engine.ts

import type {
  Page, PageInput, PageFilters, GetPageOpts,
  Chunk, ChunkInput, StaleChunkRow, StalePageRow,
  SearchResult, SearchOpts,
  Link, GraphNode, GraphPath,
  TimelineEntry, TimelineInput, TimelineOpts,
  RawData,
  PageVersion,
  BrainStats, BrainHealth,
  IngestLogEntry, IngestLogInput,
  EngineConfig,
  CodeEdgeInput, CodeEdgeResult,
  EvalCandidate, EvalCandidateInput,
  EvalCaptureFailure, EvalCaptureFailureReason,
  SalienceOpts, SalienceResult, AnomaliesOpts, AnomalyResult,
  EmotionalWeightInputRow, EmotionalWeightWriteRow,
  DomainBankSampleOpts, CorpusSampleOpts, DomainBankRow,
  AdjacencyRow,
  EnrichCandidatesOpts, EnrichCandidate,
} from './types.ts';

/**
 * v0.27.1: file row for binary-asset metadata. Mirrors the `files` table
 * shape on both engines (Postgres has had it since v0.18; PGLite gets it
 * via migration v36).
 */
/**
 * Options for `traverseGraph`.
 *
 * `frontierCap`: when set, the BFS recursive term applies a parenthesized
 * `LIMIT N ORDER BY slug,id` so each iteration emits at most N rows. This
 * is the "approximately per-layer" cap discussed in the T8 plan — Postgres'
 * recursive CTE caps per ITERATION, not strictly per BFS LAYER (BFS layer
 * boundaries map to recursive iterations only when fan-out is bounded).
 * For hub-fanout graphs the cap fires early and bounds the work. Default:
 * unset = no cap (back-compat; existing callers see no change).
 *
 * NOTE: a truncation-detection signal (`onTruncation` callback) was
 * designed but the v1 algorithm had both false-positive (organic count ==
 * cap) and false-negative (LIMIT-before-DISTINCT in diamond graphs) cases
 * caught by adversarial review. The signal is deferred until a
 * dedupe-then-cap SQL rewrite + real Postgres parity coverage lands. See
 * TODOS.md → "T8 truncation signal" entry. Callers that need to detect
 * truncation can compare `result.length` against expected fanout bounds
 * as a coarse-but-honest signal in the interim.
 */
/**
 * v0.38: bare row shape returned by `BrainEngine.listAllSources()`.
 * Kept lean (no per-source page_count) so the autopilot tick stays O(1)
 * SQL queries regardless of source count. `sources-ops.SourceListEntry`
 * is the enriched application-layer shape.
 */
export interface SourceRow {
  id: string;
  name: string | null;
  local_path: string | null;
  last_sync_at: Date | null;
  config: Record<string, unknown>;
}

export interface TraverseGraphOpts {
  sourceId?: string;
  sourceIds?: string[];
  frontierCap?: number;
}

export interface FileRow {
  id: number;
  source_id: string;
  page_slug: string | null;
  page_id: number | null;
  filename: string;
  storage_path: string;
  mime_type: string | null;
  size_bytes: number | null;
  content_hash: string;
  metadata: Record<string, unknown>;
  created_at: Date;
}

/**
 * v0.27.1: spec for upsertFile. Identity is (source_id, storage_path).
 * Re-upserting the same identity with a different content_hash updates the
 * row in place (image was replaced); same content_hash is a no-op.
 */
export interface FileSpec {
  source_id?: string;
  page_slug?: string | null;
  page_id?: number | null;
  filename: string;
  storage_path: string;
  mime_type?: string | null;
  size_bytes?: number | null;
  content_hash: string;
  metadata?: Record<string, unknown>;
}

/**
 * v0.41.18.0 — shared opts for engine batch primitives that self-retry on
 * transient connection errors. Threaded through addLinksBatch /
 * addTimelineEntriesBatch / upsertChunks.
 *
 * Retry semantics: each batch primitive wraps its internal SQL in
 * `withRetry(BULK_RETRY_OPTS)` (default `{maxRetries:3, delayMs:1000,
 * delayMaxMs:10000, jitter:'decorrelated'}`). Callers MUST NOT add their own
 * `withRetry` wrapper around these methods — that produces 3×3=9 retry
 * attempts under failure, amplifying load on a recovering circuit breaker.
 * CI lint guard `scripts/check-no-double-retry.sh` enforces the rule.
 *
 * - `auditSite`: typed label for the JSONL audit emission (`~/.gbrain/audit/
 *   batch-retry-YYYY-Www.jsonl`). Must be a member of `BATCH_AUDIT_SITES`
 *   in `src/core/retry.ts`. The CI lint guard `scripts/check-batch-audit-
 *   site.sh` validates every string-literal value at build time.
 * - `signal`: AbortSignal that aborts mid-retry-sleep on SIGTERM/SIGINT.
 *   `MinionWorker.shutdownAbort.signal` is the canonical source.
 */
import type { BatchAuditSite } from './retry.ts';
export interface BatchOpts {
  auditSite?: BatchAuditSite;
  signal?: AbortSignal;
}

/** Input row for addLinksBatch. Optional fields default to '' (matches NOT NULL DDL). */
export interface LinkBatchInput {
  from_slug: string;
  to_slug: string;
  link_type?: string;
  context?: string;
  /**
   * Provenance (v0.13+). Pass 'frontmatter' for edges derived from YAML
   * frontmatter, 'markdown' for [Name](path) refs, 'manual' for user-created.
   * NULL means "legacy / unknown" and is only used by pre-v0.13 rows; new
   * writes should always set this. Missing on input defaults to 'markdown'.
   */
  link_source?: string;
  /** For link_source='frontmatter': slug of the page whose frontmatter created this edge. */
  origin_slug?: string;
  /** Frontmatter field name (e.g. 'key_people', 'investors'). */
  origin_field?: string;
  /**
   * v0.18.0: source id for each endpoint. When omitted, the engine JOINs
   * against `source_id='default'`. Pass explicit values when the edge
   * lives in a non-default source OR crosses sources.
   *
   * Without these fields, the batch JOIN `pages.slug = v.from_slug` fans
   * out across every source containing that slug, silently creating wrong
   * edges in a multi-source brain. The source_id filter eliminates the
   * fan-out. Origin pages (frontmatter provenance) get their own
   * source_id so reconciliation can't delete edges from another source's
   * frontmatter.
   */
  from_source_id?: string;
  to_source_id?: string;
  origin_source_id?: string;
  /**
   * v0.41.18.0 (A10, codex finding #12): distinguishes "plain body mention"
   * (NULL or 'plain') from "verb-pattern-derived typed NER" ('typed_ner')
   * within link_source='mentions'. Backed by v98 schema column. NOT in
   * the links UNIQUE constraint — same (from, to, type, source, origin)
   * tuple with different link_kind collides DO NOTHING. Default NULL =
   * legacy / unknown / pre-v98 semantics.
   */
  link_kind?: string;
}

/** Input row for addTimelineEntriesBatch. Optional fields default to '' (matches NOT NULL DDL). */
export interface TimelineBatchInput {
  slug: string;
  date: string;
  source?: string;
  summary: string;
  detail?: string;
  /**
   * v0.18.0: source id for the owning page. When omitted, the engine JOINs
   * against `source_id='default'`. Without this, two pages sharing the
   * same slug across sources would fan out timeline rows to both.
   */
  source_id?: string;
}

/**
 * A single dedicated database connection, isolated from the engine's pool.
 *
 * Used by migration paths that need session-level GUCs (e.g.
 * `SET statement_timeout = '600000'` before a `CREATE INDEX CONCURRENTLY`)
 * without leaking into the shared pool, and by write-quiesce designs
 * that need a session-lifetime Postgres advisory lock that survives
 * across transaction boundaries.
 *
 * On Postgres: backed by postgres-js `sql.reserve()`; the same backend
 * process serves every `executeRaw` call within the callback. Released
 * automatically when the callback returns or throws.
 *
 * On PGLite: a thin pass-through. PGLite has no pool, so every call is
 * already on the single backing connection. The interface is still
 * exposed so cross-engine callers don't need to branch.
 *
 * Not safe to call from inside `transaction()`. The transaction holds a
 * different backend; reserving a second one can deadlock on a row the
 * transaction itself is waiting to write.
 */
export interface ReservedConnection {
  /**
   * v0.41.18.0 (A20, codex #7): optional 3rd-arg `opts.signal` lets callers
   * actually cancel a running query. Init nudge (3s wallclock cap) wires an
   * AbortController whose timer fires at 3s; queries that haven't returned
   * by then get cancelled (Postgres: query.cancel(); PGLite: in-process,
   * Promise.race against signal-rejection — documented gap because PGLite
   * has no kernel-level cancellation).
   */
  executeRaw<T = Record<string, unknown>>(
    sql: string,
    params?: unknown[],
    opts?: { signal?: AbortSignal },
  ): Promise<T[]>;
}

/**
 * v0.28: Takes — typed/weighted/attributed claims, indexed in Postgres.
 * Markdown is source of truth (fenced table on the page); this row is the
 * derived index. Page-scoped via page_id (NOT slug — slug is unique only
 * within a source). `(page_id, row_num)` is the natural unique key.
 */
// v0.38: TakeKind opens from closed 4-element union to string (T3/T10).
// Pre-v0.38, kinds {fact|take|bet|hunch} were enforced by DB CHECK
// (migrations v41/v48) AND by this TS closed union. Codex outside-voice
// review caught that dropping the CHECK without also widening the TS
// type "moves inconsistency around" — raw SQL and old clients could
// poison rows that runtime-validate cleanly. v0.38 migration v76 drops
// the CHECK; this widens the type. Runtime validation moves to the
// active schema pack's `takes_kinds:` declaration. The annotation
// primitive's seed list in gbrain-base reproduces {fact|take|bet|hunch}
// so existing behavior is unchanged; packs can extend to {finding|
// hypothesis|observation|...} per domain.
export interface TakeKindLiteral { kind: string }
export type TakeKind = string;

/** Input row for addTakesBatch. */
export interface TakeBatchInput {
  page_id: number;
  row_num: number;
  claim: string;
  kind: TakeKind;
  holder: string;
  weight?: number;          // 0..1, default 0.5; clamped server-side
  since_date?: string;      // ISO date 'YYYY-MM-DD'
  until_date?: string;
  source?: string;
  superseded_by?: number | null;
  active?: boolean;         // default true
}

/** Take row as returned by listTakes / searchTakes. */
export interface Take {
  id: number;
  page_id: number;
  page_slug: string;        // joined from pages
  row_num: number;
  claim: string;
  kind: TakeKind;
  holder: string;
  weight: number;
  since_date: string | null;
  until_date: string | null;
  source: string | null;
  superseded_by: number | null;
  active: boolean;
  resolved_at: string | null;
  resolved_outcome: boolean | null;
  /**
   * v0.30.0: 3-state outcome label. v0.36.1.1 added 'unresolvable' as a 4th
   * state for verdicts where evidence was insufficient to grade. Sits
   * alongside `resolved_outcome` for back-compat. New writes populate both;
   * legacy v0.28-resolved rows have `resolved_quality` backfilled by
   * migration v40 from the boolean. Null on unresolved rows. Schema CHECK
   * (widened in v74) enforces (quality, outcome) consistency:
   * `correct` ↔ `outcome=true`, `incorrect` ↔ `outcome=false`,
   * `partial` ↔ `outcome=NULL`, `unresolvable` ↔ `outcome=NULL`.
   */
  resolved_quality: 'correct' | 'incorrect' | 'partial' | 'unresolvable' | null;
  resolved_value: number | null;
  resolved_unit: string | null;
  resolved_source: string | null;
  resolved_by: string | null;
  created_at: string;
  updated_at: string;
}

export interface TakesListOpts {
  page_id?: number;
  page_slug?: string;       // resolved via JOIN
  holder?: string;
  kind?: TakeKind;
  active?: boolean;         // default true (only active rows)
  resolved?: boolean;       // true = only resolved; false = only unresolved; undefined = both
  /** Per-token MCP allow-list. Server applies AND holder = ANY($takesHoldersAllowList) when set. */
  takesHoldersAllowList?: string[];
  sortBy?: 'weight' | 'since_date' | 'created_at';
  limit?: number;
  offset?: number;
}

