<6 hex>.<ext>`).
  - Non-leaf (directory) segments: plain truncate-and-disambiguate
    (`<truncated-name>-<6 hex>`); directory names don't carry semantic
    extensions worth preserving.
  - Defensive fallback when `path.extname` returns a pathologically long
    "extension" (e.g. `_.aaaa…aaa` after the dotfile underscore prefix
    rewrite turns a long hidden file into a non-dotfile with a 300-char
    "extension"): collapse to whole-segment truncation rather than
    leaving the cap unmet.

+6 unit tests covering: long leaf (regression case), long leaf under a
preserved directory, long non-leaf segment, deeply nested mixed-length,
exact-255 boundary (no truncation), and the dotfile + truncation
interaction.

* 🛡️ fix: Cap flattened storage key against NAME_MAX in processCodeOutput (codex review P1)

Per-segment caps on the path-preserving form aren't enough. Once segments
are joined with `__` for the storage key, deeply-nested or moderately
long paths can still produce a flat form that overflows once
`${file_id}__` is prepended — `${file_id}__a__b__c.csv` for a 3-level
100-char-each path is ~344 chars, well past filesystem NAME_MAX (255).
saveBuffer then trips ENAMETOOLONG and falls back to a download URL,
and the artifact never persists / primes.

`flattenArtifactPath` gets an optional `maxLength` parameter. When set,
the function truncates the flat form to fit, preserving the leaf
extension with the same disambiguating-hex-suffix shape sanitizeFilename
uses. Default (`undefined`) keeps existing call sites uncapped — the cap
is opt-in for callers that are actually building a filesystem key.
Pathologically long "extensions" from `path.extname` (e.g. `.aaaa…aaa`)
fall back to whole-key truncation rather than leaving the cap unmet.

processCodeOutput composes the storage key after `file_id` is known and
passes `255 - file_id.length - 2` as the budget so the full
`${file_id}__${flatName}` string fits in one filesystem path component.

+7 unit tests in files.spec.ts:
  - Pass-through when no maxLength supplied (cap is opt-in).
  - Pass-through when flat form fits within maxLength.
  - Truncation with leaf extension preserved (the regression case).
  - Leaf-only overflow with extension preservation.
  - Pathological long-extension fallback (whole-key truncation).
  - No-extension stem truncation.
  - Boundary equality (off-by-one guard).

+1 integration test in process.spec.js: processCodeOutput passes the
file_id-aware budget (`255 - file_id.length - 2`) to flattenArtifactPath.

114/114 across files.spec.ts + Files/Code (49 + 65).

* 🛡️ fix: Determinize + clamp artifact-path truncation (codex review P2 ×2)

Two follow-ups to Codex review on the path/flat-key cap:

1. **Deterministic truncation suffixes**. The previous helpers used
   `crypto.randomBytes(3)` for the disambiguator, mirroring
   `sanitizeFilename`'s shape. That made the truncated form non-
   deterministic: a re-upload of the same long filename would compute a
   *different* storage key, orphaning the previous on-disk file under
   the reused `file_id` returned by `claimCodeFile`.

   New `deterministicHexSuffix(input)` helper hashes the input with
   SHA-256 and takes the first 6 hex chars. Same input → same suffix
   (storage key stable across re-uploads); different inputs sharing a
   truncation prefix still get different suffixes (collision avoidance).
   24 bits ≈ 16M values is collision-safe for our scale (single-digit
   artifacts per turn per (filename, conversationId) bucket).

   Applied to `truncateLeafSegment`, `truncateDirSegment`, and
   `flattenArtifactPath` — every truncation site in the new helpers.
   `sanitizeFilename` (pre-existing) is intentionally left alone; its
   tests rely on the random-bytes mock and it's outside this PR's scope.

2. **Final clamp on flattenArtifactPath result**. The old `Math.max(1,
   maxLength - ext.length - 7)` floor could let the result slip past
   `maxLength` when the extension was nearly as large as the budget
   (e.g. `maxLength=5`, `ext=".txt"`: budget computed as 0, but result
   was `-<6 hex>.txt` = 11 chars). Drop the `Math.max(1, …)` floor and
   add a final `truncated.slice(0, maxLength)` so the contract holds
   for any input. Also short-circuit `maxLength <= 0` to `''` for
   pathological budgets.

Tests updated to compute the expected hash inline (the existing
`randomBytes` mock doesn't apply to the new code path), plus 4 new
regression tests:
  - sanitizeArtifactPath: same input → same output, different inputs →
    different outputs (determinism + collision avoidance).
  - flattenArtifactPath: same input → same output, different inputs
    sharing a truncation prefix → different outputs.
  - flattenArtifactPath: clamp holds when ext.length > maxLength - 7.
  - flattenArtifactPath: returns '' for maxLength <= 0.

53 unit tests pass. 65 integration tests pass.

* 🛡️ fix: Total-path cap + basename for classifier (codex P2 + comprehensive review)

Four follow-ups from the latest reviews on this PR:

1. **Codex P2: total-path cap in sanitizeArtifactPath**. Per-segment
   caps weren't enough — a deeply nested path (3+ at-cap segments) can
   still produce a joined form past Mongo's 1024-byte indexed-key limit
   (4.0 and earlier reject; later versions configurable). Added
   `ARTIFACT_PATH_TOTAL_MAX = 512` and a leaf-only fallback when the
   joined form exceeds it. Same shape as the absolute-path /
   `..`-traversal fallbacks above; the leaf is already segment-capped to
   ≤255, so the final result stays within bounds.

2. **Codex P2: pass basename to classifier/extractor in process.js**.
   With the path-preserving sanitizer, `safeName` can now be a nested
   string like `reports.v1/Makefile`. The classifier's `extensionOf`
   reads that as `v1/Makefile` (the slice after the dot in the directory
   name) and the bare-name branch rejects because it sees a `.`
   anywhere. Result: extensionless artifacts under dotted folders
   (Makefile, Dockerfile, etc.) get misclassified as `other` and skip
   text extraction. Pass `path.basename(safeName)` to both
   `classifyCodeArtifact` and `extractCodeArtifactText` so
   classification matches what the old flat-name flow produced.

3. **Review nit: drop dead `sanitizeFilename` mock in process.spec.js**.
   process.js no longer imports `sanitizeFilename`; the mock was
   misleading dead code.

4. **Review nit: rename misleading `'embedded parent traversal'` test**.
   `path.posix.normalize('a/../escape.txt')` resolves to `escape.txt`
   which goes through the normal segment-split path, not the
   `sanitizeFilename` fallback. Test name now says "resolves embedded
   parent traversal via path normalization" to match the actual code
   path.

+3 regression tests:
  - sanitizeArtifactPath falls back to leaf-only when joined > 512.
  - sanitizeArtifactPath keeps nested path within the 512 budget.
  - process.spec: passes basename (`Makefile` from `reports.v1/Makefile`)
    to classifyCodeArtifact + extractCodeArtifactText.

Existing "caps every segment in a deeply-nested path" test now uses 2
segments (not 3) so the joined form stays under the new total cap; the
3-segment scenario is covered by the new fallback test instead.

55 unit + 66 integration = 121/121 pass.

* 📝 docs: Correct sanitizeArtifactPath JSDoc to match actual schema index

Two doc-only fixes from the latest comprehensive review (both NIT):

1. **Index field list was wrong**. JSDoc claimed the compound unique
   index was `{ file_id, filename, conversationId, context }`. The
   actual index in `packages/data-schemas/src/schema/file.ts:92-95` is
   `{ filename, conversationId, context, tenantId }` with a partial
   filter for `context: FileContext.execute_code`. The cap rationale
   (Mongo 4.0 indexed-key limit) is correct and unchanged; just the
   field list was wrong. Added the schema file path so future readers
   can find the source of truth.

