feat: add Research repository profile

plans/research-core-adaptation-v2/milestone-0-execution-dag.md

@@ -0,0 +1,69 @@
+# Milestone 0 Execution DAG
+
+```yaml
+objective: reconcile Research Core Adaptation V2 with the checked-out Nashsu core without changing production behavior
+root_owner: current Codex root session
+requested_model: GPT-5.6 Sol High
+model_verification: unavailable in this task surface
+
+nodes:
+  - id: package-intake
+    kind: root
+    depends_on: []
+    outcome: verify the complete handoff and extract its constraints and code anchors
+    status: completed
+
+  - id: repository-baseline
+    kind: root
+    depends_on: [package-intake]
+    outcome: acquire the canonical repository, pin the exact version, and create a feature branch
+    status: completed
+
+  - id: scout-frontend-ingest
+    kind: root
+    archetype: scout-equivalent
+    depends_on: [repository-baseline]
+    outcome: map templates, schema routing, source import, queues, review persistence, page merge, and tests
+    write_scope: read-only
+    status: completed
+
+  - id: scout-backend-api
+    kind: root
+    archetype: scout-equivalent
+    depends_on: [repository-baseline]
+    outcome: map Rust persistence, local API routing, graph/search behavior, and project resolution
+    write_scope: read-only
+    status: completed
+
+  - id: scout-mcp-models
+    kind: root
+    archetype: scout-equivalent
+    depends_on: [repository-baseline]
+    outcome: map MCP registration and binding, model routing, and integration-test surfaces
+    write_scope: read-only
+    status: completed
+
+  - id: baseline-validation
+    kind: root
+    depends_on: [scout-frontend-ingest, scout-backend-api, scout-mcp-models]
+    outcome: run existing builds and tests and attempt the canonical desktop launch
+    status: completed-with-findings
+
+  - id: root-reconciliation
+    kind: root
+    depends_on: [baseline-validation]
+    outcome: reconcile reports, identify contradicted assumptions, and choose a proposed PR sequence
+    status: completed
+
+  - id: milestone-0-report
+    kind: root
+    depends_on: [root-reconciliation]
+    outcome: publish the root-owned intake report; make no production change
+    status: completed
+```
+
+Delegation note: the installed Codex CLI reports stable `multi_agent`, but this
+task runtime exposes no spawn/subagent tool. Following the handoff fallback, the
+three non-overlapping read-only scouting passes were performed sequentially by
+the root. No alternate orchestration runtime was installed.
+