/** Search result row from searchTakes / searchTakesVector. */
export interface TakeHit {
  take_id: number;
  page_id: number;
  page_slug: string;
  row_num: number;
  claim: string;
  kind: TakeKind;
  holder: string;
  weight: number;
  score: number;            // search rank score (ts_rank for keyword, 1-cos_dist for vector)
}

/** v0.28 stale-takes row (mirrors StaleChunkRow shape). Embedding column intentionally omitted. */
export interface StaleTakeRow {
  take_id: number;
  page_slug: string;
  row_num: number;
  claim: string;
}

/** Resolution metadata for resolveTake. */
export interface TakeResolution {
  /**
   * v0.30.0: primary 3-state input; v0.36.1.1 widened to 4-state with
   * 'unresolvable'. When set, takes precedence over `outcome` and the engine
   * writes both columns (quality directly; outcome derived:
   * `correct→true`, `incorrect→false`, `partial→null`, `unresolvable→null`).
   * `unresolvable` marks rows where the judge ran but evidence was
   * insufficient to grade; surfaces in `TakesScorecard.unresolvable_count`.
   */
  quality?: 'correct' | 'incorrect' | 'partial' | 'unresolvable';
  /**
   * v0.28 back-compat input. Keep submitting for v0.28 callers; the engine
   * derives quality (`true→correct`, `false→incorrect`). When `quality` is
   * also set, `quality` wins. When neither is set, the engine throws.
   * Mutually-exclusive with `quality === 'partial'` because partial isn't
   * binary.
   */
  outcome?: boolean;
  value?: number;
  unit?: string;       // 'usd' | 'pct' | 'count' | other
  source?: string;
  resolvedBy: string;  // slug or 'garry'
}

/** v0.30.0: scorecard aggregate. */
export interface TakesScorecard {
  total_bets: number;
  /**
   * Count of resolved rows where `resolved_quality IN
   * ('correct','incorrect','partial')`. v0.36.1.1 deliberately keeps this
   * 3-state semantic to preserve historical comparisons. Unresolvable rows
   * land in the sibling `unresolvable_count` field instead.
   */
  resolved: number;
  correct: number;
  incorrect: number;
  partial: number;
  /** Accuracy = correct / (correct + incorrect). NULL when n=0. */
  accuracy: number | null;
  /**
   * Brier score over rows where `resolved_quality IN ('correct','incorrect')`.
   * Maps `correct→1`, `incorrect→0`, computes `mean((weight − outcome)²)`.
   * Lower is better; 0 = perfect; 0.25 = always-50% baseline.
   * Excludes partial AND unresolvable — both hide signal; the dedicated
   * `partial_rate` and `unresolvable_rate` fields surface them separately.
   * NULL when no correct+incorrect rows.
   */
  brier: number | null;
  /** partial / resolved. NULL when n=0. */
  partial_rate: number | null;
  /**
   * v0.36.1.1: count of rows where `resolved_quality = 'unresolvable'`.
   * Sibling field to `resolved` so historical comparisons against pre-v80
   * scorecards stay valid; `resolved` retains its 3-state meaning, and
   * unresolvable rows count here separately. Optional for SDK back-compat —
   * downstream consumers constructing TakesScorecard fixtures shouldn't have
   * to update on a hotfix. `finalizeScorecard` always populates it.
   */
  unresolvable_count?: number;
  /**
   * v0.37.2.0: `unresolvable_count / (resolved + unresolvable_count)`. NULL
   * when both are 0. Surfaces the spec's headline calibration signal:
   * "what fraction of grade-attempted takes couldn't be graded?" — high
   * values signal weak evidence retrieval rather than wrong predictions.
   * Optional for SDK back-compat; see `unresolvable_count` note above.
   */
  unresolvable_rate?: number | null;
}

export interface TakesScorecardOpts {
  holder?: string;
  domainPrefix?: string; // e.g. 'companies/' to scope the scorecard
  since?: string;        // ISO date 'YYYY-MM-DD'
  until?: string;        // ISO date 'YYYY-MM-DD'
}

/** v0.30.0: calibration curve bucket. */
export interface CalibrationBucket {
  /** Lower bound of the weight bucket, inclusive. */
  bucket_lo: number;
  /** Upper bound, exclusive (except for the final bucket which is inclusive of 1.0). */
  bucket_hi: number;
  /** Count of resolved correct+incorrect bets falling in this weight range. */
  n: number;
  /** correct / n. NULL when n=0. */
  observed: number | null;
  /** mean(weight) within the bucket — what was predicted on average. NULL when n=0. */
  predicted: number | null;
}

export interface CalibrationCurveOpts {
  holder?: string;
  bucketSize?: number; // default 0.1
}

/** Synthesis evidence row input (provenance from think synthesis pages). */
export interface SynthesisEvidenceInput {
  synthesis_page_id: number;
  take_page_id: number;
  take_row_num: number;
  citation_index: number;
}

/** Dream-cycle Haiku verdict on whether a transcript is worth processing. */
export interface DreamVerdict {
  worth_processing: boolean;
  reasons: string[];
  judged_at: string;
}

/** Input shape for putDreamVerdict — judged_at defaults to now() server-side. */
export interface DreamVerdictInput {
  worth_processing: boolean;
  reasons: string[];
}

// ============================================================
// v0.31 Hot Memory: facts table + recall surface
// ============================================================

/** Allowed `facts.kind` values. Different decay halflives apply per kind. */
export type FactKind = 'event' | 'preference' | 'commitment' | 'belief' | 'fact';

export const ALL_FACT_KINDS: readonly FactKind[] = [
  'event', 'preference', 'commitment', 'belief', 'fact',
] as const;

/** Visibility tier on a fact row. Mirrors takes' world-default ACL contract (D21). */
export type FactVisibility = 'private' | 'world';

/** Status returned by insertFact. */
export type FactInsertStatus = 'inserted' | 'duplicate' | 'superseded';

/** A fact row read from the facts table. */
export interface FactRow {
  id: number;
  source_id: string;
  entity_slug: string | null;
  fact: string;
  kind: FactKind;
  visibility: FactVisibility;
  /**
   * v0.31.2: salience tier the LLM assigned at extraction time. Surfaces
   * to consumers (recall response, daily-page writer, admin dashboard,
   * agents reading via MCP `_meta.brain_hot_memory`). Pre-v45 brains had
   * no notability column; migration v46 backfills with default 'medium'.
   */
  notability: 'high' | 'medium' | 'low';
  context: string | null;
  valid_from: Date;
  valid_until: Date | null;
  expired_at: Date | null;
  superseded_by: number | null;
  consolidated_at: Date | null;
  consolidated_into: number | null;
  source: string;
  source_session: string | null;
  confidence: number;
  embedding: Float32Array | null;
  embedded_at: Date | null;
  created_at: Date;
}

/** Input for insertFact. source_id supplied via the ctx arg. */
export interface NewFact {
  fact: string;
  kind?: FactKind;                     // default 'fact'
  entity_slug?: string | null;
  visibility?: FactVisibility;          // default 'private'
  context?: string | null;
  valid_from?: Date;                   // default now()
  valid_until?: Date | null;
  source: string;                       // 'mcp:put_page' | 'mcp:extract_facts' | 'cli:think' | etc
  source_session?: string | null;
  confidence?: number;                  // [0,1], default 1.0
  notability?: 'high' | 'medium' | 'low'; // salience filter for extraction gate
  embedding?: Float32Array | null;     // pre-computed; if null, insertFact computes via gateway
  /**
   * v0.35.4 (D-CDX-5) — typed-claim fields. Optional. When populated,
   * `gbrain eval trajectory` + `find_trajectory` MCP op consume them for
   * chronological regression detection and drift_score. `claim_metric` is
   * normalized to lowercase snake_case by the extraction layer before
   * this method sees it; the engine stores verbatim.
   */
  claim_metric?: string | null;
  claim_value?: number | null;
  claim_unit?: string | null;
  claim_period?: string | null;
  /**
   * v0.40.2.0 — event-shaped row marker ('meeting', 'job_change',
   * 'location_change', etc). Mutually informational with `claim_metric`:
   * a row can have either, both, or neither. Persisted into
   * `facts.event_type` (migration v89). Existing callers don't need to
   * set this — leaving it undefined preserves pre-v0.40 behavior.
   */
  event_type?: string | null;
}

/** Options shared by list-facts methods. */
export interface FactListOpts {
  /** Hide expired_at IS NOT NULL rows. Default true. */
  activeOnly?: boolean;
  limit?: number;
  offset?: number;
  /** Restrict to specific kinds. Default: all kinds. */
  kinds?: FactKind[];
  /**
   * Visibility filter. When undefined, returns all. When set, only matches
   * are returned. Remote (untrusted) callers must supply ['world'].
   */
  visibility?: FactVisibility[];
}

/** Per-source operational health snapshot consumed by `gbrain doctor`. */
export interface FactsHealth {
  source_id: string;
  total_active: number;          // facts where expired_at IS NULL
  total_today: number;           // created in last 24h
  total_week: number;            // created in last 7d
  total_expired: number;         // expired_at IS NOT NULL
  total_consolidated: number;    // consolidated_at IS NOT NULL
  top_entities: Array<{ entity_slug: string; count: number }>;
  /** Optional counters fed by the queue / classifier — populated when those modules report. */
  drop_counter?: number;
  classifier_fail_counter?: number;
  p50_latency_ms?: number;
  p99_latency_ms?: number;
}

/**
 * v0.35.4 (D-CDX-6) — Options for `BrainEngine.findTrajectory`.
 *
 * `sourceId` (scalar fast path) and `sourceIds` (federated array) follow
 * the v0.34.1.0 search* pattern: when `sourceIds` is set the engine
 * applies `WHERE source_id = ANY($N::text[])`; otherwise scalar predicate
 * with `sourceId ?? 'default'`.
 *
 * `remote` (D-CDX-1) gates the visibility filter: when true the engine
 * adds `AND visibility = 'world'`, mirroring `recall`'s posture for
 * untrusted callers. Local CLI keeps `remote: false` and sees both
 * private + world facts.
 */
export interface TrajectoryOpts {
  entitySlug: string;
  /** Single-source scope; default 'default' when both this and sourceIds are unset. */
  sourceId?: string;
  /** Federated array scope (mutually exclusive with sourceId; the array wins when set). */
  sourceIds?: string[];
  /** When true, filters to visibility='world' only. Set by MCP layer from ctx.remote. */
  remote?: boolean;
  /** Metric filter. When set, only facts with this canonical metric label participate. */
  metric?: string;
  /**
   * v0.40.2.0 — kind filter. Default 'all'. Defensive opt that future-proofs
   * the API now that event_type rows live alongside metric rows in the same
   * table. Existing callers (founder-scorecard, eval-trajectory) pass
   * 'metric' explicitly for clarity (no behavior change since their
   * downstream math already skips NULL-metric rows). Richer event-shape
   * filtering (job_change vs meeting vs location) is a v0.40.3+ TODO once
   * the event schema gets structured fields.
   *   - 'metric': only rows with claim_metric IS NOT NULL
   *   - 'event':  only rows with event_type IS NOT NULL
   *   - 'all':    both (default)
   */
  kind?: 'metric' | 'event' | 'all';
  /** Lower bound on valid_from (inclusive). YYYY-MM-DD or full ISO. */
  since?: string | Date;
  /** Upper bound on valid_from (inclusive). YYYY-MM-DD or full ISO. */
  until?: string | Date;
  /** Cap on points returned. Default 100, max 500. */
  limit?: number;
}