2. **Trade-off acknowledgement**. The reviewer noted that the
   leaf-only fallback loses directory structure, which means the
   model's `cat /mnt/data/<deep>/<path>/file.txt` would 404 on the
   pathological-depth case — partially re-introducing the original
   flat-name bug for >512-char paths. This is intentional (DB write
   failure is strictly worse than losing structure), but the trade-off
   wasn't called out explicitly in the JSDoc. Added a paragraph
   acknowledging it and noting that the cap is monotonically better
   than the pre-PR behavior, where ALL artifacts were treated this way
   regardless of depth.

No code or test changes — pure JSDoc correction. Tests still 55/0.

* 🛡️ fix: Disambiguate sanitized artifact names to keep claimCodeFile keys unique (codex P2)

`sanitizeArtifactPath` is not injective — multiple raw inputs can collapse
onto the same regex-and-normalize output. Codex's example:
`reports 2026/out.csv` and `reports_2026/out.csv` both sanitize to
`reports_2026/out.csv`. `claimCodeFile` is keyed on the schema's compound
unique `(filename, conversationId, context, tenantId)` index, so the
later upload silently matches the earlier record and overwrites the first
artifact's bytes via the reused `file_id` — a single conversation can
drop files when both names are valid in the sandbox.

This collision space isn't strictly new — pre-PR `sanitizeFilename`
(basename-only) had the same property — but the path-preserving form
gives us enough information to fix it for the first time.

**Fix.** When character-level sanitization changed something (regex
replacement, path normalization, dotfile prefix, empty-segment collapse),
embed a deterministic SHA-256 prefix of the **raw input** in the leaf
segment via the new `embedDisambiguatorInLeaf` helper. Same raw input →
same safe form (idempotent for re-uploads); different raw inputs that
would have collided → different safe forms.

**Why "character-level"** specifically:
- The disambiguator fires when `preCapJoined !== inputName` (post-regex
  + dotfile + empty-segment, BUT pre-truncation).
- Truncation alone is already disambiguated by `truncateLeafSegment`'s
  own seg-hash; firing the input-hash branch on truncation would just
  stack a second hash for no collision-avoidance benefit and clutter
  human-readable filenames.

**Three known collision shapes covered:**
1. `out 1.csv` vs `out_1.csv` (and `out@1.csv` vs `out#1.csv`, etc.)
2. `dir//file.txt` vs `dir/file.txt` (empty-segment collapse)
3. `.x` vs `_.x` (dotfile-prefix step)

**Disambiguator + truncation interaction:** for very long mutated leaves,
`truncateLeafSegment` caps at 255 first, then `embedDisambiguatorInLeaf`
re-trims to insert the input hash. The seg-hash from the first pass is
replaced by the input-hash from the second pass — that's intentional
(input-hash is the load-bearing collision-avoidance suffix; seg-hash was
only ever decorative once the input-hash exists). Final clamp ensures
the result never exceeds `ARTIFACT_PATH_SEGMENT_MAX` regardless of input.

**Disambiguator + total-cap fallback:** when joined > 512, we fall back
to the leaf-only form. The leaf has already had the disambiguator
embedded, so collision avoidance survives the pathological-depth case.

**`embedDisambiguatorInLeaf`** uses `dot <= 1` to detect "no real
extension" (covers extensionless names AND dotfile-prefixed leaves like
`_.hidden` — without this, `_.hidden` would split as stem `_` + ext
`.hidden` and produce the awkward `_-<hash>.hidden`).

**Updated 5 existing tests** that asserted the old collision-prone
outputs — they now verify the disambiguator-included form. The
character-level-only firing rule was load-bearing here: tests for
"clean inputs (no mutation)" and "long inputs (truncation only)" still
pass without any disambiguator clutter.

**+7 regression tests** in a new `collision avoidance (Codex review P2)`
describe block:
1. Different raw inputs sanitizing to the same form get distinct safes
2. Whitespace-vs-underscore in directory segment
3. Dotfile-prefix collision
4. Idempotency: same raw → same safe across calls
5. Clean inputs skip the disambiguator (cosmetic guarantee)
6. Disambiguator survives leaf truncation (long mutated leaf)
7. Disambiguator survives total-cap fallback (pathological depth)

62 unit + 66 integration = 128/128 pass.
* 🪟 feat: Render Source-Code Artifacts in the Side Panel (CODE bucket)

PR #12832 wired markdown / mermaid / html / .jsx-tsx tool outputs through
the side-panel artifact pipeline but explicitly punted on code files:

> Everything else (csv, py, json, xls/docx/pptx, …) keeps PR #12829's
> inline behaviour — dedicated viewers will land in follow-ups.

This adds the code-file viewer. A `simple_graph.py` (and every other
common source file) now opens in the side panel alongside markdown,
mermaid, html, and react artifacts instead of falling back to the
inline `<pre>` rendering.

**Design.** New `CODE: 'application/vnd.code'` bucket reuses the static-
markdown sandpack template — `useArtifactProps` pre-wraps the source as
a fenced code block (` ```python\n...\n``` `) before handing it to
`getMarkdownFiles`. The fence carries a `language-<x>` class through
`marked`, so a future highlighter swap-in (e.g. drop `highlight.js`
into the markdown template) picks up syntax colors automatically. The
`react-ts` (sandpack) template's React boot cost is avoided since
source files don't need it.

**Single source of truth for languages.** New `CODE_EXTENSION_TO_LANGUAGE`
map drives BOTH:
  - `EXTENSION_TO_TOOL_ARTIFACT_TYPE` routing (presence in this map =
    code file). Adding a new language is one entry.
  - The fenced-block language hint (exported as `languageForFilename`).

Identifiers follow the GitHub / `highlight.js` convention so the future
highlighter pickup is automatic.

**Scope.** Programming languages + stylesheets + shell + sql/graphql +
build files (Dockerfile/Makefile/HCL). Pure data formats
(CSV/TSV/JSON/JSONL/NDJSON/XML/YAML/TOML) and config dotfiles
(`.env`/`.ini`/`.conf`/`.cfg`) are intentionally NOT routed in this
pass — they're better served by dedicated viewers (CSV table view,
etc.) or remain inline. Adding them later is a one-entry change in
the map.

**JSX/TSX kept on the React (sandpack) bucket.** They're React component
sources; the existing live-preview should win over the static CODE
bucket. Plain `.js`/`.ts` source goes through CODE.

**MIME-type fallback.** The codeapi backend serves `text/x-python`,
`text/x-typescript`, etc. as `Content-Type` for source files, so a
file whose extension was stripped/renamed upstream still routes to
CODE via the MIME map.

**Empty-text gate.** CODE joins MARKDOWN/PLAIN_TEXT in the empty-text
exception (an empty `.py` is still a Python file). HTML/REACT/MERMAID
still require text — their viewers (sandpack/mermaid.js) error on
empty input.

**Files changed:**
- `client/src/utils/artifacts.ts` — `CODE` bucket constant,
  `CODE_EXTENSION_TO_LANGUAGE` map, exported `isCodeExtension` and
  `languageForFilename` helpers, extension/MIME routing additions,
  template + dependencies entries, empty-text gate exception, helper
  hoisting (extensionOf / baseMime moved up so the language map can
  reference them).
- `client/src/hooks/Artifacts/useArtifactProps.ts` — exported
  `wrapAsFencedCodeBlock`, CODE branch that wraps the source then
  routes through `getMarkdownFiles`.

**Tests (+22):**
- 8 parameterized routing cases (.py, .js, .go, .rs, .css, .sh, .sql,
  .kt) verify the CODE bucket fires.
- Extension wins when MIME is generic octet-stream (Python has no
  magic bytes; common case).
- Regression: jsx/tsx STAY on REACT bucket (no live-preview regression).
- Regression: data formats (CSV/JSON/YAML/TOML) and config dotfiles
  (.env/.ini) do NOT route to CODE.
- Empty-text exception for CODE (empty Python file is still a Python file).
- `useArtifactProps`: CODE → content.md / static template, fenced-block
  shape, language hint, unknown-extension fallback to raw extension,
  no-extension empty hint, index.html via markdown template.
- `wrapAsFencedCodeBlock`: language hint, empty hint, single-trailing-
  newline trim, multi-newline preservation, empty-source emit.

