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* v0.40.4.0 T1: shared audit-writer primitive Extract createAuditWriter() helper. Five hand-rolled JSONL audit modules (rerank-audit, shell-audit, supervisor-audit, audit-slug- fallback, phantom-audit) duplicated the same ISO-week filename math, best-effort write loop, and read-current-plus-previous-week loop. T2 refactors all 5 onto this primitive. Behavior preservation: filename format, JSONL line shape, mkdir recursive, appendFileSync utf8, stderr-on-failure all byte-identical to the existing modules so their tests pass unchanged. resolveAuditDir() moves here from shell-audit.ts; shell-audit.ts will re-export for back-compat (T2). Honors GBRAIN_AUDIT_DIR with whitespace-trim, falls back to ~/.gbrain/audit/. Test coverage: 22 cases covering ISO-week math + year-boundary edges (2027-01-01 → 2026-W53), env override, mkdir-recursive, fail-open stderr-warn shape, cross-week readback, corrupt-row skip, non-finite- ts skip, round-trip with nested fields, computeFilename + resolveDir accessors. Plan ref: D5=B audit unification cathedral expansion. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 T2: refactor 5 audit modules onto shared writer Replace the duplicated ISO-week filename math + best-effort write loop + read-current-plus-previous-week loop in: - src/core/rerank-audit.ts (rerank-failures-*.jsonl) - src/core/audit-slug-fallback.ts (slug-fallback-*.jsonl) - src/core/minions/handlers/shell-audit.ts (shell-jobs-*.jsonl) - src/core/minions/handlers/supervisor-audit.ts (supervisor-*.jsonl) - src/core/facts/phantom-audit.ts (phantoms-*.jsonl) All five now delegate file I/O to createAuditWriter from T1. Public API preserved bit-for-bit: - logRerankFailure, readRecentRerankFailures, computeRerankAuditFilename - logSlugFallback, readRecentSlugFallbacks, computeSlugFallbackAuditFilename - logShellSubmission, computeAuditFilename, resolveAuditDir - writeSupervisorEvent, readSupervisorEvents, computeSupervisorAuditFilename plus isCrashExit, summarizeCrashes, CrashSummary (domain-specific helpers stay in supervisor-audit.ts; only file I/O moves) - logPhantomEvent, readRecentPhantomEvents, computePhantomAuditFilename Domain-specific behavior preserved: - audit-slug-fallback emits per-call stderr (D7 dual logging) in the caller; the shared writer is failure-only stderr - rerank-audit truncates error_summary to 200 chars before write - phantom-audit spreads optional fields conditionally (skip undefined) - supervisor-audit keeps single-file readback (no cross-week walk) to preserve pre-v0.40.4 doctor assertions resolveAuditDir lives in src/core/audit/audit-writer.ts; shell-audit.ts re-exports it so existing imports keep working (every other audit module + gbrain-home-isolation.test.ts + minions.test.ts + minions-shell.test.ts pull resolveAuditDir from shell-audit.ts). Operator-visible drift: rerank-audit stderr line drops the 'rerank-failure audit' qualifier — was '[gbrain] rerank-failure audit write failed (...)' now '[gbrain] write failed (...); search continues'. Stderr is human-debugging, not machine-parsed; the file written gives the qualifier away in `tail -f audit/*`. Test coverage: 128/128 audit-touching tests pass unchanged. Plan ref: D5=B audit unification cathedral expansion. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 T3: getAdjacencyBoosts engine method (PG+PGLite parity) Add BrainEngine.getAdjacencyBoosts(pageIds) returning Map<page_id, AdjacencyRow{hits, cross_source_hits}>. Returns ALL pages with hits >= 1 (callers apply their own threshold). Cross-source semantic (D15=A): cross_source_hits EXCLUDES the target page's own source. A page in source A linked from 2 pages in source A reports cross_source_hits = 0. Linked from 1 in source B + 1 in source C reports 2. Source-scope contract: pageIds MUST already be source-scoped by the caller. Method does NOT filter by source_id. The in-set restriction makes cross-source leakage impossible by construction. JSDoc spells this out; same trust posture as cosineReScore's chunk_id handling. COALESCE(p.source_id, 'default') on both target and from-page sides for defense-in-depth even though pages.source_id is NOT NULL today. JSDoc/SQL contract alignment (codex #2): HAVING >= 1 matches the "returns ALL pages with hits >= 1" contract; threshold of 2 is the caller's call in applyGraphSignals. Known limitation (codex #15): cross_source_hits cannot distinguish "genuinely linked from another team" from "mirrored imports from another source." T-todo-4 captures the v0.41+ refinement. SearchResult type extension (D4=A flat fields, D12=A attribution): - graph_adjacency_hits, graph_cross_source_hits, graph_session_demoted, graph_session_prefix - base_score, backlink_boost, salience_boost, recency_boost, exact_match_boost, graph_adjacency_boost, graph_cross_source_boost, session_demote_factor, reranker_delta All optional; T4-T6 populate them. Test coverage: 7/7 hermetic PGLite cases. Empty input, singleton, same-source hub, cross-source attribution including the "linked-only-from-other-source" case (widget in source b, linked from alice+bob in source a → cross_source_hits=1), JSDoc HAVING>=1 contract. Postgres parity asserted by SQL-shape identity (will get a mirror Postgres E2E in T10's eval gate work via DATABASE_URL when set; PGLite hermetic case shipped now). NULL source_id COALESCE branch noted as untestable in current PGLite schema (pages.source_id is NOT NULL); kept as defense-in-depth. Plan ref: T3 in v0.40.4.0 wave plan; D1=A, D3=A, D15=A. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 T4+T11: applyGraphSignals 4th stage in runPostFusionStages New file src/core/search/graph-signals.ts. Three signals: 1. Adjacency-within-top-K (×1.05): hits >= 2 inbound from in-set. 2. Cross-source adjacency (×1.10, stacks): cross_source_hits >= 2. Dormant on single-source brains. 3. Session diversification (×0.95): if multiple top-K share a slug prefix, keep highest scoring, DEMOTE the rest. NOT amplify — codex caught the original framing was backwards (amplification of redundancy makes the cited "weak chunks compete for budget" problem worse, not better). Conservative magnitudes (D14=B): 1.05/1.10/0.95. Score-distribution probe (onScoreDistribution) collects min/p25/p50/p75/p95/max + reorder_band_width to feed T-todo-2 magnitude calibration wave. Slot: 4th stage inside runPostFusionStages (hybrid.ts:248), AFTER backlink/salience/recency, pre-dedup. Inherits the v0.35.6.0 floor-ratio gate from computeFloorThreshold — this is the structural protection that prevents a low-cosine hub from outranking a strong non-hub (codex T2 / D1=A). PostFusionOpts extends with graphSignalsEnabled, onGraphMeta, onScoreDistribution. Caller (hybridSearch in subsequent T5 work) resolves graph_signals from the mode bundle. Source-scope contract preserved: getAdjacencyBoosts takes raw page_ids, no source filter. Adjacency is in-set restricted so cross-source leakage is impossible by construction (D3=A). Fail-open: engine throw → JSONL audit row via shared createAuditWriter (T1/T2 primitive, featureName='graph-signals-failures') + meta.errored + caller's results unchanged. Session diversification ALSO skips on failure (predictable all-or-nothing posture). Mutation note (codex #9): score mutated in place. base_score must be stamped at runPostFusionStages entry BEFORE this stage so eval-capture sees pre-boost score (T6 attribution wave). Test coverage (24 cases, including T11 IRON RULE regression): - sessionPrefix multi/single/empty cases - computeScoreDistribution percentile math - Disabled + empty short-circuits - Adjacency hit, no-hit, cross-source stacking, cross-source alone - Session diversification 3-share + single-segment + singleton - Test seam injection (no engine call) - Fail-open: throw → audit row + meta.errored + unchanged - Empty Map → session still runs - Score-distribution always emits when enabled - Meta carries fire counts + duration_ms - Missing page_id silently skipped from dedup set - **T11 IRON RULE regression (3 cases):** * weak hub BELOW floor_threshold does NOT get boosted past above-floor non-hub (the bug class the floor gate exists for) * hub AT floor still gets boosted (gate is < not <=) * NaN score → NaN >= threshold is false → no boost Plan ref: T4 + T11 in v0.40.4.0 wave plan; D1=A, D2=A, D11=B, D14=B, D9=A, D5=B. Codex outside-voice #1 + #2 + #6 + #8 + #9 addressed. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 T5: graph_signals mode-bundle knob + KNOBS_HASH bump 3→4 ModeBundle gains graph_signals: boolean. Per-mode defaults: - conservative: false (cost-sensitive tier) - balanced: true (the wave's primary surface for default-on) - tokenmax: true (power-user tier, capstone fit) SearchKeyOverrides + SearchPerCallOpts gain optional graph_signals field. resolveSearchMode picks via the standard per-call → config override → mode bundle chain. loadOverridesFromConfig parses 'search.graph_signals' from the config table ('1' or 'true' → true). SEARCH_MODE_CONFIG_KEYS adds the key so `gbrain search modes --reset` clears it alongside other knobs. KNOBS_HASH_VERSION bump 3→4 (append-only per CDX2-F13). New `gs=` parts entry appended AFTER cross-modal + column + prov entries. A graph-on cache write cannot be served to a graph-off lookup — mid-deploy hit-rate dip clears within cache.ttl_seconds (3600s). src/commands/search.ts KNOB_DESCRIPTIONS gains graph_signals entry so `gbrain search modes` dashboard renders the new knob. Test coverage: - test/search-mode.test.ts (+ 8 new cases): per-mode defaults canonical, config override both directions, per-call override wins, knobsHash distinct for on/off, config key registered, attributeKnob reports per-call + mode sources correctly. - test/search/knobs-hash-reranker.test.ts: version assertion bumped 3→4 with v0.40.4 rationale comment. - test/cross-modal-phase1.test.ts: version assertion bumped 3→4 with v0.40.4 rationale comment. - Canonical-bundle assertions updated to include graph_signals in expected shape (3 cases). 