/**
 * A single point in an entity's claim trajectory. Carries the typed-claim
 * fields when populated (drives regression detection), the underlying
 * fact text (for display), provenance (source_session, source_markdown_slug),
 * and the raw embedding so the caller can compute drift_score without a
 * second SQL round-trip.
 */
export interface TrajectoryPoint {
  fact_id: number;
  valid_from: Date;
  metric: string | null;
  value: number | null;
  unit: string | null;
  period: string | null;
  /**
   * v0.40.2.0 — event-shaped row marker (e.g. 'meeting', 'job_change',
   * 'location_change'). Mutually informational with metric: a row can have
   * (a) metric set + event_type null (typed claim like MRR=$50K),
   * (b) metric null + event_type set (event like "last met Marco"), or
   * (c) both null (legacy free-text fact row from pre-v0.35.4 brains).
   * Both founder-scorecard's per-metric math and eval-trajectory's
   * regression analysis already skip null-metric rows, so event-only
   * rows ride through invisibly to those callers.
   */
  event_type: string | null;
  text: string;
  source_session: string | null;
  source_markdown_slug: string | null;
  /** Raw embedding for drift computation; null when the fact was inserted without one. */
  embedding: Float32Array | null;
}

/** Maximum results returned by search operations. Internal bulk operations (listPages) are not clamped. */
export const MAX_SEARCH_LIMIT = 100;

/** Clamp a user-provided search limit to a safe range. */
export function clampSearchLimit(limit: number | undefined, defaultLimit = 20, cap = MAX_SEARCH_LIMIT): number {
  if (limit === undefined || limit === null || !Number.isFinite(limit) || Number.isNaN(limit)) return defaultLimit;
  if (limit <= 0) return defaultLimit;
  return Math.min(Math.floor(limit), cap);
}

export interface BrainEngine {
  /** Discriminator: lets migrations and other consumers branch on engine kind without instanceof + dynamic imports. */
  readonly kind: 'postgres' | 'pglite';

  // Lifecycle
  connect(config: EngineConfig): Promise<void>;
  disconnect(): Promise<void>;
  initSchema(): Promise<void>;
  transaction<T>(fn: (engine: BrainEngine) => Promise<T>): Promise<T>;
  /**
   * Run `fn` with a dedicated connection (Postgres: reserved backend;
   * PGLite: pass-through). See `ReservedConnection` for semantics and
   * usage constraints. Release is automatic.
   */
  withReservedConnection<T>(fn: (conn: ReservedConnection) => Promise<T>): Promise<T>;

  // Pages CRUD
  /**
   * Fetch a page by slug.
   * v0.26.5: by default soft-deleted rows return null (matches the search
   * filter contract). Pass `opts.includeDeleted: true` to surface them with
   * `deleted_at` populated — used by `gbrain pages purge-deleted` listing,
   * by `restore_page` flow, and by operator diagnostics.
   */
  getPage(slug: string, opts?: GetPageOpts): Promise<Page | null>;
  /**
   * Insert or update a page. When `opts.sourceId` is omitted, the row is
   * written under the schema DEFAULT ('default'). When provided, `source_id`
   * is included in the INSERT column list so ON CONFLICT (source_id, slug)
   * DO UPDATE actually targets the intended row instead of fabricating a
   * duplicate at (default, slug). Multi-source brains MUST pass sourceId.
   */
  putPage(slug: string, page: PageInput, opts?: { sourceId?: string }): Promise<Page>;
  /**
   * v0.41.13 (#1309) — identity-based dedup pre-check for the import pipeline.
   *
   * Returns the first matching `{slug, id}` whose `(source_id, …)` matches
   * the supplied identity signal, OR null when nothing matches.
   *
   * Identity precedence (a row matches if EITHER fires):
   *   - `content_hash = $hash` AND `deleted_at IS NULL`
   *   - `frontmatter->>'id' = $frontmatterId` AND `$frontmatterId IS NOT NULL`
   *     AND `deleted_at IS NULL`
   *
   * Background: the overlapping-ingest-roots bug class (infiniteGameExp,
   * issue #1309) created two pages per file when a user ran `gbrain import
   * /vault/Subdir/` then `gbrain import /vault/` — the slug-shape changed
   * but the content + external ID were identical. Pre-fix, the import
   * pipeline dedup-checked by `getPage(slug)` alone and missed the
   * cross-slug duplicate. This method gives the importer a deterministic
   * way to identify true duplicates BEFORE insert.
   *
   * Per codex review: the optional `?` shape lets existing test doubles
   * compile without changes. Callers must defensively check
   * `engine.findDuplicatePage?.(...)` and fall through on undefined.
   * `deleted_at IS NULL` is deliberate — a soft-deleted page should NOT
   * block a legitimate re-import under a new slug.
   */
  findDuplicatePage?(
    sourceId: string,
    opts: { hash: string; frontmatterId?: string | null },
  ): Promise<{ slug: string; id: number } | null>;
  /**
   * Hard-delete a page row. Cascades to content_chunks, page_links,
   * chunk_relations via existing FK ON DELETE CASCADE.
   *
   * v0.26.5: this is no longer the public-facing `delete_page` op handler —
   * the op now soft-deletes via `softDeletePage` instead. `deletePage` stays
   * as the underlying primitive used by `purgeDeletedPages` and by callers
   * that explicitly want hard-delete semantics (e.g. test setup teardown).
   */
  /**
   * v0.18.0+ multi-source: `opts.sourceId` scopes the DELETE so a source-A
   * delete doesn't hard-delete the same-slug pages in sources B/C/D. Without
   * it, the bare DELETE matches every row with that slug across all sources.
   * Cascades through content_chunks / page_links / chunk_relations via FKs.
   *
   * v0.41.19.0 (CDX-11): single-row primitive used by `purgeDeletedPages`,
   * `gbrain sync` (one path per call), test setup teardown, and the v0.41.19.0
   * sync-delete decompose path (when `deletePages` throws on a 500-row batch,
   * the sync loop falls back to per-slug `deletePage` to log unrecoverable
   * failures to `failedFiles`). `gbrain sync` calls this on EVERY run that
   * sees a deleted file — it is NOT admin-only.
   */
  deletePage(slug: string, opts?: { sourceId?: string }): Promise<void>;
  /**
   * v0.41.19.0 — batch delete: single SQL round-trip via
   * `DELETE FROM pages WHERE slug = ANY($1::text[]) AND source_id = $2
   *  RETURNING slug`. Cascades through content_chunks / page_links (×3) /
   * tags / raw_data / timeline_entries / page_versions via FKs declared in
   * `src/schema.sql`. `files.page_id` and `links.origin_page_id` go SET
   * NULL per their FK definitions.
   *
   * SINGLE-BATCH PRIMITIVE: caller is responsible for chunking the input to
   * `<= DELETE_BATCH_SIZE` entries per call (see
   * `src/core/engine-constants.ts`). Matches the `addLinksBatch` convention
   * — engine assumes well-behaved input, caller owns the slicing.
   *
   * Returns the slugs of rows ACTUALLY DELETED (order undefined). Callers
   * use this to filter their own `pagesAffected` tracking so downstream
   * phases don't waste lookups on phantom slugs (paths that were in the
   * deletion list but had no DB row).
   *
   * ATOMICITY: one statement, one transaction. The whole batch commits or
   * the whole batch rolls back. Coarser than the per-row `deletePage`
   * cadence — a mid-loop abort or transient connection failure can roll
   * back up to `DELETE_BATCH_SIZE - 1` successful deletes from the
   * in-flight batch. `gbrain sync` is idempotent (next run picks them up
   * via git diff); other callers should account for the contract.
   *
   * sourceId is REQUIRED (no `'default'` fallback). This is asymmetric with
   * `deletePage` (which keeps the optional/'default' fallback for back-
   * compat). Filed as v0.42+ TODO to tighten `deletePage` to match once a
   * full caller audit confirms every site threads `sourceId`.
   */
  deletePages(slugs: string[], opts: { sourceId: string }): Promise<string[]>;
  /**
   * v0.41.19.0 — batch path → slug resolution. Single SQL round-trip via
   * `SELECT slug, source_path FROM pages WHERE source_path = ANY($1::text[])
   *  AND source_id = $2`. Returns `Map<path, slug>`; paths NOT in the map
   * have no `source_path` row in the DB and the caller is expected to fall
   * back to `resolveSlugForPath(path)` for the path-derived slug.
   *
   * Mirrors the contract of the single-call `resolveSlugByPathOrSourcePath`
   * helper in `src/commands/sync.ts`, batched. As of v0.41.19.0, that
   * single-call helper is implemented on top of this method (one Map
   * allocation per single-path call; negligible cost; one owner of the SQL
   * + fallback semantics).
   *
   * SINGLE-BATCH PRIMITIVE: caller chunks to `<= DELETE_BATCH_SIZE`.
   *
   * Empty `paths` short-circuits to an empty Map without touching the DB.
   */
  resolveSlugsByPaths(
    paths: string[],
    opts: { sourceId: string },
  ): Promise<Map<string, string>>;
  /**
   * v0.26.5 — set `deleted_at = now()` on a page. Returns the slug if a row
   * was soft-deleted, null if no row matched (already soft-deleted OR not found).
   * Idempotent-as-null. The page stays in the DB and cascade rows (chunks,
   * links) stay intact; the autopilot purge phase hard-deletes after 72h.
   */
  softDeletePage(slug: string, opts?: { sourceId?: string }): Promise<{ slug: string } | null>;
  /**
   * v0.26.5 — clear `deleted_at` on a soft-deleted page. Returns true iff a
   * row was restored. False if the slug is unknown OR the page is not
   * currently soft-deleted (idempotent-as-false).
   */
  restorePage(slug: string, opts?: { sourceId?: string }): Promise<boolean>;
  /**
   * v0.26.5 — hard-delete pages whose `deleted_at` is older than the cutoff.
   * Called by the autopilot purge phase and by the `gbrain pages purge-deleted`
   * CLI escape hatch. Cascades through existing FKs.
   */
  purgeDeletedPages(olderThanHours: number): Promise<{ slugs: string[]; count: number }>;
  /**
   * v0.26.5: by default `listPages` excludes soft-deleted rows. Set
   * `filters.includeDeleted: true` to surface them.
   */
  listPages(filters?: PageFilters): Promise<Page[]>;
  /**
   * Fuzzy slug resolver.
   *
   * v0.41.13 (#1436): `opts.sourceId` scopes the search to a single source;
   * `opts.sourceIds` to an array (federated_read OAuth tier). Pre-fix the
   * resolver was unscoped, so MCP `get_page` with `fuzzy: true` would
   * return candidates from sources the caller couldn't actually access.
   * Source-bleed via fuzzy resolution was the bug class infiniteGameExp
   * reported as #1436. When neither opt is set, the original unscoped
   * behavior is preserved for back-compat with internal callers (the
   * `gbrain query --resolve` CLI path, etc.). Field names match the
   * `sourceScopeOpts(ctx)` helper output so callers can spread directly.
   */
  resolveSlugs(partial: string, opts?: { sourceId?: string; sourceIds?: string[] }): Promise<string[]>;
  /**
   * Returns the slug of every page in the brain. Used by batch commands as a
   * mutation-immune iteration source (alternative to listPages OFFSET pagination,
   * which is unstable when ordering by updated_at and writes are happening).
   *
   * v0.31.8 (D12): `opts.sourceId` scopes the result to a single source
   * (used by the source-aware reconcileLinks path so wikilink resolution
   * doesn't span unrelated sources). When omitted, returns the union of
   * slugs across every source (pre-v0.31.8 behavior).
   */
  getAllSlugs(opts?: { sourceId?: string }): Promise<Set<string>>;

  /**
   * v0.32.8: cross-source page enumeration. Returns one row per (slug,
   * source_id) pair across the brain, ordered by (source_id, slug) for
   * deterministic iteration on large brains. Used by extract-takes,
   * extract, and integrity to replace the `getAllSlugs() → getPage(slug)`
   * N+1 pattern, which silently defaulted to source_id='default' and
   * skipped non-default-source pages.
   *
   * Cheap by design: only slug + source_id, not the full Page row. For
   * loops that need page.compiled_truth / timeline / frontmatter, use
   * `forEachPage` from src/core/engine-iter.ts instead.
   */
  listAllPageRefs(): Promise<Array<{ slug: string; source_id: string }>>;