87/87 in artifact-impacted tests; 155/155 across the broader artifact
suite. No regressions in pre-existing markdown/mermaid/HTML/REACT/text
behavior.

* 🛡️ fix: Bare-filename routing + adaptive fence delimiter (codex P2 ×2)

Two follow-ups from Codex review on the CODE bucket:

1. **Bare-filename routing for extensionless build files (Codex P2).**
   `Dockerfile`, `Makefile`, `Gemfile`, `Rakefile`, `Vagrantfile`,
   `Brewfile` have no `.` in their basename — `extensionOf` returns
   `''` and the extension map can't match, so they fell through to
   inline rendering despite being in `CODE_EXTENSION_TO_LANGUAGE`.

   New `bareNameOf` helper returns the lowercased basename for
   extensionless filenames (returns `''` for files with a `.` so the
   extension and bare-name paths don't double-match). Both
   `detectArtifactTypeFromFile` and `languageForFilename` consult it as
   a second lookup against the same `CODE_EXTENSION_TO_LANGUAGE` map,
   so adding a new build file is one entry. Path-aware: takes the
   basename so `proj/Dockerfile` (path-preserving sanitizer output)
   still routes correctly.

   Added the four extra Ruby build-script names while I was here.

2. **Adaptive fence delimiter (Codex P2).** A hardcoded ` ``` ` fence
   breaks when the source contains a line starting with ` ``` ` —
   for example, a JS file containing a markdown-shaped template
   literal:
       const md = `
       ```
       hello
       ```
       `;
   CommonMark closes a fence on a line whose backtick run matches-or-
   exceeds the opener, so `marked` would close the outer fence at
   the inner `\`\`\`` and the rest of the file would render as
   markdown — corrupting the artifact and potentially altering
   formatting / links outside `<code>`.

   New `longestLeadingBacktickRun(source)` scans for the longest
   start-of-line backtick run in the payload. Fence length =
   `max(3, longest + 1)` — strictly more than any internal run, so
   `marked` can never close the outer fence early. Only escalates
   when needed; the common case still uses a triple-backtick fence.

   Inline backticks (mid-line) don't count — they're not fence
   delimiters. Only column-zero runs trigger escalation, so e.g.
   a Python file with ` `inline ``` here` ` keeps the 3-fence.

+11 regression tests:
  - 8 parameterized cases: `Dockerfile`/`Makefile`/`Gemfile`/etc. route
    to CODE via bare-name fallback (case-insensitive on basename).
  - Path-aware: `proj/Dockerfile` recognized.
  - No double-match: `dockerfile.dev` (with extension) returns null.
  - Unknown extensionless files (`README`, `LICENSE`) stay null.
  - 4-backtick fence when source has ` ``` ` at start-of-line.
  - 5-backtick fence when source has ` ```` ` at start-of-line.
  - 3-backtick fence (default) for ordinary code.
  - Inline backticks don't escalate.
  - Source starting with backtick run at offset 0.

Plus 6 new `languageForFilename` tests covering bare-name fallback
and path-awareness.

108/108 in artifact-impacted tests (was 87, +21 tests). No regressions.

* 🛡️ fix: Indented fence detection + basename-scoped extensionOf (codex P2/P3)

Two follow-ups from the latest Codex review on the CODE bucket:

1. **Indented backtick runs (Codex P2).** `longestLeadingBacktickRun`
   was scanning `^(`+)` — column 0 only. CommonMark allows fence
   closers to be indented up to 3 spaces, so a JS source containing
   an indented `\`\`\`` (e.g. inside a template literal embedded in a
   class method) would still terminate our outer fence and the
   remainder would render as markdown.

   Updated regex to `^ {0,3}(`+)`. Tabs are not allowed in fence
   indentation (CommonMark expands them to 4 spaces, which is over
   the 3-space limit), so spaces alone suffice. Backticks indented
   4+ spaces are CommonMark "indented code blocks" — they can't
   terminate a fence, so we correctly don't escalate for them.

2. **`extensionOf` path-laden output (Codex P3).** `extensionOf` took
   `lastIndexOf('.')` across the FULL path string, so
   `pkg.v1/Dockerfile` yielded the nonsensical "extension"
   `v1/dockerfile`. `languageForFilename` returned that as the language
   hint (broken `language-v1/dockerfile` class on the fenced block),
   AND the routing's bare-name fallback couldn't fire because the
   extension lookup returned non-empty.

   New `basenameOf` helper strips path separators; `extensionOf` and
   `bareNameOf` both go through it. After the fix:
     - `pkg.v1/Dockerfile` → `extensionOf` returns `''` → `bareNameOf`
       returns `dockerfile` → routes to CODE with correct language.
     - `pkg.v1/main.go` → `extensionOf` returns `go` → routes correctly.
     - `pkg.v1/script.py` → `extensionOf` returns `py` → routes correctly.

+10 regression tests:
  - 5 parameterized cases covering 1-3 space indent at fence lengths
    3, 4, 5 (escalation kicks in correctly).
  - 4-space indent does NOT escalate (CommonMark indented-code-block
    territory; can't close a fence).
  - `pkg.v1/Dockerfile` and `a.b.c/Makefile` route to CODE +
    `languageForFilename` returns `dockerfile`/`makefile`.
  - Dotted-directory files (`pkg.v1/main.go`, `a.b.c/script.py`) still
    route correctly via the basename-scoped extension parse.

118/118 in artifact-impacted tests (was 108, +10 tests). No regressions.

* 🛡️ fix: Comprehensive review polish + MIME-derived language hint (codex P3)

Resolves all 8 valid findings from the comprehensive review and the
follow-up Codex P3 on the same PR. None are user-visible bugs; the set
spans correctness guards, dead-code removal, organization, and test
coverage.

**Comprehensive review #1 — Remove dead `isCodeExtension` export.**
Function was exported with zero callers anywhere in the codebase.

**Comprehensive review #2 — Guard the for-loop against silent overwrites.**
The `for (ext of CODE_EXTENSION_TO_LANGUAGE)` loop blindly assigned
each language extension to the CODE bucket. If a future contributor
added `jsx` or `tsx` to the language map (a natural mistake — they
ARE source code), the loop would silently overwrite the REACT bucket
entries and break the sandpack live-preview with no compile-time or
runtime error. Added `if (ext in EXTENSION_TO_TOOL_ARTIFACT_TYPE) continue`
so explicit map entries always win.

**Comprehensive review #3 — Add `fileToArtifact` end-to-end test for CODE.**
Routing was tested via `detectArtifactTypeFromFile`; full Artifact
construction (id / type / title / content / messageId / language) for
CODE was not. Added 5 new `fileToArtifact` cases.

**Comprehensive review #4 — Move pure utilities out of the hook file.**
`wrapAsFencedCodeBlock` and `longestLeadingBacktickRun` are pure
string transformations with no React dependencies. Moved both to
`utils/artifacts.ts`. Test files updated to import from the new
location.

**Comprehensive review #5 — Correct the MIME-map "mirrors" comment.**
Comment claimed the MIME map mirrored `CODE_EXTENSION_TO_LANGUAGE`, but
covered ~21 of ~60 entries. Reworded to "best-effort COMMON-CASE list,
not an exhaustive mirror" with the rationale (extension routing is
primary; MIME is a stripped-filename fallback).

**Comprehensive review #6 — Drop `lang ? lang : ''` ternary.**
`lang` is typed `string`; the only falsy value is `''`. Removed.
(Replaced via the MIME-fallback rewrite of `wrapAsFencedCodeBlock`,
where `lang` is now used directly without the ternary.)

**Comprehensive review #7 — Avoid double `basenameOf` computation.**
`extensionOf(filename)` and `bareNameOf(filename)` both internally
called `basenameOf` — when the extension lookup missed,
`detectArtifactTypeFromFile` paid for two parses of the same path.
Split into private `extensionFromBasename` / `bareNameFromBasename`
helpers; the caller computes `basenameOf` once and threads it through.