plans/research-core-adaptation-v2/milestone-0-fresh-intake.md

@@ -0,0 +1,153 @@
+# Nashsu Research Core Adaptation V2 — Milestone 0 Fresh Intake
+
+## Status
+
+The implementation map is coherent enough to scope later work, but the baseline
+is not fully green. No production code, dependency, lockfile, schema, or runtime
+was changed. Milestone 1 was not started.
+
+Nashsu/llm_wiki remains the sole canonical product and knowledge core.
+AtomicStrata, AutoSci, OpenKB, Synto, Open Knowledge CLI, llm-wiki-okf, OKF, and
+additional orchestration runtimes remain outside the implementation boundary.
+OpenDeepWiki remains a future lazy, repository-scoped, non-canonical adjunct.
+
+## Exact baseline
+
+- Repository: `https://github.com/nashsu/llm_wiki.git`
+- Baseline branch: `main`
+- Intake branch: `codex/research-core-m0-intake`
+- Commit: `969e7e8d9e2903af0e3ed0be85c97639511e845c`
+- Describe: `v0.6.4-8-g969e7e8`
+- Commit: `fix: harden provider and import routing`
+- Commit date: `2026-07-16T17:04:21+08:00`
+- App/package/Cargo/Tauri version: `0.6.4`
+- MCP package version: `0.4.25`
+- Handoff: all 25 manifest entries matched their declared SHA-256 and byte size.
+
+The workspace initially contained no Nashsu checkout, so the current upstream
+repository was cloned before inspection.
+
+## Orchestration and capability check
+
+- Codex CLI: `0.142.5`
+- CLI feature state: `multi_agent = stable/true`;
+  `multi_agent_v2 = under-development/false`;
+  `enable_fanout = under-development/false`.
+- Official Codex documentation describes direct subagents, a default nesting
+  depth of one, and built-in `worker` and `explorer` roles.
+- This task runtime exposed no spawn/subagent tool, so no worker was delegated.
+  The root performed three sequential, isolated, read-only scout-equivalent
+  passes: frontend/ingest, Rust/API, and MCP/model routing.
+- The requested GPT-5.6 Sol High identity/reasoning setting is not inspectable
+  or configurable from this task surface, so it cannot be independently
+  verified.
+
+The compact DAG is in `milestone-0-execution-dag.md`.
+
+## Root implementation map
+
+| Capability | Current authority and behavior | Adaptation consequence |
+| --- | --- | --- |
+| Template materialization | `src/lib/templates.ts` defines schema, purpose, and extra directories. `src-tauri/src/commands/project.rs` creates the base project; `src/components/project/create-project-dialog.tsx` then writes the selected template files/directories. | Research Profile v2 must update the existing two-stage path, not add a creator. |
+| Schema routing | `src/lib/wiki-schema.ts` parses the `## Page Types` table dynamically and maps type to directory. In ingest, generated blocks are checked against this routing before write. Other schema prose mostly guides prompts. | Add `repository` to the Research table; do not build a generic schema engine. |
+| Fixed page-type surfaces | `src/lib/wiki-page-types.ts`, knowledge-tree and activity icon maps, `src/lib/wiki-type-style.ts`, and i18n labels contain known-type lists. Graph affinity and review-page creation also have fixed maps but safe fallbacks. | Milestone 1 must update user-visible/generation lists and test dynamic fallback surfaces. |
+| Source import | `src/lib/source-lifecycle.ts` copies files into `raw/sources`, preprocesses them, and immediately calls `enqueueSourceIngest` when an ingest model is usable. | Candidate registration must be inserted before enqueue for Research projects only; reuse import/copy logic. |
+| Ingest queue | `src/lib/ingest-queue.ts::enqueueBatch`; state is project-scoped in `.llm-wiki/ingest-queue.json`. It supports pause, restart recovery, retry, cancellation, stable project identity, and serial processing. | Candidate batch include/watch/exclude should feed this queue; no second queue. |
+| Ingest and merge | `src/lib/ingest.ts` performs analysis/generation, validates schema routing, creates review items, and writes through `mergePageContent`. `src/lib/page-merge.ts` unions `sources`, `tags`, and `related`, locks `type`, `title`, and `created`, and writes history backups. | Corpus bootstrap and Research writes must use normal ingest/merge/review behavior. |
+| Review persistence | `src/stores/review-store.ts`; `.llm-wiki/review.json` through `src/lib/persist.ts` and autosave. The Rust API reads and patches the same file. | Extend existing review/activity patterns; do not add a review store. |
+| Search/index | Rust search in `src-tauri/src/commands/search.rs` backs desktop invoke and API search. Index rebuild groups pages dynamically from frontmatter. Embeddings are optional. | `repository` should become searchable without a new index; add acceptance coverage. |
+| Graph | Desktop uses the TypeScript wiki graph path. API/MCP use a separate Rust `build_graph` in `api_server.rs`; the API currently excludes `query` nodes. Both derive types dynamically. | Repository visibility should work, but graph parity is an existing architectural discrepancy to resolve or document. |
+| Model routing | Desktop chat and ingest use `src/lib/llm-task-routing.ts` with separate `chat` and `ingest` presets. Image captioning is passed the ingest-side configuration. Embedding has separate embedding settings. Rust API/MCP chat uses `project_llm_config`, global config, and project overrides but does not apply `taskModelRouting.chatPresetId`. | Preserve current desktop routing; add parity tests before relying on MCP chat for acceptance. |
+| Local API | `src-tauri/src/api_server.rs`, port `19828`, prefix `/api/v1`; exposes health, projects, files, reviews, search, graph, source rescan, chat, and cancellation with auth, bind, rate, size, and path controls. | Extend the API only when a required Research operation cannot use an existing endpoint. |