  /**
   * v0.38 — lean per-source enumeration for hot-loop callers (autopilot
   * dispatch, doctor freshness check). Returns the bare row shape sources-ops
   * needs without the N+1 per-source page_count enrichment in
   * `sources-ops.listSources`.
   *
   * Defaults filter out archived sources. When `localPathOnly` is true,
   * also filters `local_path IS NOT NULL` so the autopilot fan-out doesn't
   * dispatch jobs for pure-DB sources whose handler would fall back to
   * the global sync.repo_path (codex r1 P1-4).
   *
   * `config` is returned as `Record<string, unknown>` — both engines
   * already parse the JSONB at the boundary (Postgres-js returns
   * parsed objects; PGLite returns objects via its built-in JSONB
   * codec). Callers reading `config['last_full_cycle_at']` get a string.
   */
  listAllSources(opts?: {
    includeArchived?: boolean;
    localPathOnly?: boolean;
  }): Promise<SourceRow[]>;

  /**
   * v0.38 — atomic JSONB merge into sources.config. Uses Postgres's
   * `config || $patch::jsonb` operator so concurrent writers don't
   * stomp each other (last write wins, but no read-modify-write race).
   *
   * Primary caller: runCycle's exit hook writes
   *   { last_full_cycle_at: '<ISO>' }
   * after a successful per-source cycle so autopilot's freshness gate
   * can read it next tick. Resolves codex round-1 P0-5 (write site for
   * last_full_cycle_at was unspecified pre-PR).
   *
   * Returns true if a row was updated (source exists), false otherwise
   * (silently no-ops on unknown sourceId — caller decides whether that's
   * a problem).
   */
  updateSourceConfig(sourceId: string, patch: Record<string, unknown>): Promise<boolean>;

  /**
   * v0.37.0 — prefix-stratified page sampling for `gbrain brainstorm` / `gbrain lsd`
   * domain-bank module. Takes a caller-supplied prefix list (cached at the domain-bank
   * layer per D3), returns one page per prefix tiebroken by `connection_count`
   * (LEFT JOIN to page_links, count of inbound links).
   *
   * Stale-bias (D5 / LSD): when `opts.staleBias === true`, ROW_NUMBER() ORDER BY
   * prefers pages with `last_retrieved_at IS NULL` (never retrieved) > pages older
   * than `staleThresholdDays` (default 90) > recently-retrieved.
   *
   * Source scoping (D5, codex r2 #2 fix): `sourceId` (scalar) and `sourceIds`
   * (array, wins over scalar) per the [source-id-canonical-thread] pattern.
   * Both threaded from day 1 even though v0.37.0 callers are CLI-local — D7
   * MCP exposure ships zero-refactor.
   *
   * Soft-deleted pages (deleted_at IS NOT NULL) excluded automatically.
   */
  listPrefixSampledPages(opts: DomainBankSampleOpts): Promise<DomainBankRow[]>;

  /**
   * v0.37.0 — corpus-sampling fallback for `gbrain brainstorm` when prefix-stratified
   * can't fill M (small brain, single-prefix corpus). Random sample of N pages with
   * the same exclusion + source-scope semantics as `listPrefixSampledPages`.
   * Deterministic with `opts.seed` set; falls back to RANDOM() otherwise.
   *
   * Returns the same `DomainBankRow` shape so the orchestrator can union both
   * sources of pages and dedup by slug+source_id.
   */
  listCorpusSample(opts: CorpusSampleOpts): Promise<DomainBankRow[]>;

  // Search
  searchKeyword(query: string, opts?: SearchOpts): Promise<SearchResult[]>;
  searchVector(embedding: Float32Array, opts?: SearchOpts): Promise<SearchResult[]>;
  /**
   * Hydrate embeddings for chunks already known by id. v0.36 (D9):
   * optional `column` parameter selects which content_chunks column to
   * fetch from (default 'embedding'). The dynamic-embedding-column
   * search path hands its resolved column name here so cosineReScore
   * rehydrates in the right embedding space — otherwise vector search
   * against `embedding_voyage` would HNSW-rank against Voyage but
   * rescore against OpenAI vectors (NaN / wrong rankings).
   *
   * The column name MUST be regex-validated by the caller (resolveEmbed-
   * dingColumn rejects bad names). Engines identifier-quote on
   * interpolation as defense in depth (D12).
   */
  getEmbeddingsByChunkIds(ids: number[], column?: string): Promise<Map<number, Float32Array>>;

  // Chunks
  /**
   * Replace the chunk set for a page. Internal page-id lookup is sourceId-
   * scoped when `opts.sourceId` is given; without it, the schema DEFAULT
   * matches and bare-slug lookup blows up if the same slug exists in
   * multiple sources (Postgres 21000).
   */
  /**
   * v0.41.18.0: internal SQL wrapped in `withRetry(BULK_RETRY_OPTS)` against
   * transient connection errors (Supavisor circuit-breaker recovery).
   * Idempotent under replay via single-statement DELETE+INSERT in implicit tx
   * — Postgres rolls back automatically on conn drop, so commit-ambiguous
   * failure replays to the same end state. Callers MUST NOT wrap externally;
   * see {@link BatchOpts} retry-contract block.
   */
  upsertChunks(slug: string, chunks: ChunkInput[], opts?: { sourceId?: string } & BatchOpts): Promise<void>;
  /**
   * Read every chunk for a page. `opts.sourceId` source-scopes the page
   * lookup; without it, multi-source brains return chunks from every
   * same-slug source (importCodeFile uses this for incremental embedding
   * reuse, which would then attach the wrong source's embeddings).
   */
  getChunks(slug: string, opts?: { sourceId?: string }): Promise<Chunk[]>;
  /**
   * Count chunks across the brain where embedding IS NULL.
   * Pre-flight short-circuit for `embed --stale` so a 100%-embedded brain
   * does no further work after a single SELECT count(*) (~50 bytes wire).
   *
   * `opts.sourceId` scopes the count to a single source. When omitted,
   * counts across every source in the brain. Operators running
   * `gbrain embed --stale --source media-corpus` expect only that
   * source's NULLs touched; the caller threads `sourceId` here.
   */
  countStaleChunks(opts?: { sourceId?: string; signature?: string }): Promise<number>;
  /**
   * Sum of LENGTH(chunk_text) over stale chunks — the character-count
   * backlog the embed phase / embed-backfill will process. Sibling of
   * countStaleChunks (same stale predicate + embed_skip filter + optional
   * sourceId scope); used by the `gbrain sync --all` cost preview to price
   * the embedding backlog via estimateCostFromChars. Returns 0 on an
   * empty/fully-embedded brain.
   *
   * v0.41.31: `signature` (optional) widens "stale" to ALSO include chunks
   * whose page `embedding_signature` is set AND differs from the current
   * model signature (a model/dims swap). NULL signature is GRANDFATHERED
   * (never counted) so the post-migration corpus isn't flagged en masse.
   * Omit `signature` for the legacy `embedding IS NULL`-only count.
   */
  sumStaleChunkChars(opts?: { sourceId?: string; signature?: string }): Promise<number>;
  /**
   * Stamp `pages.embedding_signature = signature` for one page. Called after
   * a page's chunks are (re)embedded so a later model swap can detect it as
   * stale. Idempotent. No-op if the page doesn't exist.
   */
  setPageEmbeddingSignature(slug: string, opts: { sourceId?: string; signature: string }): Promise<void>;
  /**
   * NULL out the embeddings (and embedded_at) of every chunk whose page
   * `embedding_signature` is set AND differs from `signature` — i.e. pages
   * embedded under a now-stale model. Returns the chunk count invalidated.
   * The embed-stale loop calls this BEFORE listStaleChunks so signature-
   * drift pages flow through the existing NULL-embedding cursor (keeps
   * listStaleChunks's keyset pagination untouched). GRANDFATHER: NULL
   * signature is never invalidated. `sourceId` scopes the sweep.
   */
  invalidateStaleSignatureEmbeddings(opts: { signature: string; sourceId?: string }): Promise<number>;
  /**
   * Return every chunk where embedding IS NULL, with the metadata needed
   * to call embedBatch + upsertChunks. The `embedding` column is omitted
   * by design — stale rows have NULL embeddings, so shipping them wastes
   * wire bytes for no gain. Caller groups by slug, embeds, and re-upserts.
   *
   * v0.33.3: cursor-paginated — yields up to `batchSize` rows per call
   * (default 2000) to stay within Supabase's statement_timeout. Pass the
   * last row's `(page_id, chunk_index)` as `afterPageId`/`afterChunkIndex`
   * to fetch the next page.  When fewer than `batchSize` rows come back,
   * the caller has reached the end.
   *
   * `opts.sourceId` scopes the scan to a single source (matches the
   * countStaleChunks contract). Paired with embedAllStale's --source
   * support.
   */
  listStaleChunks(opts?: {
    batchSize?: number;
    afterPageId?: number;
    afterChunkIndex?: number;
    sourceId?: string;
    // v0.41.18.0 (A13, codex #9): pagination order. Default 'page_id'
    // (legacy stable cursor). 'updated_desc' joins pages and orders by
    // p.updated_at DESC NULLS LAST, p.id, cc.chunk_index — backed by
    // idx_pages_updated_at_desc + content_chunks_stale_idx partial.
    orderBy?: 'page_id' | 'updated_desc';
    // For 'updated_desc' cursor: previous row's updated_at, page_id, chunk_index.
    // ISO-8601 string for cross-engine compatibility (postgres.js + PGLite
    // both round-trip TIMESTAMPTZ as Date | string; ISO string is the
    // common denominator on the wire).
    afterUpdatedAt?: string | null;
  }): Promise<StaleChunkRow[]>;
  /**
   * Delete every chunk for a page. Internal page-id lookup is sourceId-scoped
   * when `opts.sourceId` is given; otherwise the bare-slug subquery returns
   * the wrong row count in multi-source brains.
   */
  deleteChunks(slug: string, opts?: { sourceId?: string }): Promise<void>;

  // ============================================================
  // v0.42.7 (#1696): link/timeline extraction freshness watermark.
  // A page is stale for extraction when its links_extracted_at is NULL,
  // older than the extractor version stamp, or older than its updated_at
  // (edited-since-extract — the MCP put_page / sync --no-extract path).
  // Powers `gbrain extract --stale` + the `links_extraction_lag` doctor check.
  // ============================================================
  /**
   * Count pages needing (re)extraction. `versionTs` is the ISO-8601
   * `LINK_EXTRACTOR_VERSION_TS` string (bound `::timestamptz`); when omitted,
   * only the NULL + edited-since arms apply. Soft-deleted pages excluded.
   */
  countStalePagesForExtraction(opts?: { sourceId?: string; versionTs?: string }): Promise<number>;
  /**
   * List a keyset page (ordered by `id`, `id > afterPageId`) of stale pages
   * WITH their content so the caller extracts without an N+1 `getPage`. Same
   * stale predicate as countStalePagesForExtraction. Caller passes a SMALL
   * batchSize (page bodies are unbounded — 25MB transcript pages exist) and
   * applies its own per-batch byte budget.
   */
  listStalePagesForExtraction(opts: {
    batchSize: number;
    afterPageId?: number;
    sourceId?: string;
    versionTs?: string;
  }): Promise<StalePageRow[]>;
  /**
   * Stamp `links_extracted_at` for a batch of pages keyed on the unique
   * `(slug, source_id)` pair (unnest idiom, mirrors addLinksBatch).
   * Short-circuits on empty input. Called AFTER the link/timeline flush so a
   * crash mid-batch leaves pages unstamped and they re-extract next run.
   *
   * Each ref may carry its own `extractedAt`; refs that omit it use the
   * `defaultExtractedAt` arg. `gbrain extract --stale` passes the row's READ
   * `updated_at` per ref (v0.42.7 D4 race fix) so a concurrent edit landing
   * between the SELECT and this stamp advances `updated_at` past the stamped
   * value → the page stays stale → re-extracted next run, never marked
   * fresh-with-the-old-content. Sync / DB-extract sites omit per-ref values and
   * pass `now()` (the page was just imported, so `now() >= updated_at`).
   */
  markPagesExtractedBatch(refs: Array<{ slug: string; source_id: string; extractedAt?: string }>, defaultExtractedAt: string): Promise<void>;