**Comprehensive review #8 — Trim verbose Dockerfile/Makefile comment.**
Inline comment block in the language map duplicated `bareNameOf`'s
JSDoc. Replaced with a one-line pointer.

**Codex P3 — MIME fallback for the CODE language hint.**
`detectArtifactTypeFromFile` routes `{ filename: 'noext', type:
'text/x-python' }` to CODE via the MIME bucket map, but then
`useArtifactProps` derived the language hint from `artifact.title`
ONLY — and `noext` has no extension, so `languageForFilename` returned
empty and the fenced block emitted with no `language-` class. The
future highlighter swap-in would lose syntax-color metadata for these
files.

  - New `MIME_TO_LANGUAGE` map covering the language MIMEs codeapi
    actually emits.
  - `languageForFilename(filename, mime?)` now takes an optional MIME
    second arg and falls back to it after the extension and bare-name
    paths.
  - `fileToArtifact` resolves the language at construction time
    (using both filename AND `attachment.type`) and stores it on
    `artifact.language`. The hook reads `artifact.language` directly
    rather than re-deriving from `title` alone, so the MIME signal
    survives end-to-end.
  - Title-derived fallback in the hook covers older callers that
    don't populate `language`.

Tests:
  +10 cases for the comprehensive review findings (CODE end-to-end
  via `fileToArtifact`, language storage, non-CODE language
  un-set).
  +6 cases for the MIME fallback (`languageForFilename(name, mime)`
  ordering, MIME parameter stripping, extension/bare-name vs MIME
  precedence, empty signal).
  +2 hook tests for `artifact.language` pre-resolved vs title-fallback.

131/131 in directly-impacted files (was 118, +13).
199/199 across the broader artifact suite. No regressions.

Pre-existing TypeScript errors in `a11y/`, `Agents/`, `Auth/`,
`Mermaid.tsx`, etc. are unrelated to this PR (verified by checking
`tsc --noEmit` on origin/dev — same errors).
…ne (#12866)

* 🛂 fix: Skip Re-Download of Inherited Code-Env Files (No More 403 Storms)

When a bash/code-interpreter call lists or operates on inputs the user
already owns (skill files primed via primeInvokedSkills, files inherited
from a prior session), codeapi echoes those files back in the tool
result with `inherited: true`. We were treating every entry as a
generated artifact and calling processCodeOutput on each, which:

1. Hit `/api/files/code/download/<session_id>/<file_id>` with the
   user's session key. Skill files are uploaded under the skill's
   entity_id, so every download 403'd — producing dozens of
   "Unauthorized download" log lines per turn.

2. Surfaced those inputs as ghost file chips in the UI even though
   they were never generated by the run.

3. Wasted a download round-trip even when no auth boundary was
   crossed — the file is already persisted at its origin.

Fix: skip files where `file.inherited === true` in all three
artifact-files loops (`tools.js`, `createToolEndCallback`, and
`createResponsesToolEndCallback`). Skill files remain available to
subsequent calls via primeInvokedSkills / session inheritance — we
just don't redundantly re-download them.

Pairs with codeapi-side change that adds the `inherited` flag.

* 🔒 feat: Mark Skill Files as `read_only` During Code-Env Priming

Pairs with codeapi `read_only` upload flag (ClickHouse/ai#1345). When
LibreChat primes a skill into the code-env, every file in the batch
(SKILL.md plus all bundled scripts/schemas/docs) is now uploaded with
`read_only: true`. Codeapi seals these inputs at the filesystem layer
(chmod 444) and the walker echoes the original refs as `inherited:
true` regardless of whether sandboxed code modified the bytes on disk.

Without this, the previous PR's `inherited` skip handled only the
unchanged case. A modified skill file (pip writing pyc near a .py, a
script accidentally truncating LICENSE.txt, etc.) still flowed through
the modified-input branch on codeapi, got a fresh user-owned file_id,
uploaded as a "generated" artifact, and surfaced in the UI as a chip
the user couldn't actually authorize a download for.

Changes:

- `api/server/services/Files/Code/crud.js`:
  `batchUploadCodeEnvFiles({ ..., read_only })` forwards the flag as
  a multipart form field. Default `false` preserves existing behavior
  for user-attached files and prior-session inheritance.

- `packages/api/src/agents/skillFiles.ts`: type signature gains
  `read_only?: boolean`; `primeSkillFiles` passes `true`.

- `packages/api/src/agents/skillFiles.spec.ts`: assert the upload call
  carries `read_only: true`.

The flag is intentionally not skill-specific. Any future
infrastructure-input flow (system fixtures, cached datasets, etc.) can
opt in the same way.
…pend (#12868)

* 💎 fix: Stop Double-Counting Cache Tokens for Gemini/OpenAI in Usage Spend (#12855)

Different providers report `usage_metadata.input_tokens` with different
semantics:

  - Anthropic / Bedrock: `input_tokens` EXCLUDES cache; cache reads/writes
    arrive separately and must be added to get the total prompt size.
  - Gemini / OpenAI: `input_tokens` ALREADY INCLUDES cached tokens
    (Google's `promptTokenCount`, OpenAI's `prompt_tokens`). Their
    `input_token_details.cache_*` are subsets of `input_tokens`.

`recordCollectedUsage` treated both schemes as additive, so for cache-hit
requests on Gemini/OpenAI it added cache tokens on top of an
`input_tokens` value that already contained them — overcharging users by
the cache_hit_rate (e.g., ~67% cache hit ≈ 1.67x overcharge). This
matches the issue reporter's GCP billing comparison.

Adds a small `splitUsage` helper that classifies the provider by model
name and computes `inputOnly` (the non-cached portion) plus the
all-inclusive `totalInput` for both the spend math and the returned
`input_tokens` summary. The helper defaults to additive semantics (the
historical behavior) so unknown providers are unaffected.

Updates existing OpenAI-shaped tests that previously asserted the buggy
additive math, and adds Gemini regression tests using the exact numbers
from the issue report (input=11125, cache_read=7441 → input=3684).

Anthropic / Bedrock paths remain bit-identical to before.

* 🔧 refactor: Classify Cache-Token Semantics by Provider, Not Model Name

Follows up the previous commit. Replaces a model-name regex
(`gemini|gpt|o[1-9]|chatgpt`) with an explicit `Providers` enum lookup
keyed off the `usage.provider` field — `UsageMetadata.provider` already
exists in `IJobStore.ts` but was never being populated.

  - `callbacks.js#ModelEndHandler` now attaches `usage.provider` from
    `agentContext.provider` alongside `usage.model`.
  - `usage.ts` uses a `SUBSET_PROVIDERS` set (`openAI`, `azureOpenAI`,
    `google`, `vertexai`, `xai`, `deepseek`, `openrouter`, `moonshot`)
    backed by the canonical `Providers` enum from
    `librechat-data-provider`.
  - `xai`, `deepseek`, `openrouter`, `moonshot` extend `ChatOpenAI` so
    they inherit subset semantics (verified in node_modules).
  - Defaults to additive when `usage.provider` is missing, so the title
    flow (which doesn't propagate provider) and any pre-this-PR usage
    entries keep their existing behavior.

Tests: switch fixtures from model-name signaling to explicit `provider`
field, plus a Vertex AI case and a "missing provider" fallback case.
…12840)

When GOOGLE_KEY=user_provided is set as an endpoint config, the
loadAuthValues() function in credentials.js would pass the literal
string 'user_provided' to tools via the || fallback chain. This caused
Gemini Image Tools to fail at runtime with an invalid API key error,
as initializeGeminiClient() received the sentinel value instead of a
real key.

The fix aligns loadAuthValues() with checkPluginAuth() in format.ts,
which already correctly excludes user_provided and empty/whitespace
values. Now loadAuthValues() skips these values and continues to the
next field in the fallback chain or falls through to user DB values.