+| MCP | `mcp-server` is a thin HTTP client over the desktop API. It registers 10 tools: status, projects, set-project, files, read-file, reviews, search, chat, graph, and rescan-sources. | Keep MCP thin; no filesystem scan or independent retrieval implementation. |
+| Project selection | Stable UUID in `.llm-wiki/project.json`; global `app-state.json` registry; API accepts stable ID, exact path, or `current`; MCP can pin a process to a project and rejects conflicting overrides. | Candidate and corpus state must key by stable project identity and remain project-scoped. |
+
+Representative `.llm-wiki/` state includes `project.json`,
+`ingest-queue.json`, `ingest-cache.json`, `ingest-progress/`,
+`ingest-warnings.log`, `review.json`, `lint.json`, `file-snapshot.json`,
+`file-change-queue.json`, `dedup-queue.json`, `dedup-not-duplicates.json`,
+`scheduled-import-db.json`, `image-caption-cache.json`, `conversations.json`,
+`chats/`, `chat-preferences.json`, `history/`, `page-history/`, `lancedb/`, and
+project `skills/`. Candidate screening needs one new small project-scoped file,
+not a replacement for any of these.
+
+## Handoff anchor reconciliation
+
+All named high-value anchors still exist. The paths are useful, but three
+assumptions require correction:
+
+1. Schema routing is already substantially dynamic. Adding a page type does not
+   require Rust index/search/graph type registration, although fixed generation
+   and UI presentation lists still need updates.
+2. Desktop and API/MCP graph generation are not one shared backend. The API has
+   its own Rust graph builder and intentionally drops `query` nodes.
+3. Desktop task-model routing and API/MCP chat routing are not equivalent. The
+   Rust API does not currently consume the chat task preset.
+
+Additional baseline findings:
+
+- The Research template's shared frontmatter example lists only base types even
+  though the same schema defines `thesis`, `methodology`, and `finding`.
+- Import currently means copy plus immediate enqueue; there is no candidate
+  registration/screening state.
+- `npm ci` at the root is not reproducible from the checked-in lockfile:
+  `@emnapi/core@1.11.2` and `@emnapi/runtime@1.11.2` are missing and
+  `@emnapi/wasi-threads` resolves at an invalid locked version. Dependencies
+  were materialized with `npm install --package-lock=false`; the lockfile was
+  preserved.
+- Existing tests strongly cover page merge preservation and TypeScript task
+  routing. Research template form state is tested, but full Research project
+  materialization is not. MCP client tests prove HTTP calls, but there is no
+  explicit architectural regression test forbidding direct filesystem scans.
+
+## Validation evidence
+
+| Command | Result |
+| --- | --- |
+| `npm run test:mocks -- --reporter=dot` | PASS: 117 files, 1,707 tests. |
+| `npm run build` | PASS: TypeScript and Vite production build; existing chunk/dynamic-import warnings only. |
+| `npm run mcp:test` | PASS: 20 tests. |
+| `npm run test:llm` | FAIL: 6 failed, 3 passed, 70 skipped. Three fake embedding-server tests receive `undefined`; three Origin tests send `http://localhost` instead of the endpoint origin. External provider suites were skipped because credentials/endpoints were unavailable. |
+| `cargo test -q` | PASS: 338 passed, 1 ignored; existing compiler warnings only. |
+| `npm run tauri dev` | PASS: desktop binary launched; Vite served `http://localhost:1420/`; Clip Server listened on `127.0.0.1:19827`; API listened on `127.0.0.1:19828/api/v1`. |
+| Local API smoke | PASS: health 200 (`version: 0.6.4`), CORS preflight 204. Projects returned the expected 401 because the fresh state requires auth but has no token configured; MCP is disabled. |
+
+The first Rust/launch attempts failed when the data volume had about 118 MiB
+free. After space was restored, both completed. The build consumed most of the
+new headroom and left about 1 GiB free.
+
+The computer-use skill is installed, but this task surface does not expose its
+required action tool. The app and services were launched and probed, but
+click-driven creation/import/review/search/graph flows were therefore not
+manually exercised.
+
+## Proposed PR sequence
+
+1. **M0 baseline stabilization:** add the canonical-core ADR, repair root
+   lockfile reproducibility, document the full local stack, add missing Research
+   materialization/MCP-boundary regressions, and decide whether the six
+   real-contract failures are code or stale test expectations. Add an
+   authenticated full-stack fixture for API/MCP acceptance.
+2. **M1 Research Profile v2:** add only `repository` and
+   `wiki/repositories/`; keep flat frontmatter; update the fixed surfaces above;
+   add creation, routing, rendering, search/graph visibility, and safe-merge
+   tests.
+3. **M2 candidate intake:** add a small Research-only project store and
+   include/watch/exclude UI; register without ingest; batch-enqueue through the
+   existing queue.
+4. **M3 screening and progress:** structured screening output, migration and
+   restart tests, and existing activity/review integration.
+5. **M4 bounded corpus bootstrap:** inventory, group, cluster synthesis, and
+   global synthesis through normal compiled pages and merge/review.
+6. **M5 MCP/API parity:** expose only missing Research operations, resolve
+   graph/model-routing parity, and keep MCP as an API client.
+7. **M6 OpenDeepWiki adjunct:** lazy repository registration and
+   commit-pinned evidence only; never canonical.
+
+## Root decision and remaining uncertainty
+
+The extension seams are clear and no new core runtime or generic abstraction is
+justified. Before Milestone 1, disposition the six real-contract failures and
+perform one authenticated, click-driven baseline pass through current
+Research creation, import, review, search, graph, API, and MCP behavior. The
+remaining evidence gaps are not permission to broaden Milestone 1.