  // Links
  /**
   * Single-row link insert. linkSource defaults to 'markdown' for back-compat
   * with pre-v0.13 callers. Pass 'frontmatter' + originSlug + originField for
   * frontmatter-derived edges; 'manual' for user-initiated edges.
   */
  /**
   * v0.18.0+ multi-source: each endpoint can live in a different source.
   * `opts.fromSourceId` / `opts.toSourceId` / `opts.originSourceId` default to
   * 'default'. Without these, the original cross-product `FROM pages f, pages t`
   * fanned out across every source containing the slug.
   */
  addLink(
    from: string,
    to: string,
    context?: string,
    linkType?: string,
    linkSource?: string,
    originSlug?: string,
    originField?: string,
    opts?: { fromSourceId?: string; toSourceId?: string; originSourceId?: string },
  ): Promise<void>;
  /**
   * Bulk insert links via a single multi-row INSERT...SELECT FROM (VALUES) JOIN pages
   * statement with ON CONFLICT DO NOTHING. Returns the count of rows actually inserted
   * (RETURNING clause excludes conflicts and JOIN-dropped rows whose slugs don't exist).
   * Used by extract.ts to avoid 47K sequential round-trips on large brains.
   */
  /**
   * v0.41.18.0: internal SQL wrapped in `withRetry(BULK_RETRY_OPTS)`.
   * Idempotent via `ON CONFLICT (from_page_id, to_page_id, link_type,
   * link_source, origin_page_id) DO NOTHING` — composite key is the semantic
   * uniqueness. Replay-after-partial-success: 2nd attempt finds conflicts,
   * returns 0 from RETURNING. Caller-visible edge: linksCreated undercounts
   * on commit-ambiguous replay. Cosmetic (audit JSONL captures the truth).
   * Callers MUST NOT wrap externally; see {@link BatchOpts} retry contract.
   */
  addLinksBatch(links: LinkBatchInput[], opts?: BatchOpts): Promise<number>;
  /**
   * Remove links from `from` to `to`. If linkType is provided, only that specific
   * (from, to, type) row is removed. If omitted, ALL link types between the pair
   * are removed (matches pre-multi-type-link behavior). linkSource additionally
   * constrains the delete to a specific provenance ('frontmatter', 'markdown',
   * 'manual') — used by runAutoLink reconciliation to avoid deleting edges from
   * other provenances when pruning frontmatter-derived edges.
   */
  removeLink(
    from: string,
    to: string,
    linkType?: string,
    linkSource?: string,
    opts?: { fromSourceId?: string; toSourceId?: string },
  ): Promise<void>;
  /**
   * v0.31.8 (D12 + D16): `opts.sourceId` source-scopes the from-page lookup.
   * When omitted, the read returns links from every same-slug page across
   * sources (pre-v0.31.8 behavior; preserved via two-branch query in both
   * engines). When set, the from-page filter becomes
   * `WHERE f.slug = $1 AND f.source_id = $X`.
   */
  getLinks(slug: string, opts?: { sourceId?: string }): Promise<Link[]>;
  /**
   * v0.31.8 (D12 + D16): same `opts.sourceId` semantics as `getLinks`,
   * applied to the to-page side of the join.
   */
  getBacklinks(slug: string, opts?: { sourceId?: string }): Promise<Link[]>;
  /**
   * Fuzzy-match a display name to a page slug using pg_trgm similarity.
   * Zero embedding cost, zero LLM cost — designed for the v0.13 resolver used
   * during migration/batch backfill where 5K+ lookups must stay sub-second.
   *
   * Returns the best match whose title similarity is at or above `minSimilarity`
   * (default 0.55). If `dirPrefix` is given (e.g. 'people' or 'companies'),
   * only slugs starting with that prefix are considered. Returns null when no
   * page meets the threshold.
   *
   * Uses the `%` trigram operator (GIN-indexed) + the standard `similarity()`
   * function. Both engines support pg_trgm (PGLite 0.3+, Postgres always).
   */
  findByTitleFuzzy(
    name: string,
    dirPrefix?: string,
    minSimilarity?: number,
  ): Promise<{ slug: string; similarity: number } | null>;
  /**
   * v0.34.1 (#861 — P0 leak seal): `opts.sourceId` / `opts.sourceIds`
   * constrain visited nodes to a single source or array of sources.
   * Pre-fix, the walk ignored source scope and an authenticated MCP
   * client could enumerate cross-source topology + page metadata via
   * the graph op. MCP-bound callers MUST pass the auth'd scope; local
   * CLI callers omit it for the historical unscoped behavior.
   */
  traverseGraph(
    slug: string,
    depth?: number,
    opts?: TraverseGraphOpts,
  ): Promise<GraphNode[]>;
  /**
   * Edge-based graph traversal with optional type and direction filters.
   * Returns a list of edges (GraphPath[]) instead of nodes. Supports:
   * - linkType: per-edge filter, only follows matching edges (per-edge semantics)
   * - direction: 'in' (follow to->from), 'out' (follow from->to), 'both'
   * - depth: max depth from root (default 5)
   * - sourceId/sourceIds: v0.34.1 source-isolation filter, see traverseGraph
   * Uses cycle prevention (visited array in recursive CTE).
   */
  traversePaths(
    slug: string,
    opts?: { depth?: number; linkType?: string; direction?: 'in' | 'out' | 'both'; sourceId?: string; sourceIds?: string[] },
  ): Promise<GraphPath[]>;
  /**
   * For a list of slugs, return how many inbound links each has.
   * Used by hybrid search backlink boost. Single SQL query, not N+1.
   * Slugs with zero inbound links are present in the map with value 0.
   */
  getBacklinkCounts(slugs: string[]): Promise<Map<string, number>>;
  /**
   * v0.40.4 — for a list of page_ids, return adjacency aggregates
   * restricted to the subgraph induced by them. Returns ALL pages with
   * `hits >= 1` (callers apply their own threshold). Empty input → empty
   * Map, no SQL.
   *
   * Returned shape per page (AdjacencyRow):
   *   - `hits`: distinct from_page_id count, in-set
   *   - `cross_source_hits`: distinct OTHER source_ids count (excluding
   *     target's own source), in-set
   *
   * SOURCE-SCOPE CONTRACT: pageIds MUST already be source-scoped by the
   * caller. This method does NOT filter by source_id. Adjacency is
   * page-id keyed and the in-set restriction makes cross-source leakage
   * impossible BY CONSTRUCTION (a leaked-in page_id from another source
   * would have to also appear in the caller's input set, which the
   * caller is responsible for preventing). The only consumer in v0.40.4
   * is hybridSearch via runPostFusionStages, which is source-scoped
   * upstream. Same trust posture as `cosineReScore`'s chunk_id handling.
   *
   * Known limitation: cross_source_hits doesn't distinguish "genuinely
   * linked from another team" from "mirrored imports from another
   * source" (codex outside-voice #15). T-todo-4 captures the v0.41+
   * sync-topology-aware refinement.
   */
  getAdjacencyBoosts(pageIds: number[]): Promise<Map<number, AdjacencyRow>>;
  /**
   * v0.42 (issue #1699): for a list of page_ids, return their
   * `frontmatter.content_flag` markers (reason + detail). Used by hybrid
   * search to stamp `SearchResult.content_flag` post-fusion — the
   * agent-warning channel for fuzzy markup-heavy / oversize pages that
   * stay searchable. Single SQL query, not N+1. Pages without the marker
   * get no entry in the map. Empty input → empty map (no query).
   */
  getContentFlagsByPageIds(
    pageIds: number[],
  ): Promise<Map<number, { reason: string; detail: string }>>;
  /**
   * v0.27.0: for a list of slugs, return their updated_at timestamps (or created_at fallback).
   * Used by hybrid search recency boost. Single SQL query, not N+1.
   * Slugs with no timestamp get no entry in the map.
   *
   * @deprecated v0.29.1: prefer getEffectiveDates (composite-keyed, multi-source-safe).
   * Kept for back-compat with PR #618 callers.
   */
  getPageTimestamps(slugs: string[]): Promise<Map<string, Date>>;
  /**
   * v0.29.1: for a list of (slug, source_id) refs, return COALESCE(effective_date,
   * updated_at) per ref. Single SQL query. Composite-keyed map (key format:
   * `${source_id}::${slug}`) so multi-source brains don't conflate pages with
   * the same slug across sources (codex pass-1 finding #3).
   *
   * Drives the new applyRecencyBoost post-fusion stage. Returns NULL for refs
   * with no row; map omits them.
   */
  getEffectiveDates(refs: Array<{slug: string; source_id: string}>): Promise<Map<string, Date>>;
  /**
   * v0.29.1: for a list of (slug, source_id) refs, return the salience score
   * (emotional_weight × 5 + ln(1 + take_count)) per ref. Single SQL query.
   * Composite-keyed (`${source_id}::${slug}`) like getEffectiveDates.
   *
   * Drives the new applySalienceBoost post-fusion stage. Pages with no row
   * (or zero emotional_weight + zero takes) get score = 0; the boost stage
   * skips them.
   */
  getSalienceScores(refs: Array<{slug: string; source_id: string}>): Promise<Map<string, number>>;
  /**
   * Return every page with no inbound links.
   * Domain comes from the frontmatter `domain` field (null if unset).
   * The caller filters pseudo-pages + derives display domain.
   * Used by `gbrain orphans` and `runCycle`'s orphan sweep phase.
   *
   * v0.41.29.0: scopes the CANDIDATE set to one source (`sourceId`, from
   * `gbrain doctor/orphans --source` + single-source MCP clients) or a
   * federated set (`sourceIds`, from `allowedSources` MCP clients). The
   * inbound-link side is NOT scoped — a page in source X linked FROM
   * source Y is genuinely reachable, so it is not an orphan of X. Omit
   * `opts` for the brain-wide behavior (unchanged). When both are set,
   * `sourceIds` wins (mirrors `sourceScopeOpts` precedence).
   */
  findOrphanPages(opts?: {
    sourceId?: string;
    sourceIds?: string[];
  }): Promise<Array<{ slug: string; title: string; domain: string | null }>>;

  // Tags
  /**
   * v0.18.0+ multi-source: `opts.sourceId` scopes the page-id lookup. When
   * omitted, the schema DEFAULT 'default' applies; in multi-source brains
   * with the same slug across sources the bare-slug lookup returns >1 row
   * and the INSERT/DELETE fails with Postgres 21000.
   */
  addTag(slug: string, tag: string, opts?: { sourceId?: string }): Promise<void>;
  removeTag(slug: string, tag: string, opts?: { sourceId?: string }): Promise<void>;
  getTags(slug: string, opts?: { sourceId?: string }): Promise<string[]>;