Added regression tests covering:
- user_provided sentinel is skipped, DB value used instead
- Fallback chain continues past user_provided to next field
- Empty and whitespace env values are skipped
- Real env values are returned correctly
- Optional fields with sentinel values handled gracefully
)

* fix: graceful MCP OAuth revoke cleanup when tokens are missing (#12754)

`maybeUninstallOAuthMCP` in `api/server/controllers/UserController.js`
aborts before the DB-delete and flow-state cleanup steps whenever
`MCPTokenStorage.getTokens` throws `ReauthenticationRequiredError` —
which is exactly what happens when a user clicks "Revoke" on an MCP
server whose backend is already dead and whose refresh token is gone.
The resulting error is both surfaced to the log as a red line and, more
importantly, leaks the DB token row and OAuth flow state.

Wrap the token retrieval in try/catch following the same best-effort
pattern already used for the two `revokeOAuthToken` calls. On
`ReauthenticationRequiredError`, skip revocation silently (info log)
and continue to the cleanup steps. On any other unexpected error, log
a warning and continue — cleanup must always run.

Exported `maybeUninstallOAuthMCP` for direct unit testing and added
`api/server/controllers/__tests__/maybeUninstallOAuthMCP.spec.js` with
8 cases: early-return guards (non-MCP key, non-OAuth server, missing
client info), happy path (both tokens revoked + cleanup), both
failure-to-retrieve paths (ReauthenticationRequiredError and arbitrary
error — cleanup still runs in both), single-token path, and
revocation-call failures (cleanup still runs).

Fixes #12754.

* test: use instanceof check against real ReauthenticationRequiredError

Follow-up to the previous commit on this branch. Two changes:

1. `UserController.maybeUninstallOAuthMCP` now checks
   `error instanceof ReauthenticationRequiredError` using the real
   class imported from `@librechat/api`, instead of comparing
   `error?.name === 'ReauthenticationRequiredError'`. The name-string
   check matched any unrelated error that happened to have the same
   `.name`; the `instanceof` check is a proper identity test.

2. The accompanying spec's jest mock for `@librechat/api` now
   exposes a `ReauthenticationRequiredError` class, and the test
   imports it from that mock so the `instanceof` comparison in the
   production code holds during the test. Without this, the two
   "skips revocation ... still runs cleanup" tests threw
   `TypeError: Right-hand side of 'instanceof' is not an object`
   because the mock left the class undefined.

All 8 tests in the spec pass.
…2765)

Most of the codebase already supports the concept of *not* using a reranker w/
web search, except there was no way to initially setup an absent reranker
component.

Now there's a special path for skipping the reranker auth when loading web
search config, which allows for skipping the reranker when using web search.
…er Error (#12834)

* fix(sse): treat responseCode===0 as transport failure, not server error

When a long-running model response (e.g. gpt-5.4 with web_search:true)
takes longer than the browser's idle connection timeout, the SSE transport
drops and sse.js fires an error event with responseCode=0 and e.data set
to the raw response buffer (non-JSON SSE text).

The previous guard `!responseCode` is truthy for both 0 (transport drop)
and undefined (genuine server-sent error event), so the client incorrectly
entered the server-error branch, tried to JSON.parse raw SSE text, logged
"Failed to parse server error", and showed the user a red error banner --
even though the backend continued processing and delivered the final answer
seconds later.

Fix 1 (client): change guard from `!responseCode` to `responseCode == null`
so that only undefined/null (no HTTP status at all) triggers the server-error
parse path. responseCode===0 now correctly falls through to the reconnect path.

Fix 2 (backend): after res.flushHeaders() the response is already committed
as SSE. The fallback branch that wrote res.status(404).json() was an HTTP/SSE
protocol violation. Replace with an SSE-conformant event:error frame + res.end().

* fix(sse): use onError helper on subscribe failure + add regression tests

Replace silent res.end() with onError('Failed to subscribe to stream')
so the client receives a parseable SSE error event instead of a stream
that closes with no signal. The previous res.end() left the UI stuck
in "submitting" state because no error/abort/final event ever fired.

Also adds two missing test cases for the responseCode guard change:
- responseCode === 0 with raw SSE buffer data must NOT call errorHandler
  (transport failure should reconnect, not display garbage)
- responseCode == null with JSON error data MUST call errorHandler
  (server-sent error events should still surface to the user)

---------

Co-authored-by: Danny Avila <danny@librechat.ai>
* fix(code): preserve code env upload filepaths

* chore: Reorder import statements in crud.js
* 🧹 chore: Strip code-execution boilerplate from tool output

The bash executor in `@librechat/agents` appends two kinds of noise to
every successful run:

1. Trailing `Note:` paragraphs — long behavioral hints repeating
   rules already in the system prompt ("Files from previous executions
   are automatically available...", "Files in 'Available files' are
   inputs..."). Re-stating these on every tool call adds ~50 tokens of
   waste per call, which compounds across long agent traces.

2. Per-file `| <annotation>` suffixes on every line of `Generated
   files:` / `Available files (...):`. The two section headers already
   convey the new-vs-known distinction; the per-file annotations are
   redundant *and* phrased inconsistently ("downloaded by the user"
   vs. "displayed to the user" vs. "known to the user").

Strip both in a small `cleanCodeToolOutput` helper invoked from
`packages/api/src/agents/handlers.ts` for every tool listed in
`CODE_EXECUTION_TOOLS`. Non-code-execution tools pass through
unchanged. The cleaning happens *after* tool resolution but *before*
downstream consumers (model context, SSE forwarding, persistence) see
the content, so subsequent model turns get the lean output.

* 🩹 fix: Polish code-execution attachment rendering

Three rough edges visible in code-interpreter conversations:

1. **Sandbox-internal `.dirkeep` placeholders leak as file chips.** The
   bash executor creates `.dirkeep` inside any new directory so the
   stateless container preserves the folder across executions. After
   `sanitizeArtifactPath`'s `_` prefix and 6-hex collision suffix it
   surfaces as `_.dirkeep-<hash>` — a 0-byte chip with no value to the
   user, sometimes hiding the real artifact behind it. New
   `isInternalSandboxArtifact` helper filters them out of every
   routing path (`Attachment`, `AttachmentGroup`, `LogContent`).

2. **The `-<hash>` collision suffix is visible in chip labels.** The
   suffix is collision-avoidance machinery; users only need to see the
   canonical name. New `displayFilename` strips it for display while
   leaving the on-disk `attachment.filename` untouched so downloads
   resolve. Applied across `FileContainer`, `ToolArtifactCard`,
   `ToolMermaidArtifact`, and `LogContent`'s text-attachment label
   path.

3. **0-byte / placeholder files outrank real artifacts in render
   order.** Bucket sort by salience (non-empty before empty) sinks
   stragglers to the bottom. Stable sort preserves arrival order for
   peers.

Added regression tests cover the new helpers, the dirkeep filter
across buckets, and the within-bucket salience ordering.

* 🩹 fix: Don't auto-open artifact panel on history navigation

Navigating to a previous conversation full of code-execution artifacts
would auto-open the side panel and focus the most-recent artifact —
the same code path that fires for fresh streaming artifacts. Users
expect that "auto-open" behavior only when an artifact arrives via
SSE, not when they revisit an old chat.

Two-part gate:

1. `ToolArtifactCard`'s focus effect captures `isSubmitting` at first
   render via a ref. A card mounted *during* a stream means a new
   artifact arrived → steal panel focus (legacy behavior). A card
   mounted while `isSubmitting === false` is part of conversation
   history → leave focus alone.

2. `Presentation`'s panel-render condition gains `currentArtifactId
   != null`. With (1) keeping `currentArtifactId` null on history
   load, the panel stops rendering at all on navigation — even if
   `artifactsVisibility` was left `true` by a prior conversation.
   User clicks on a chip to re-open (the click handler is unchanged
   and unconditional).

Test seeds `isSubmittingFamily(0)` per case: existing tests opt into
streaming (default `true`) so legacy auto-focus assertions still hold;
new tests for history-load opt into `streaming: false` and verify
no auto-focus + click-to-open still works.