plans/research-core-adaptation-v2/milestone-1-execution-dag.md

@@ -0,0 +1,62 @@
+# Milestone 1 Execution DAG
+
+```yaml
+objective: extend the existing Research template with the repository page type and directory while preserving all existing projects and templates
+root_owner: current Codex root session
+
+nodes:
+  - id: root-scope
+    kind: root
+    depends_on: []
+    outcome: pin accepted seams and exact fixed page-type surfaces from Milestone 0
+    status: completed
+
+  - id: tests-red
+    kind: root
+    archetype: verifier
+    depends_on: [root-scope]
+    outcome: add failing behavior tests for creation, routing, rendering, search/graph visibility, and safe merge
+    write_scope: test files only
+    status: completed
+
+  - id: profile-builder
+    kind: root
+    archetype: builder
+    depends_on: [tests-red]
+    outcome: add only the Research repository type/directory and update required fixed surfaces
+    write_scope: accepted template and page-type presentation files
+    status: completed
+
+  - id: focused-verification
+    kind: root
+    archetype: verifier
+    depends_on: [profile-builder]
+    outcome: pass focused tests and typechecking
+    write_scope: read-only except generated test/build artifacts
+    status: completed
+
+  - id: independent-review
+    kind: root
+    archetype: reviewer
+    depends_on: [focused-verification]
+    outcome: review the complete diff independently against repository standards and the handoff
+    write_scope: read-only
+    status: completed
+
+  - id: root-integration
+    kind: root
+    depends_on: [independent-review]
+    outcome: resolve findings and run the full verification matrix
+    status: completed
+
+  - id: commit
+    kind: root
+    depends_on: [root-integration]
+    outcome: commit the accepted Milestone 0 evidence and Milestone 1 implementation
+    status: completed
+```
+
+Delegation note: this task runtime exposes no subagent/spawn tool. The root
+therefore collapses builder, verifier, and reviewer roles into explicit
+sequential passes with non-overlapping phases. Architecture and integration
+remain root-owned.

src-tauri/src/api_server.rs

@@ -2184,6 +2184,39 @@ mod tests {
         assert!(!is_public_project_rel("wiki/.draft.md"));
     }
 