  // Timeline
  /**
   * Insert a timeline entry. By default verifies the page exists and throws if not.
   * Pass opts.skipExistenceCheck=true for batch operations where the slug is already
   * known to exist (e.g., from a getAllSlugs() snapshot). Duplicates are silently
   * deduplicated by the (page_id, date, summary) UNIQUE index (ON CONFLICT DO NOTHING).
   */
  /**
   * Insert a timeline entry. By default verifies the page exists and throws if not.
   * `opts.skipExistenceCheck` skips the pre-check for batch loops where the slug
   * is already known to exist. `opts.sourceId` source-scopes both the existence
   * check AND the page-id lookup inside the INSERT — required for multi-source
   * brains where the slug exists in 2+ sources.
   */
  addTimelineEntry(
    slug: string,
    entry: TimelineInput,
    opts?: { skipExistenceCheck?: boolean; sourceId?: string },
  ): Promise<void>;
  /**
   * Bulk insert timeline entries via a single multi-row INSERT...SELECT FROM (VALUES)
   * JOIN pages statement with ON CONFLICT DO NOTHING. Returns the count of rows
   * actually inserted (RETURNING excludes conflicts and JOIN-dropped rows whose
   * slugs don't exist). Used by extract.ts to avoid sequential round-trips.
   */
  /**
   * v0.41.18.0: internal SQL wrapped in `withRetry(BULK_RETRY_OPTS)`.
   * Idempotent via composite-key conflict (page_id, kind, when_text, body).
   * Same caller-visible undercount caveat as {@link addLinksBatch}.
   * Callers MUST NOT wrap externally; see {@link BatchOpts} retry contract.
   */
  addTimelineEntriesBatch(entries: TimelineBatchInput[], opts?: BatchOpts): Promise<number>;
  getTimeline(slug: string, opts?: TimelineOpts): Promise<TimelineEntry[]>;

  // Raw data
  /**
   * v0.31.8 (D21): `opts.sourceId` source-scopes the page-id lookup. When
   * omitted, the write targets the bare slug (pre-v0.31.8 behavior); the
   * Postgres 21000 hazard for multi-source brains exists on this path.
   * Multi-source callers MUST pass sourceId to land on the intended row.
   */
  putRawData(slug: string, source: string, data: object, opts?: { sourceId?: string }): Promise<void>;
  /**
   * v0.31.8 (D21): `opts.sourceId` source-scopes the page-id lookup. Without
   * it, multi-source brains return raw_data rows from every same-slug page
   * (preserved via two-branch query for back-compat).
   */
  getRawData(slug: string, source?: string, opts?: { sourceId?: string }): Promise<RawData[]>;

  // Files (v0.27.1: binary asset metadata + storage_path. Image bytes never
  // enter the DB; storage_path references a path inside the brain repo or an
  // external store).
  upsertFile(spec: FileSpec): Promise<{ id: number; created: boolean }>;
  getFile(sourceId: string, storagePath: string): Promise<FileRow | null>;
  listFilesForPage(pageId: number): Promise<FileRow[]>;

  // ============================================================
  // v0.28: Takes (typed/weighted/attributed claims) + synthesis evidence
  // ============================================================
  /**
   * Bulk insert/upsert takes. Uses `unnest()` (Postgres) or manual `$N`
   * placeholders (PGLite). Idempotency: ON CONFLICT (page_id, row_num) DO UPDATE
   * — re-extract on a changed claim/weight updates the row in place.
   * Returns the number of rows inserted OR updated.
   *
   * Weight outside [0, 1] is clamped server-side and surfaces a stderr
   * warning per call (`TAKES_WEIGHT_CLAMPED`). Invalid `kind` values
   * fail the whole batch via the CHECK constraint — caller is responsible
   * for parser validation upstream.
   */
  addTakesBatch(rows: TakeBatchInput[]): Promise<number>;

  /** List takes filtered by holder/kind/active/etc. Resolves page_slug via JOIN. */
  listTakes(opts?: TakesListOpts): Promise<Take[]>;

  /**
   * Keyword search across active takes. Uses pg_trgm similarity over claim text.
   * Honors `takesHoldersAllowList` via WHERE filter so MCP-bound calls cannot
   * retrieve holders outside the token's allow-list.
   */
  searchTakes(query: string, opts?: SearchOpts & { takesHoldersAllowList?: string[] }): Promise<TakeHit[]>;

  /**
   * Vector search across active takes. Cosine distance against `embedding`.
   * Skipped (returns []) when no embedding column has been populated yet.
   */
  searchTakesVector(
    embedding: Float32Array,
    opts?: SearchOpts & { takesHoldersAllowList?: string[] },
  ): Promise<TakeHit[]>;

  /** Look up embeddings by take id (mirrors getEmbeddingsByChunkIds). */
  getTakeEmbeddings(ids: number[]): Promise<Map<number, Float32Array>>;

  /** Pre-flight count for `gbrain embed --stale`. WHERE active AND embedding IS NULL. */
  countStaleTakes(): Promise<number>;

  /** List stale takes (no embedding column in payload — same pattern as listStaleChunks). */
  listStaleTakes(): Promise<StaleTakeRow[]>;

  /**
   * Update a take's mutable fields. May NOT change claim/kind/holder per the
   * supersession invariants — those route through supersedeTake. Throws
   * `TAKE_ROW_NOT_FOUND` when (page_id, row_num) doesn't exist.
   */
  updateTake(
    pageId: number,
    rowNum: number,
    fields: { weight?: number; since_date?: string; source?: string },
  ): Promise<void>;

  /**
   * Supersede the take at (page_id, oldRow). Marks old row active=false +
   * sets superseded_by; appends new row at the next row_num for the page;
   * returns both row_nums. Atomic (transactional). Cycle prevention: if newRow
   * sets superseded_by pointing to a chain that comes back to oldRow, throws
   * `TAKES_SUPERSEDE_CYCLE`. Resolved bets (`resolved_at IS NOT NULL`) cannot
   * be superseded — throws `TAKE_RESOLVED_IMMUTABLE`.
   */
  supersedeTake(
    pageId: number,
    oldRow: number,
    newRow: Omit<TakeBatchInput, 'page_id' | 'row_num' | 'superseded_by'>,
  ): Promise<{ oldRow: number; newRow: number }>;

  /**
   * Resolve a bet (or take). Sets resolved_* columns. Immutable: re-resolve
   * attempts throw `TAKE_ALREADY_RESOLVED`. Use supersede to express a new bet.
   *
   * v0.30.0: accepts either `quality` (3-state, primary) or `outcome` (boolean,
   * back-compat). When both set, `quality` wins. The engine writes BOTH columns
   * derived from whichever input was given: `quality='correct'/'incorrect'` →
   * `outcome=true/false`; `quality='partial'` → `outcome=NULL`. The schema
   * `takes_resolution_consistency` CHECK constraint catches contradictory
   * states at the DB layer as a defense-in-depth backstop.
   */
  resolveTake(pageId: number, rowNum: number, resolution: TakeResolution): Promise<void>;

  /**
   * v0.30.0: aggregate calibration scorecard. Pure SQL aggregation; no LLM.
   * Counts resolved bets, computes accuracy, Brier score (correct+incorrect
   * only), and `partial_rate`. Filtering: `holder` scopes to one identity;
   * `domainPrefix` scopes to a slug-prefix (e.g. `companies/`); `since`/`until`
   * scope to a `since_date` window.
   *
   * Privacy (D4 from plan): `allowList` is REQUIRED in the TS signature.
   * The engine applies `WHERE holder = ANY($allowList)` INSIDE the GROUP BY
   * so hidden-holder rows contribute zero to aggregates. Pass an empty array
   * to enforce zero-results; pass `undefined` only from server-side trusted
   * callers that have already verified the request is unrestricted.
   */
  getScorecard(opts: TakesScorecardOpts, allowList: string[] | undefined): Promise<TakesScorecard>;

  /**
   * v0.30.0: calibration curve. Bins resolved correct+incorrect bets by stated
   * weight (default bucket size 0.1) and reports observed vs predicted frequency
   * per bucket. Same allow-list contract as `getScorecard`. Excludes partial
   * (consistent with Brier — partial has no binary outcome to compare against).
   */
  getCalibrationCurve(opts: CalibrationCurveOpts, allowList: string[] | undefined): Promise<CalibrationBucket[]>;

  /** Persist think provenance. ON CONFLICT DO NOTHING; returns rows inserted. */
  addSynthesisEvidence(rows: SynthesisEvidenceInput[]): Promise<number>;

  // Dream-cycle significance verdict cache (v0.23).
  // Keyed by (file_path, content_hash). Distinct from raw_data, which is
  // page-scoped — transcripts being judged aren't pages yet.
  getDreamVerdict(filePath: string, contentHash: string): Promise<DreamVerdict | null>;
  putDreamVerdict(filePath: string, contentHash: string, verdict: DreamVerdictInput): Promise<void>;

  // ============================================================
  // v0.32.6 Contradiction probe — batched takes fetch + cache + trends
  // ============================================================

  /**
   * Batch fetch: for each page_id in the input array, return the page's
   * currently-active takes. Single query under the hood (`WHERE page_id =
   * ANY($1) AND active = true`); replaces the O(K) loop of listTakes calls
   * the contradiction probe would otherwise pay per probe-query.
   *
   * Returns a Map keyed on page_id; pages with no active takes get an empty
   * array (NOT undefined) so callers can avoid existence checks.
   *
   * Honors `takesHoldersAllowList` for MCP scope enforcement (mirrors
   * listTakes contract). Pass undefined from trusted local callers.
   */
  listActiveTakesForPages(
    pageIds: number[],
    opts?: { takesHoldersAllowList?: string[] },
  ): Promise<Map<number, Take[]>>;

  /**
   * Persist a single contradiction-probe run row. Caller supplies a full
   * `ContradictionsRunRow`-shaped object; the engine inserts as-is.
   *
   * Idempotent on `run_id`: re-inserting an existing run_id is a no-op
   * (caller passes ISO-timestamp-shaped run_ids that won't collide
   * unintentionally). Returns true iff a row was inserted.
   */
  writeContradictionsRun(row: {
    run_id: string;
    judge_model: string;
    prompt_version: string;
    queries_evaluated: number;
    queries_with_contradiction: number;
    total_contradictions_flagged: number;
    wilson_ci_lower: number;
    wilson_ci_upper: number;
    judge_errors_total: number;
    cost_usd_total: number;
    duration_ms: number;
    source_tier_breakdown: Record<string, unknown>;
    report_json: Record<string, unknown>;
  }): Promise<boolean>;

  /**
   * Load contradiction-probe run history within the last N days, ordered
   * newest first. Used by `gbrain eval suspected-contradictions trend` and
   * by the doctor `contradictions` check. `report_json` and
   * `source_tier_breakdown` are parsed JSONB columns.
   */
  loadContradictionsTrend(days: number): Promise<Array<{
    run_id: string;
    ran_at: string;
    judge_model: string;
    queries_evaluated: number;
    queries_with_contradiction: number;
    total_contradictions_flagged: number;
    wilson_ci_lower: number;
    wilson_ci_upper: number;
    judge_errors_total: number;
    cost_usd_total: number;
    duration_ms: number;
    source_tier_breakdown: Record<string, unknown>;
    report_json: Record<string, unknown>;
  }>>;

  /**
   * Cache lookup for the contradiction probe's persistent judge cache (P2).
   * Returns the verdict JSON if a row exists with matching key AND non-expired
   * `expires_at`. NULL means cache miss (judge call needed).
   *
   * Key shape mirrors the table primary key: (chunk_a_hash, chunk_b_hash,
   * model_id, prompt_version, truncation_policy). Codex's outside-voice
   * critique fixed the key to include prompt_version + truncation_policy so
   * prompt edits cleanly invalidate prior verdicts.
   */
  getContradictionCacheEntry(key: {
    chunk_a_hash: string;
    chunk_b_hash: string;
    model_id: string;
    prompt_version: string;
    truncation_policy: string;
  }): Promise<Record<string, unknown> | null>;

  /**
   * Upsert a contradiction-probe judge verdict into the persistent cache.
   * `ttl_seconds` controls expires_at (default 30 days from now). Caller
   * supplies pre-hashed chunk text + the verdict to cache.
   *
   * ON CONFLICT DO UPDATE so re-runs refresh expires_at; this is the simplest
   * shape for "I judged the same pair again with the same config, slide the
   * TTL forward."
   */
  putContradictionCacheEntry(opts: {
    chunk_a_hash: string;
    chunk_b_hash: string;
    model_id: string;
    prompt_version: string;
    truncation_policy: string;
    verdict: Record<string, unknown>;
    ttl_seconds?: number;
  }): Promise<void>;