* 🩹 fix: Force panel visible on streaming artifact arrival

The previous commit gated `setCurrentArtifactId` on `isSubmitting` but
left `artifactsVisibility` untouched. When a user had explicitly
closed the panel earlier in the session, a fresh SSE artifact would
set `currentArtifactId` (so the chip read "click to close") but
`Presentation`'s render condition still required `visibility === true`
— net effect: the card claimed to be open, the panel stayed hidden.

Streaming arrivals now also call `setVisible(true)`, which is the
explicit "auto-open when first created" behavior the user asked for.
History mounts (`isSubmitting === false`) still leave both focus and
visibility alone, so navigating to an old conversation does not
re-open the panel.

Two regression tests added: one asserts streaming flips visibility on
even when seeded false, the other asserts history mounts leave a
seeded-false visibility alone.

* 🧹 chore: Tighten code-execution attachment polish per audit feedback

Resolves the eight actionable findings from the comprehensive audit:

- Scope `displayFilename` out of `FileContainer`: opt-in via a new
  `displayName` prop. User-uploaded chips (input area, persisted
  message files) keep their raw filename, eliminating the false-positive
  class where `report-abc123.pdf` was silently rewritten to `report.pdf`.
  Code-execution artifact paths in `Attachment.tsx` explicitly compute
  the de-suffixed name and pass it through.
- Tighten `TRAILING_NOTES_PATTERN` to anchor on the two known boilerplate
  openings (`Files from previous executions`, `Files in "Available files"`),
  so a user-authored `Note:` line preceded by a blank line in stdout no
  longer gets eaten along with everything after it.
- `ToolMermaidArtifact`: compute `visibleFilename` once and reuse for
  title, content, and the download `aria-label` (was using the raw
  `attachment.filename` for the aria-label, creating a screen-reader
  inconsistency).
- `ToolArtifactCard`: read `isSubmittingFamily(0)` once via a
  non-subscribing `useRecoilCallback`, instead of subscribing for the
  full lifetime to a value the ref only ever needs at first render.
- Extract `bySalience` and `byEntrySalience` comparators from
  `attachmentTypes.ts`, replacing the ten duplicated sort lambdas in
  `Attachment.tsx` and `LogContent.tsx`.
- Treat `attachmentSalience({ bytes: undefined })` as neutral (`0`)
  rather than empty (`1`); only an explicit `bytes === 0` sinks. Stops
  non-code-exec sources (web-search inline results, files where the
  schema omits the byte count) from silently sinking past real content.
- Pin the click-history test to the panel-open button by name instead
  of relying on `getByRole('button', { pressed: false })`, which
  matched by DOM order.
- Add the missing blank line between adjacent `it(...)` blocks.
- Drop the verbose narrating comments in `FileContainer` along with the
  removed `displayFilename` import.

Adds three regression tests for the new behavior (FileContainer raw
filename, artifact-context displayName flow, user-authored `Note:` line
preserved through cleanup) and updates the salience test for the new
neutral-undefined semantics.

* 🧹 chore: Drop redundant `@testing-library/jest-dom` import in FileContainer spec

`client/test/setupTests.js` already imports the matchers globally for every
Jest test in the client workspace, so the explicit import here was dead code.
Removing it brings the spec in line with the broader convention used by
`ArtifactRouting.test.tsx`, `LogContent.test.tsx`, and `attachmentTypes.test.ts`.

* 🛡️ fix: Narrow `.dirkeep`/`.gitkeep` filter to the sandbox-specific form

`isInternalSandboxArtifact` was filtering bare `.dirkeep` / `.gitkeep`
along with the post-sanitization form. Bare versions never originate
from the bash executor (the dotfile rewrite + disambiguator step in
`sanitizeArtifactPath` always produces `_.dirkeep-<6 hex>`), so the only
real-world source of a bare `.gitkeep` is project scaffolding the user
uploaded — silently hiding it from every attachment bucket meant the
file disappeared with no way to surface or download it.

Tightening to `^_\.(?:dirkeep|gitkeep)-[0-9a-f]{6}$` keeps the
sandbox-placeholder filter intact while letting user-uploaded markers
render normally. Tests inverted accordingly: bare forms now expected to
render; only the post-sanitization form is filtered.

* 🩹 fix: Address comprehensive-review findings on attachment helpers

Five findings from the latest pass:

- **MAJOR — `displayFilename` false-positive on extensionless 6-hex.**
  The previous regex `/-[0-9a-f]{6}(?=\.[^.]+$|$)/` stripped any leaf
  ending in `-XXXXXX` regardless of context, so a user-named
  `build-a1b2c3` (script-emitted hash artifact, no extension) lost its
  tail and rendered as `build`. Split into two narrower patterns:
  `COLLISION_SUFFIX_BEFORE_EXT` only matches when followed by an
  extension; `SANITIZED_DOTFILE_TRAILING_SUFFIX` only fires when the
  leaf starts with `_.` AND ends with `-XXXXXX` — the unambiguous
  fingerprint of `sanitizeArtifactPath`'s dotfile rewrite.

- **MINOR — `isInternalSandboxArtifact` filter too aggressive.**
  `(file.bytes ?? 0) > 0` treated undefined bytes as zero, falling
  through to the regex check. Tightened to `file.bytes !== 0`: only
  an *explicit* zero counts as the empty-placeholder shape worth
  hiding. Non-code-exec sources without `bytes` populated render
  normally now.

- **MINOR — `getValue()` could throw on a degenerate atom state.**
  Switched the snapshot read in `ToolArtifactCard` to
  `valueMaybe() ?? false` so a transient error / loading state on the
  upstream selector doesn't crash card mount. The `false` default is
  the right history-fallback (don't auto-open if we can't classify).

- **NIT — `attachmentSalience` / `bySalience` over-broad signature.**
  Removed the test-only `{ bytes?: number }` arm; functions now accept
  `TAttachment` directly. The internal `bytes` read still goes through
  a cast since not every TAttachment branch declares it. Tests updated
  to use the existing `baseAttachment(...)` helper.

- **MINOR — Missing regression test for extensionless 6-hex.**
  Added `'build-a1b2c3'` and `'out/blob-deadbe'` cases that pin the
  preservation behavior, plus an `isInternalSandboxArtifact` test that
  asserts undefined-bytes attachments are not filtered.

* 🩹 fix: Make code-file artifacts click-to-open only

Removes mount-time auto-open from `ToolArtifactCard`. Streaming
arrivals no longer hijack the panel — even a freshly-emitted SSE
artifact registers silently in `artifactsState` and waits for the
user to click. Combined with `Presentation`'s
`currentArtifactId != null` render gate, the panel stays closed
across history navigation, page reload, and SSE arrival.

Click is the only path that opens the panel. `handleOpen` is
unchanged: first click focuses + reveals, second click on the same
chip closes.

Dropped:
- `useRecoilCallback` snapshot read of `isSubmittingFamily(0)`
- `mountedDuringStreamRef` ref + lazy-init block
- The whole focus + visibility effect (was effect 3)
- `useRef` import (now unused)

Tests:
- `ArtifactRouting.test.tsx` rewritten to exercise the click path:
  registers-on-mount-without-focus, click-to-open-then-close, multi-
  card-no-auto-focus, click-when-visibility-was-false. The streaming
  state is no longer seeded; both `renderWith` and `renderWithProbe`
  collapsed back to plain `RecoilRoot`.
- `LogContent.test.tsx` flips its panel-routing assertions from
  `pressed: true` (which asserted auto-focus) to `pressed: false`
  with a chip-title check (which asserts the panel card rendered
  but stayed unfocused).

* Revert "🩹 fix: Make code-file artifacts click-to-open only"

This reverts commit 6761531.

* 🩹 fix: Exclude CODE bucket from streaming auto-open

Narrows the previous-commit revert: rich-preview artifacts (HTML,
React, Markdown, plain text) keep the legacy SSE auto-open UX, but
the CODE bucket (`.py`, `.js`, `.cpp`, `Dockerfile`, `Makefile`, …)
stays click-to-open even on streaming.