+    #[test]
+    fn api_graph_includes_repository_pages_with_their_declared_type() {
+        let root = test_project_dir();
+        let repository_dir = root.join("wiki/repositories");
+        let concept_dir = root.join("wiki/concepts");
+        fs::create_dir_all(&repository_dir).unwrap();
+        fs::create_dir_all(&concept_dir).unwrap();
+        fs::write(
+            repository_dir.join("nashsu-llm-wiki.md"),
+            "---\ntype: repository\ntitle: Nashsu / llm_wiki\n---\n\n[[knowledge-core]]",
+        )
+        .unwrap();
+        fs::write(
+            concept_dir.join("knowledge-core.md"),
+            "---\ntype: concept\ntitle: Knowledge Core\n---\n\n[[nashsu-llm-wiki]]",
+        )
+        .unwrap();
+
+        let (nodes, edges) = build_graph(root.to_str().unwrap()).unwrap();
+        let repository = nodes
+            .iter()
+            .find(|node| node.id == "nashsu-llm-wiki")
+            .unwrap();
+
+        assert_eq!(repository.node_type, "repository");
+        assert_eq!(
+            repository.path,
+            "wiki/repositories/nashsu-llm-wiki.md"
+        );
+        assert_eq!(edges.len(), 1);
+        let _ = fs::remove_dir_all(root);
+    }
+
     #[test]
     fn review_query_defaults_to_unresolved_items() {
         let root = test_project_dir();

src-tauri/src/commands/search.rs

@@ -2038,6 +2038,34 @@ mod tests {
         let _ = fs::remove_dir_all(root);
     }
 
+    #[tokio::test]
+    async fn keyword_search_includes_repository_pages_in_custom_wiki_directories() {
+        let root = tmp_project();
+        write_page(
+            &root,
+            "wiki/repositories/nashsu-llm-wiki.md",
+            "---\ntype: repository\ntitle: Nashsu / llm_wiki\n---\n\nCanonical research knowledge core implementation.",
+        );
+
+        let out = search_project_inner(
+            root.to_string_lossy().to_string(),
+            "canonical research knowledge core".into(),
+            20,
+            false,
+            None,
+        )
+        .await
+        .unwrap();
+
+        assert_eq!(out.results.len(), 1);
+        assert_eq!(
+            out.results[0].path,
+            "wiki/repositories/nashsu-llm-wiki.md"
+        );
+        assert_eq!(out.results[0].title, "Nashsu / llm_wiki");
+        let _ = fs::remove_dir_all(root);
+    }
+
     #[tokio::test]
     async fn keyword_search_always_blends_available_graph_neighbors() {
         let root = tmp_project();

src/components/chat/chat-message.tsx

@@ -9,7 +9,7 @@ import "katex/dist/katex.min.css"
 import {
   Bot, User, FileText, BookmarkPlus, ChevronDown, ChevronRight, RefreshCw, Copy, Check,
   Users, Lightbulb, BookOpen, HelpCircle, GitMerge, BarChart3, Layout, Globe,
-  TrendingUp, Target, Sparkles, Image as ImageIcon, FileSearch, Terminal,
+  TrendingUp, Target, GitBranch, Sparkles, Image as ImageIcon, FileSearch, Terminal,
 } from "lucide-react"
 import { openUrl } from "@tauri-apps/plugin-opener"
 import { useWikiStore } from "@/stores/wiki-store"
@@ -655,6 +655,7 @@ const REF_TYPE_CONFIG: Record<string, { icon: typeof FileText; color: string }>
   finding: { icon: TrendingUp, color: "text-purple-500" },
   thesis: { icon: Target, color: "text-rose-500" },
   methodology: { icon: BookOpen, color: "text-teal-500" },
+  repository: { icon: GitBranch, color: "text-sky-500" },
   overview: { icon: Layout, color: "text-yellow-500" },
   clip: { icon: Globe, color: "text-blue-400" },
   external: { icon: Globe, color: "text-sky-500" },

src/components/graph/graph-view.tsx

@@ -35,6 +35,7 @@ const NODE_TYPE_COLORS: Record<string, string> = {
   finding: "#a855f7",    // purple-500
   thesis: "#f43f5e",     // rose-500
   methodology: "#14b8a6", // teal-500
+  repository: "#38bdf8", // sky-400
   other: "#94a3b8",     // slate-400
 }
 
@@ -728,6 +729,7 @@ export function GraphView() {
       finding: t("graph.nodeTypeLabels.finding"),
       thesis: t("graph.nodeTypeLabels.thesis"),
       methodology: t("graph.nodeTypeLabels.methodology"),
+      repository: t("graph.nodeTypeLabels.repository"),
       other: t("graph.nodeTypeLabels.other"),
     })
   }, [t])