  /**
   * Sweep expired cache entries. Returns count deleted. Periodic call from
   * cache.ts — keeps the table bounded without requiring a cron.
   */
  sweepContradictionCache(): Promise<number>;

  // ============================================================
  // v0.31 Hot memory — facts table operations
  // ============================================================
  /**
   * Insert a fact into the per-source hot memory. The handler:
   *   1. canonicalizes entity_slug against pages (caller may pre-canonicalize)
   *   2. queries findCandidateDuplicates (entity-prefiltered, k=5 cap)
   *   3. cosine ≥0.95 fast-path → mark duplicate, skip classifier
   *   4. else classifier (caller's job; this engine method handles the
   *      DB-side INSERT/UPDATE only). On insert.status === 'duplicate' or
   *      'superseded' the engine returns the existing/superseding row id.
   * Per-entity advisory lock on Postgres serializes the dedup window.
   * PGLite no-op for the lock (single-process).
   *
   * `status` reflects what the engine wrote:
   *   'inserted'   → row inserted
   *   'duplicate'  → no new row (returns the matching candidate id)
   *   'superseded' → new row inserted; old row got expired_at + superseded_by
   */
  insertFact(
    input: NewFact,
    ctx: { source_id: string; supersedeId?: number },
  ): Promise<{ id: number; status: FactInsertStatus }>;

  /**
   * v0.32.2: batch insert for fence-extracted fact rows. Persists the
   * v51 fence columns (`row_num`, `source_markdown_slug`) alongside the
   * standard NewFact fields.
   *
   * Designed for the `extract_facts` cycle phase: wipe-then-batch-insert
   * per page. No dedup is performed here — callers (the cycle phase via
   * `deleteFactsForPage` + this) own that contract. Bypasses the
   * single-row supersede flow because fence reconciliation is the canonical
   * source-of-truth direction, not the consolidator path.
   *
   * Insertion is atomic per call: all rows commit in a single transaction
   * or none commit (the transaction rolls back on any constraint
   * violation, e.g. the v51 partial UNIQUE index on
   * `(source_id, source_markdown_slug, row_num)`).
   *
   * Returns the inserted ids in input-order so callers can correlate
   * fence-row → DB-id without a separate lookup.
   */
  insertFacts(
    rows: Array<NewFact & { row_num: number; source_markdown_slug: string }>,
    ctx: { source_id: string },
  ): Promise<{ inserted: number; ids: number[] }>;

  /**
   * v0.32.2: hard-delete every fact row scoped to a single fence page.
   *
   * Keyed on `(source_id, source_markdown_slug)`. Used by the
   * `extract_facts` cycle phase before re-inserting from the fence — the
   * fence is canonical, the DB is the derived index, so each phase run
   * wipes the page-scoped index and rebuilds it from the markdown.
   *
   * Hard DELETE (not soft-delete via `expired_at`). A fence row that
   * disappears from markdown corresponds to a fact the user removed
   * entirely from history; the DB mirrors that. Forgotten facts that
   * stay in the fence as strikethrough rows survive the wipe because
   * the re-insert puts them back with `valid_until = today` per the
   * `extract-from-fence` derivation contract.
   *
   * Pre-v51 rows (NULL `source_markdown_slug`) are NEVER deleted by this
   * call — the partial UNIQUE index on `row_num IS NOT NULL` is the
   * structural guarantee that legacy rows live in a different keyspace
   * until the v0_32_2 migration backfills them. Cycle-phase callers in
   * commit 7 add the empty-fence-guard as a belt-and-suspenders check.
   */
  deleteFactsForPage(slug: string, source_id: string): Promise<{ deleted: number }>;

  /**
   * Mark a fact expired. Never DELETE. Returns true iff a row was updated.
   * Idempotent-as-false (already expired returns false without changing state).
   */
  expireFact(id: number, opts?: { supersededBy?: number; at?: Date }): Promise<boolean>;

  /** List active facts about an entity within a source, newest first. */
  listFactsByEntity(
    source_id: string,
    entitySlug: string,
    opts?: FactListOpts,
  ): Promise<FactRow[]>;

  /** List facts created since a given timestamp within a source. */
  listFactsSince(
    source_id: string,
    since: Date,
    opts?: FactListOpts & { entitySlug?: string },
  ): Promise<FactRow[]>;

  /** List facts captured under a session id within a source. */
  listFactsBySession(
    source_id: string,
    sessionId: string,
    opts?: FactListOpts,
  ): Promise<FactRow[]>;

  /**
   * Audit log: facts that were superseded (expired_at + superseded_by both set),
   * newest first. Drives `gbrain recall --supersessions`.
   */
  listSupersessions(
    source_id: string,
    opts?: { since?: Date; limit?: number },
  ): Promise<FactRow[]>;

  /**
   * v0.32: count facts that haven't been promoted to takes by the consolidate
   * phase yet (active + unconsolidated). Drives `gbrain recall --pending`.
   * Single SQL: COUNT(*) WHERE consolidated_at IS NULL AND expired_at IS NULL.
   */
  countUnconsolidatedFacts(source_id: string): Promise<number>;

  /**
   * Find candidate duplicates for a new fact within a source+entity bucket.
   * Entity-prefilter is mandatory (bounds the contradiction-classifier blast
   * radius). Hard cap k=5 by default. Embedding-cosine when both sides have
   * embeddings; recency fallback otherwise.
   */
  findCandidateDuplicates(
    source_id: string,
    entitySlug: string,
    factText: string,
    opts?: { k?: number; embedding?: Float32Array },
  ): Promise<FactRow[]>;

  /**
   * Mark a fact as consolidated into a take. Sets consolidated_at + consolidated_into.
   * Never DELETE — facts stay as audit trail.
   */
  consolidateFact(id: number, takeId: number): Promise<void>;

  /**
   * v0.35.4 (D-CDX-1 + D-CDX-6) — chronological fact trajectory for an
   * entity. Returns points ordered by (valid_from ASC, id ASC) so the
   * caller can compute regressions and drift_score deterministically.
   *
   * - Source-scoped via `sourceId` (scalar) OR `sourceIds` (federated array).
   * - Visibility-filtered: when `opts.remote=true`, only `visibility='world'`
   *   facts are returned. Trusted local callers see both private + world.
   * - Optional metric filter restricts to a single normalized metric label.
   * - Active-only by default (expired_at IS NULL); soft-deleted entities
   *   on the pages side are NOT filtered here — trajectory is a facts-table
   *   query and doesn't JOIN pages.
   */
  findTrajectory(opts: TrajectoryOpts): Promise<TrajectoryPoint[]>;

  /** Per-source operational metrics for `gbrain doctor` facts_health check. */
  getFactsHealth(source_id: string): Promise<FactsHealth>;

  // Versions
  /**
   * Snapshot a page row into page_versions. Source-scoped via `opts.sourceId`;
   * without it the bare-slug lookup snapshots whichever row Postgres returns
   * first when the slug exists across multiple sources.
   */
  createVersion(slug: string, opts?: { sourceId?: string }): Promise<PageVersion>;
  /**
   * v0.31.8 (D12 + D16): `opts.sourceId` source-scopes the page-id lookup.
   * When omitted, returns versions for every same-slug page across sources
   * (pre-v0.31.8 behavior; preserved via two-branch query).
   */
  getVersions(slug: string, opts?: { sourceId?: string }): Promise<PageVersion[]>;
  /**
   * v0.31.8 (D12): `opts.sourceId` source-scopes both the version lookup
   * and the page revert. Without it, multi-source brains can revert the
   * wrong row when the slug exists in 2+ sources.
   */
  revertToVersion(slug: string, versionId: number, opts?: { sourceId?: string }): Promise<void>;

  // Stats + health
  getStats(): Promise<BrainStats>;
  getHealth(): Promise<BrainHealth>;

  // Ingest log
  logIngest(entry: IngestLogInput): Promise<void>;
  getIngestLog(opts?: { limit?: number }): Promise<IngestLogEntry[]>;

  // Sync
  /**
   * Rename a page's slug (chunks + links + tags + timeline + versions all
   * preserved via stable page_id). `opts.sourceId` scopes the UPDATE — without
   * it, the bare `WHERE slug = old` matches every row across every source and
   * would either rename them all OR violate the (source_id, slug) UNIQUE.
   */
  updateSlug(oldSlug: string, newSlug: string, opts?: { sourceId?: string }): Promise<void>;
  rewriteLinks(oldSlug: string, newSlug: string): Promise<void>;

  /**
   * v0.42 type-unification (T2, plan D1+F10). Returns the canonical slug if
   * `slug` is registered in `slug_aliases` for any of the provided source(s);
   * otherwise returns `slug` unchanged. Defense-in-depth: also returns the
   * input when the table doesn't exist yet (pre-v104 brains).
   *
   * Accepts either a single sourceId (scalar) OR a sourceIds array
   * (federated reads). Multi-source ambiguity: when the same alias_slug
   * exists in two registered sources, returns the first match in array
   * order and emits a once-per-process stderr `multi_match` warning.
   *
   * Callers (the cluster the alias-table primitive is meant for):
   *   - src/core/entities/resolve.ts: wikilink resolver short-circuit
   *     (alias-table is authoritative; runs BEFORE fuzzy/prefix cascade)
   *   - MCP `read_page` op (canonical lookup)
   *   - Search rank stage `applyAliasResolvedBoost` (knows whether a
   *     top-K result was reached via an alias)
   *
   * Source-scoped throughout per F12 (codex outside voice) — no cross-source
   * false-positive resolution. v0.42 ships this method on both engines.
   */
  resolveSlugWithAlias(
    slug: string,
    sourceOrSources: string | readonly string[],
  ): Promise<string>;

  /**
   * T3 retrieval-cathedral — free-text alias resolution for SEARCH.
   * Given a set of NORMALIZED alias strings (normalizeAlias() output),
   * return a map alias_norm -> canonical slugs from page_aliases. An alias
   * may resolve to MORE THAN ONE slug (two pages claimed the same name) —
   * the caller reports the collision and resolves deterministically.
   *
   * Source-scoped: pass scalar `sourceId` (single-source) OR `sourceIds`
   * (federated read) — array wins when both set, matching sourceScopeOpts.
   * Empty input → empty map (no query). Throws "relation page_aliases does
   * not exist" on pre-v110 brains; the alias-hop caller wraps in try/catch
   * (isUndefinedColumnError) and degrades to no-injection (D9 fail-open).
   */
  resolveAliases(
    aliasNorms: string[],
    opts?: { sourceId?: string; sourceIds?: string[] },
  ): Promise<Map<string, Array<{ slug: string; source_id: string }>>>;

  /**
   * T3 retrieval-cathedral — WRITE side of the alias layer. Replace the full
   * alias set for one (slug, source) with `aliasNorms` (already normalized):
   * delete the page's existing page_aliases rows, insert the new set. Empty
   * `aliasNorms` just clears them. Idempotent (the unique triple). Called by
   * the ingest projection in importFromContent and the `reindex --aliases`
   * backfill so a page's declared aliases stay in lockstep with its frontmatter.
   */
  setPageAliases(
    slug: string,
    sourceId: string,
    aliasNorms: string[],
  ): Promise<void>;

  /**
   * v0.35.5 — narrow UPDATE of `pages.compiled_truth`, `pages.timeline`, and
   * `pages.content_hash` for a single slug+source. NO chunking, NO embedding,
   * NO link reconcile, NO `updated_at` advance beyond the trivial bump.
   *
   * Used by the phantom-redirect pass in `extract_facts` after appending
   * migrated fact rows to a canonical page's disk fence: we just rewrote the
   * `.md` on disk, so the DB body must match before the next reconcile reads
   * stale state. content_hash is included so the next `gbrain sync` sees the
   * canonical as unchanged and skips re-import (round-14 + codex #7 — the
   * "second cycle is a no-op" premise depends on all three columns moving
   * together).
   *
   * Skips soft-deleted rows (deleted_at filter). Idempotent — second call
   * with the same args produces the same row state.
   */
  refreshPageBody(
    slug: string,
    sourceId: string,
    compiledTruth: string,
    timeline: string,
    contentHash: string,
  ): Promise<void>;