Source-code artifacts are typically supporting helpers the agent
emits alongside a richer deliverable (a Python script that builds
the actual `.html` output, for example). Auto-opening every
helper's panel each time it gets written would shove the panel
in front of the user every tool call. The user explicitly opens
a code chip when they want to inspect it.

Implementation:
- Focus+open effect skips early when `artifact.type === CODE`.
- `artifact.type` added to the dep array so the gate re-evaluates
  if the type ever changes (it shouldn't, but the dep is honest).
- JSDoc updated to call out the carve-out.

Tests:
- New `does NOT auto-open a streaming CODE artifact (test.py is
  click-to-open)` — seeds isSubmitting=true, mounts a `.py`,
  asserts the artifact registers but currentArtifactId stays null.
- New `clicking a CODE artifact focuses it even though it skipped
  auto-open` — confirms the click path still surfaces a `.py`.
- All 25 prior auto-open tests for HTML/React/Markdown/plain-text
  buckets still pass unchanged: those types continue to auto-open
  on streaming.

* 🧹 chore: Address two NITs from the audit-fix follow-up review

- **NIT #1 (conf 60)**: Add a test for the dotfile-with-extension
  intersection (`_.config-abcdef.txt` → `.config.txt`). Both halves
  of the path were tested separately — extension-anchored suffix
  stripping and `_.` underscore restoration — but the combination
  wasn't pinned. Adds `expect(displayFilename('_.config-abcdef.txt'))
  .toBe('.config.txt')`.

- **NIT #2 (conf 25)**: Tighten the cast in `attachmentSalience` from
  the anonymous `{ bytes?: number }` shape to the concrete
  `TFile & TAttachmentMetadata` (the actual TAttachment branch that
  declares `bytes`). Same runtime behavior; a future retype of
  `TFile.bytes` will now surface here at compile time instead of
  being silently papered over.

* 🩹 fix: Stop stripping `-<6 hex>` suffixes from non-dotfile filenames

Codex's repeated P2 was correct: the `COLLISION_SUFFIX_BEFORE_EXT`
regex stripped any `-<6 hex>` immediately before an extension
regardless of context. That collapsed legitimate user-named files
like `report-deadbe.csv` and `report-beef01.csv` onto the same chip
label `report.csv`, silently merging distinct files in the UI.

The structural truth: only the dotfile shape (`_.foo-XXXXXX`) carries
an unambiguous discriminator (the leading `_.` that
`sanitizeArtifactPath` adds when rewriting a leading dot). The
extension-only case (`name-<hash>.ext`) has no such discriminator —
we can't distinguish a sanitized `report 1.csv` (which became
`report_1-<hash>.csv`) from a user-named `report-deadbe.csv` from
the filename alone.

Recovering the non-dotfile case cleanly would require a backend
`wasSanitized` metadata flag we don't have. Without it, the safer
choice is to leave non-dotfile names alone — uglier when the file
*was* sanitized, but never collapses distinct files onto a shared
label.

Changes:
- Drop `COLLISION_SUFFIX_BEFORE_EXT`. Replace
  `SANITIZED_DOTFILE_TRAILING_SUFFIX` with a unified
  `SANITIZED_DOTFILE_PATTERN` that handles both extensionless and
  with-extension dotfile shapes in one regex.
- Simplify `displayFilename` to a single match + reconstruct path.
- Update tests: drop the broad-stripping assertion
  (`output-deadbe.csv` → `output.csv`), add explicit codex-regression
  cases (`report-deadbe.csv` and `report-beef01.csv` preserve
  unchanged), document the deliberate non-recovery for sanitized
  non-dotfiles, update the AttachmentGroup→FileContainer integration
  test to reflect the narrower stripping (non-dotfile `archive-deadbe.zip`
  passes through; new dotfile `_.config-abcdef.zip` → `.config.zip`
  exercises the recoverable path).

* 🩹 fix: Scope code-tool annotation stripping to file-list sections

Codex was right: the previous global `.replace` would mutate any line
ending in one of the three annotation phrases — even legitimate
stdout. A user script doing
`echo "foo | File is already downloaded by the user"` had its output
silently scrubbed before being fed back into model context.

New `FILE_SECTION_PATTERN` captures `Generated files:` /
`Available files (...)` blocks (header + lines starting with `- /`).
Annotation stripping now only runs *within* the captured file-list
section via a nested `.replace`, so:

- Inside the section: per-file `| <ann>` suffixes still get stripped
  (line-per-file ≥ 4 files form, inline `, ` comma-separated ≤ 3
  files form — both already covered by existing patterns).
- Outside the section: stdout, stderr, blank lines, the trailing
  `Note:` paragraphs (handled by their own pattern), and any user
  text that coincidentally contains an annotation phrase pass
  through unchanged.

Tests:
- New `does NOT mutate stdout that legitimately contains an
  annotation phrase outside a file-list section` pins the codex
  regression: three coincidental phrases in stdout, no
  `Generated files:` header, all three preserved verbatim.
- New `strips annotations inside a file-list section but preserves
  identical phrases in stdout above it` covers the mixed case where
  the same phrase appears in both stdout and a file listing —
  stdout survives, listing gets cleaned, exactly one occurrence
  remains.
- All 9 prior tests still pass (file-section stripping behavior
  unchanged for both line-per-file and inline-comma layouts).
)

* 🔌 fix: Follow 307/308 redirects in MCP streamable HTTP transport

Some MCP servers (e.g. Coda) return 308 Permanent Redirect to route
doc-scoped tool calls to a different endpoint path. The fetch wrapper
used `redirect: 'manual'` for SSRF protection, which silently dropped
these redirects and caused tool calls to fail with empty error bodies.

Follow 307/308 redirects (method-preserving per RFC 7538) up to a
depth of 5. SSRF safety is preserved because the same undici Agent
with its SSRF-safe connect function validates redirect targets.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* 🛡️ fix: Harden MCP 307/308 redirect handling against SSRF and credential leaks

- Validate every redirect target against `resolveHostnameSSRF` so allowlist
  deployments (which disable connect-time SSRF protection) still block hops to
  private/reserved IPs.
- Strip `Authorization`, `Cookie`, `mcp-session-id`, and any user-injected
  headers when a 307/308 crosses an origin boundary, mirroring browser/Fetch
  behavior so a redirecting MCP server can't exfiltrate credentials.
- Cancel the intermediate response body before each next hop so undici can
  reuse pooled sockets rather than holding them until GC.
- Restructure redirect test helpers to be same-origin (matching real-world
  Coda-style routing), drop dead setup code, fix the misleading "5 hops
  successfully" test, and add coverage for SSRF-blocked redirects, cross-
  origin credential stripping, and same-origin credential preservation.

* 🛡️ fix: Also strip `serverConfig.headers` on cross-origin MCP redirects

Previously only runtime `setRequestHeaders` keys were treated as secret on a
307/308 cross-origin hop. API keys baked into `serverConfig.headers` (passed
through `requestInit.headers` at transport construction time) survived
stripping, so a malicious MCP endpoint could exfiltrate them by returning a
cross-origin `Location`. Pass the configured header keys through to
`createFetchFunction` so both runtime and config secrets are stripped.

The cross-origin credential test now also configures `serverConfig.headers`
to lock in this behavior.

* 🧹 chore: Tighten MCP redirect-stripping coverage and helper duplication

- Add `proxy-authorization` to the cross-origin forbidden header set so a
  forward-proxy credential header would also be stripped on a cross-origin
  hop, matching the Fetch-spec list.
- Strengthen the cross-origin credential test with positive assertions that
  benign protocol headers (`accept`, `content-type`) survive the hop, so a
  regression that strips everything indiscriminately would now fail.
- Extract the duplicated MCP request handler / session-teardown logic from
  three test helpers into shared `createMCPRequestHandler` and
  `closeMCPSessions` utilities.