  /**
   * v0.40.3.0 — narrow UPDATE that stamps the two CR-state columns
   * (`contextual_retrieval_mode`, `corpus_generation`) plus
   * `updated_at = now()` and nothing else.
   *
   * Used by `src/core/contextual-retrieval-service.ts:reembedPageWithContextualRetrieval`
   * at the end of its PHASE 2 transaction. Why narrow instead of routing
   * through `putPage`: stamping the CR state alone shouldn't trigger the
   * full page-version snapshot machinery (createVersion fires on every
   * putPage with an existing row, which would bloat page_versions on every
   * tier upgrade).
   *
   * Skips soft-deleted rows (deleted_at filter). Idempotent — same args
   * twice produces the same row state. Both columns are NULL-tolerant
   * (callers pass NULL for `corpusGeneration` only on the 'none' tier
   * path; 'title' and 'per_chunk_synopsis' always supply a hash).
   */
  updatePageContextualRetrievalState(
    slug: string,
    sourceId: string,
    mode: string,
    corpusGeneration: string | null,
  ): Promise<void>;

  /**
   * v0.35.5 — lossless DB-side migration of fact rows from one slug to
   * another within a single source. UPDATEs `entity_slug` and
   * `source_markdown_slug` on every active fact row whose
   * `source_markdown_slug` matches the phantom slug. Every other column
   * (embedding, valid_from, valid_until, kind, notability, confidence,
   * source_session, status, etc.) is preserved verbatim — codex #3 fix
   * for the writeFactsToFence lossy-migration trap.
   *
   * Idempotent: re-run after success finds no rows to update and returns
   * `{migrated: 0}`. Hard-deletes are out of scope; the caller wipes the
   * phantom's `.md` file separately. Scoped to one source by design —
   * cross-source migration is a separate concern.
   */
  migrateFactsToCanonical(
    phantomSlug: string,
    canonicalSlug: string,
    sourceId: string,
  ): Promise<{ migrated: number }>;

  // Config
  getConfig(key: string): Promise<string | null>;
  setConfig(key: string, value: string): Promise<void>;
  /**
   * v0.32.3 — delete a config row. Returns the number of rows deleted (0 or 1).
   * No-op when the key doesn't exist. Used by `gbrain config unset` and by
   * `gbrain search modes --reset`. Engine-agnostic.
   */
  unsetConfig(key: string): Promise<number>;
  /**
   * v0.32.3 — list config keys matching a literal prefix (e.g. "search.").
   * Used by `gbrain config unset --pattern` and the search-modes --reset path.
   * Does NOT support glob/regex on purpose — the caller knows the prefix.
   */
  listConfigKeys(prefix: string): Promise<string[]>;

  // Migration support
  runMigration(version: number, sql: string): Promise<void>;
  getChunksWithEmbeddings(slug: string, opts?: { sourceId?: string }): Promise<Chunk[]>;

  // Raw SQL (for Minions job queue and other internal modules)
  /**
   * v0.41.18.0 (A20, codex #7): optional 3rd-arg `opts.signal` lets callers
   * actually cancel a running query. Init nudge (3s wallclock cap) wires an
   * AbortController whose timer fires at 3s; queries that haven't returned
   * by then get cancelled (Postgres: query.cancel(); PGLite: in-process,
   * Promise.race against signal-rejection — documented gap because PGLite
   * has no kernel-level cancellation).
   */
  executeRaw<T = Record<string, unknown>>(
    sql: string,
    params?: unknown[],
    opts?: { signal?: AbortSignal },
  ): Promise<T[]>;

  /**
   * Like `executeRaw`, but routes through the DIRECT (session-mode) pool when
   * dual-pool is active (Supabase: port 5432), falling back to the read pool
   * otherwise. Use this for the Minion lock hot-path (`claim`/`renewLock`):
   * those statements heartbeat a lock over many seconds, and the
   * transaction-mode pooler (port 6543) recycles connections per-transaction,
   * which surfaces as `CONNECTION_ENDED` mid-heartbeat → orphaned locks →
   * silent worker wedge. The direct session pool holds the connection open for
   * the life of the worker, so heartbeats survive. Single-statement UPDATEs
   * only — same idempotency contract as `executeRaw`. On PGLite (no pooler)
   * this is identical to `executeRaw`.
   */
  executeRawDirect<T = Record<string, unknown>>(
    sql: string,
    params?: unknown[],
    opts?: { signal?: AbortSignal },
  ): Promise<T[]>;

  // ============================================================
  // v0.20.0 Cathedral II: code edges (Layer 5 populates, Layer 7 consumes)
  // ============================================================
  /**
   * Bulk-insert code edges. Resolved edges (to_chunk_id set) land in
   * code_edges_chunk; unresolved refs (to_chunk_id null, to_symbol_qualified
   * set) land in code_edges_symbol. ON CONFLICT DO NOTHING handles idempotency.
   * Returns count of rows actually inserted.
   */
  addCodeEdges(edges: CodeEdgeInput[]): Promise<number>;

  /**
   * Delete all code edges involving these chunk IDs, in BOTH directions, across
   * both code_edges_chunk and code_edges_symbol. Called by importCodeFile on
   * per-chunk invalidation (codex SP-2): when a chunk's text changed, stale
   * inbound edges from other pages pointing at the old symbol must wipe before
   * new edges write.
   */
  deleteCodeEdgesForChunks(chunkIds: number[]): Promise<void>;

  /**
   * "Who calls this symbol?" Returns UNION of code_edges_chunk +
   * code_edges_symbol matching `to_symbol_qualified = qualifiedName`.
   * Source scoping (codex SP-3): if opts.sourceId is set, filter by the
   * anchor chunk's source; if opts.allSources, ignore scoping.
   */
  getCallersOf(
    qualifiedName: string,
    opts?: { sourceId?: string; allSources?: boolean; limit?: number },
  ): Promise<CodeEdgeResult[]>;

  /**
   * "What does this symbol call?" Returns edges from chunks whose
   * from_symbol_qualified = qualifiedName. Same source-scoping semantics
   * as getCallersOf.
   */
  getCalleesOf(
    qualifiedName: string,
    opts?: { sourceId?: string; allSources?: boolean; limit?: number },
  ): Promise<CodeEdgeResult[]>;

  /**
   * All edges touching a chunk in the given direction. Used by A2 two-pass
   * retrieval to expand from anchor chunks. direction='in' returns edges
   * pointing AT the chunk; 'out' returns edges FROM it; 'both' unions.
   */
  getEdgesByChunk(
    chunkId: number,
    opts?: { direction?: 'in' | 'out' | 'both'; edgeType?: string; limit?: number },
  ): Promise<CodeEdgeResult[]>;

  /**
   * Chunk-grain keyword search. Ranks by content_chunks.search_vector
   * without the dedup-to-page pass that searchKeyword applies. Consumed
   * by A2 two-pass retrieval as its anchor source. Most callers should
   * prefer searchKeyword (external contract: page-grain best-chunk-per-page).
   */
  searchKeywordChunks(query: string, opts?: SearchOpts): Promise<SearchResult[]>;

  // Eval capture (v0.25.0 — BrainBench-Real substrate).
  // Captured at the op-layer wrapper in src/core/operations.ts; reads via
  // `gbrain eval export` (NDJSON) for sibling gbrain-evals consumption.
  // Adding these to BrainEngine is a breaking-interface change for third-
  // party engine implementers — this is why v0.25.0 is a minor bump.
  /** Insert a captured candidate. Returns the new row id. Best-effort: callers swallow failures and route them through `logEvalCaptureFailure`. */
  logEvalCandidate(input: EvalCandidateInput): Promise<number>;
  /** Read candidates by time window / limit / tool filter. Used by `gbrain eval export`. */
  listEvalCandidates(filter?: { since?: Date; limit?: number; tool?: 'query' | 'search' }): Promise<EvalCandidate[]>;
  /** Delete candidates created before `date`. Returns rows deleted. Used by `gbrain eval prune`. */
  deleteEvalCandidatesBefore(date: Date): Promise<number>;
  /** Log a capture failure so `gbrain doctor` can surface drops cross-process. Best-effort; symmetric with logEvalCandidate (failure-of-failure is lost). */
  logEvalCaptureFailure(reason: EvalCaptureFailureReason): Promise<void>;
  /** Read capture failures within an optional time window. Used by `gbrain doctor`. */
  listEvalCaptureFailures(filter?: { since?: Date }): Promise<EvalCaptureFailure[]>;

  // ============================================================
  // v0.29 — Salience + Anomaly Detection
  // ============================================================
  // The brain surfaces what's unusual and emotionally charged without being
  // asked. Cost: ~zero at query time (deterministic SQL), with backfill done
  // during the new `recompute_emotional_weight` cycle phase.

  /**
   * Batch-load tag + take inputs for the emotional-weight formula. One CTE-shaped
   * query: `pages` LEFT JOIN aggregated `tags` and aggregated `takes` (each
   * pre-aggregated in its own CTE so the page × N tags × M takes cartesian
   * product is avoided).
   *
   * If `slugs` is undefined, returns inputs for every page in the brain
   * (full-mode backfill). If provided, returns only matching slugs (incremental
   * recompute after sync / synthesize touched specific pages).
   *
   * Multi-source-aware: each row carries its `source_id` so the matching
   * `setEmotionalWeightBatch` UPDATE can composite-key correctly.
   */
  batchLoadEmotionalInputs(slugs?: string[]): Promise<EmotionalWeightInputRow[]>;

  /**
   * Apply pre-computed emotional weights in a single UPDATE. Composite-keyed
   * on `(slug, source_id)` because `pages.slug` is only unique within a
   * source — a slug-only UPDATE would fan out across sources, the same bug
   * that the v0.18.0 link batches fixed for cross-source edges.
   *
   * Returns the count of rows actually updated. Pages whose `(slug, source_id)`
   * tuple doesn't exist (race with delete) are silently skipped.
   */
  setEmotionalWeightBatch(rows: EmotionalWeightWriteRow[]): Promise<number>;

  /**
   * Salience query: pages recently touched, ranked by a deterministic
   * `(emotional_weight * 5) + ln(1 + take_count) + recency_decay` score.
   *
   * The handler computes the time boundary in JS (`now - days * 86400000`)
   * and binds it as TIMESTAMPTZ so the SQL is identical across PGLite +
   * Postgres (eng review D5 — avoids dialect drift on `interval` binding).
   */
  getRecentSalience(opts: SalienceOpts): Promise<SalienceResult[]>;

  /**
   * v0.41.39 (issue #1700) — enrich candidate selection for
   * `gbrain enrich --thin`. ONE source-aware SQL query: thin-filter +
   * per-page inbound-link count (source-correct via `to_page_id = p.id`,
   * `link_source='mentions'` excluded) + optional `enriched_at` recency
   * guard + whitelisted ORDER BY (ENRICH_ORDER_SQL) + LIMIT. Returns a
   * lightweight projection (NO page bodies) so ranking 100K stubs doesn't
   * pull every body into memory.
   *
   * Empty `opts.types` → empty result, no SQL. Source scope follows the
   * canonical scalar/array precedence (sourceIds wins over sourceId).
   */
  listEnrichCandidates(opts: EnrichCandidatesOpts): Promise<EnrichCandidate[]>;

  /**
   * Anomaly detection: cohorts (tag, type) with unusually-high page activity
   * on a target day vs baseline mean+stddev over the previous N days. Year
   * cohort is deferred to v0.30 (slug-regex year extraction is fragile).
   *
   * Baseline densifies the day series via `generate_series` zero-fill so
   * sparse-day rare cohorts don't look "normally active" — a sparse-day cohort
   * with one touch in 30 days has a low baseline mean and high sigma at 7 touches,
   * not a misleading mean of 1.
   */
  findAnomalies(opts: AnomaliesOpts): Promise<AnomalyResult[]>;
}