* 🛠️ fix: Handle `Request` inputs in MCP `customFetch` URL derivation

`customFetch` is typed to accept `UndiciRequestInfo` (`string | URL | Request`),
but `Request.prototype.toString()` returns `"[object Request]"`. The previous
implementation derived `originalOrigin` and the redirect base via
`url.toString()`, so a `Request` input would throw inside `new URL(...)` before
any network call — a regression even when no redirect was involved.

Add a `getRequestUrlString` helper that extracts the URL string for all three
shapes, track the URL string alongside the fetch input through the redirect
loop, and add parameterized tests that exercise `customFetch` with each shape.

* 🛠️ fix: Don't override `Request` input headers in MCP `buildFetchInit`

Previously `buildFetchInit` always set `headers` on the returned init —
even when neither `init.headers` nor runtime headers contributed anything.
Passing `headers: {}` to `undiciFetch` overrides the headers carried on a
`Request` input (auth tokens, MCP session, protocol negotiation), so
Request-based wrappers could fail authentication even without a redirect
in play. Skip the `headers` override entirely when there is nothing to
merge.

Adds a regression test that supplies `Authorization` and a custom header
on the `Request` itself and asserts both reach the target server.

* 🛠️ fix: Preserve `Request` method/body across MCP redirects + guard cross-origin strip

Two regressions surfaced by extending `customFetch` to accept `Request` inputs:

1. **307/308 method/body loss.** The redirect loop switches `url` to the
   new `Location` string, but the original `Request`'s method and body
   stayed bound to the (now-discarded) `Request` object. A redirected
   POST silently became a GET with no payload — the exact behavior the
   method-preserving codes are designed to prevent. Added a
   `resolveFetchInput` helper that runs once at the top of `customFetch`,
   extracts a `Request`'s method/body/headers into the shared init, and
   buffers the body via `arrayBuffer()` so 307/308 retries can replay it.

2. **Cross-origin strip crashed on absent headers.** After the previous
   fix that stopped `buildFetchInit` from setting `headers: {}`,
   `currentInit.headers` could legitimately be `undefined`. The
   cross-origin branch read it as a `Record` and called `Object.entries`
   on `undefined`, throwing `TypeError`. Guard the branch on
   `currentInit.headers != null` — when there are no headers there is
   nothing to strip.

Adds two regression tests: a POST-with-body `Request` that 308-redirects
cross-origin (asserts both method and body survive) and a no-headers
cross-origin redirect (asserts the strip path no longer crashes).

* 🛠️ fix: Forward `Request.signal` through MCP `customFetch` normalization

`resolveFetchInput` was copying method/body/headers off a `Request` input
but dropping `Request.signal` on the floor, so a caller that wired an
`AbortController` onto the `Request` for cancellation/timeouts lost that
wiring as soon as we re-shaped the input into the `(string, init)` pair
used by the redirect loop. Subsequent aborts no longer reached the
in-flight fetch — a regression from the pre-PR code, which forwarded
the original `Request` directly to undici.

Forward the signal alongside method/body/headers, with explicit
`init.signal` still winning per Fetch-spec semantics. Regression test
aborts a controller before calling \`customFetch\` with the wired
`Request` and asserts the call rejects.

* 🧪 test: Pin URL.origin contract for protocol-downgrade redirect handling

Audit follow-up. The cross-origin strip path keys off
`targetUrl.origin !== originalOrigin`, and `URL.origin` is defined as
`scheme + "://" + host + ":" + port`, so a same-host `https → http`
redirect produces a different origin and trips the strip path through
the existing logic — no separate code path needed.

Pin that contract with a small unit test so a future change to URL
semantics (or a refactor that swaps in a different comparison) doesn't
silently regress protocol-downgrade stripping. Standing up a TLS
fixture (self-signed cert, undici skip-verify, etc.) just to re-prove
the URL spec is wasted complexity.

---------

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-authored-by: Danny Avila <danny@librechat.ai>
…sConfig (#12885)

* 📥 fix: Use Endpoint-Aware Default Model on Imported Conversations

Claude conversations imported from claude.ai's data export display
"gpt-4o-mini" in the chat UI until the page is refreshed, and any
attempt to send a message before refreshing fails with "The model
'gpt-4o-mini' is not available for Anthropic."

Root cause: ImportBatchBuilder.finishConversation() unconditionally
defaulted the saved conversation's `model` field to
openAISettings.model.default, regardless of `this.endpoint`. Claude
exports don't carry a model name, so every imported Claude conversation
landed with endpoint=anthropic but model=gpt-4o-mini.

Fix: pick the default based on `this.endpoint` via a small lookup
(openAI -> gpt-4o-mini, anthropic -> claude-3-5-sonnet-latest), keeping
the existing OpenAI default as the fallback for unknown endpoints.

Fixes #12844

* 🪄 refactor: Resolve Import Default Model From `modelsConfig`

Replace the hardcoded per-endpoint default lookup added in the previous
commit with a runtime resolver that consults the same models config the
chat UI uses (`getModelsConfig` in ModelController -> `loadDefaultModels`
+ `loadConfigModels`). This way an imported conversation defaults to a
model the LibreChat instance has actually configured / discovered for
the endpoint, instead of a hardcoded constant that may not exist on this
deployment.

Resolution order:
1. First non-empty model in `modelsConfig[endpoint]`.
2. Per-endpoint hardcoded fallback (anthropic/openAI settings) if the
   runtime config is empty for the endpoint or `getModelsConfig` throws.
3. `openAISettings.model.default` if even the per-endpoint fallback is
   missing (unknown endpoint).

`importBatchBuilder.finishConversation` now accepts an optional
`defaultModel` argument; each importer resolves it once at the top via
`resolveImportDefaultModel({ endpoint, requestUserId, userRole })` and
threads it through. ChatGPT message-level model selection also falls
back to the resolved default before the hardcoded gpt-4o-mini.
…hanges (#12887)

* 🩹 fix: Sync ControlCombobox popover width with trigger after layout changes

The popover width was measured once on mount via offsetWidth. When the agent builder side panel opens after a page reload with the sidebar collapsed, the trigger button is initially measured during the layout transition (~26px) and never re-measured, leaving the agent select dropdown rendered at the far left with no options fully visible.

Use a ResizeObserver to keep buttonWidth in sync with the trigger's actual width whenever it resizes, then disconnect on unmount.

* test: cover ControlCombobox isCollapsed, no-ResizeObserver, and zero-width branches

Address review feedback:
- Use button.offsetWidth as the ResizeObserver fallback instead of
  entry.contentRect.width to avoid a content-box vs border-box mismatch in
  pre-2022 browsers that ship ResizeObserver without borderBoxSize.
- Add tests for the three previously-untested branches: isCollapsed=true
  (no observation of the trigger), ResizeObserver unavailable (sync-only
  measurement), and zero-width entries (state unchanged).

* test: lock the button.offsetWidth fallback against revert

Add a test that drives the ResizeObserver callback with borderBoxSize
absent and divergent contentRect.width vs offsetWidth (251 vs 275).
The fix would silently revert to entry.contentRect.width without this
test failing, so this pins the chosen fallback semantics.

---------

Co-authored-by: Danny Avila <danny@librechat.ai>
* Handle MCP tool cache lookup failures

* Harden MCP cached tool lookup

* Cover full MCP tool cache outage

* Guard MCP tool cache store lookup
* fix: stabilize agent prompt cache prefix

* chore: refresh agents sdk lockfile integrity

* test: format agent memory assertion

* test: type agent context fixtures

* fix: preserve MCP instruction precedence

* fix: reuse resolved conversation anchor

* fix: keep resumable startup immediate
Fixes #12912.\n\n- Clear stored MCP OAuth tokens and flow state on revoke cleanup-only paths.\n- Keep provider revocation best-effort when token and client metadata are available.\n- Add controller and function coverage for stale metadata, missing config, and cleanup failure paths.
@pull pull Bot locked and limited conversation to collaborators May 2, 2026
@pull pull Bot added the ⤵️ pull label May 2, 2026
@pull pull Bot merged commit 4e45e8e into innFactory:main May 2, 2026
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