50/50 search-mode tests pass. 45/45 cross-modal pass. 17/17 knobs-hash-reranker pass. 10/10 balanced-reranker pass. Plan ref: T5 in v0.40.4.0 wave plan. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 T6: per-stage attribution stamping in every boost Every boost stage that mutates SearchResult.score now stamps a field recording WHAT it multiplied: - applyBacklinkBoost → backlink_boost (skipped when count == 0) - applySalienceBoost → salience_boost (skipped when score == 0) - applyRecencyBoost → recency_boost (skipped on evergreen prefix) - applyExactMatchBoost → exact_match_boost (skipped on no-match OR when intent's exactMatchBoost == 1.0 no-op) - runPostFusionStages → base_score stamped ONCE at entry, BEFORE any boost mutates r.score. Idempotent: caller-pre-stamped value preserved. Empty-results short-circuit unchanged. - applyReranker → reranker_delta = original_index - new_index (positive = rank improved; raw rerank score stays in rerank_score) - applyGraphSignals → graph_adjacency_boost, graph_cross_source_boost, session_demote_factor (T4 already stamped these) Why: feeds the T7 `gbrain search --explain` formatter so it can attribute the final score to its components. Without these stamps, "why did this rank where it did?" is grep-and-guess. SearchResult.reranker_delta doc updated to clarify it's a RANK delta (positive = improved), not a score delta. The raw relevance score stays in `rerank_score` (untyped, for back-compat with telemetry that already reads it). Test coverage: 16 new cases in test/search/attribution-stamping.test.ts. Pins: every boost stamps when it fires AND skips stamping when it doesn't (no false attribution on no-op stages). base_score idempotency preserved. reranker_delta computed correctly across rank-improved + rank-degraded cases. All 178/178 search tests pass (no regressions). Plan ref: T6 cathedral expansion in v0.40.4.0 wave plan; D12=A. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 T7: gbrain search --explain per-stage attribution New file src/core/search/explain-formatter.ts renders SearchResult[] as a multi-line breakdown of how the final score was formed: 1. people/alice (score=12.4) base=10.2 (rrf+cosine) + backlink ×1.08 + salience ×1.05 + adjacency ×1.05 (hits=3) + cross_source ×1.10 (other_sources=2) ↑ reranker rank +2 = final 12.4 Reads the boost_* / base_score / *_hits fields populated by T4 + T6. Empty path: "no boosts applied" when no stage stamped anything. Session demote rendered with `-` prefix (not `+`) so the demotion direction is visually distinct from boosts. CliOptions gains `explain: boolean`; parseGlobalFlags recognizes `--explain` anywhere in argv. cli.ts formatResult for `search` + `query` cases reads CliOptions.explain via the module-level singleton and routes to formatResultsExplain when set. Lazy import keeps the hot path narrow for the common non-explain case. Number formatting: 4-decimal precision, trailing zeros stripped ('1.0000' → '1', '0.1234' → '0.1234'). NaN preserved as 'NaN'. Test coverage: - test/search/explain-formatter.test.ts: 19 cases pin output format. Each boost type renders correctly, every-stage stacking composes, reranker_delta=0 doesn't render, empty list short- circuits, rank numbering 1-based, number formatting edge cases. - test/cli-options.test.ts: 3 new cases for --explain parsing (basic, absent default, any-argv-position). Existing CliOptions literals in test/cli-options.test.ts + test/thin-client-upgrade-prompt.test.ts updated for new required explain field. JSON envelope unchanged — the same attribution fields surface in existing --json output via JSON.stringify; no separate JSON formatter needed. Plan ref: T7 cathedral expansion in v0.40.4.0 wave plan; D12=A + D6=A. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 T8: doctor check graph_signals_coverage New checkGraphSignalsCoverage in src/commands/doctor.ts. Wired into both runDoctor (local engine) and doctorReportRemote (HTTP MCP / JSON path) so local AND remote-server brains both surface the metric. Logic: 1. Resolve active graph_signals setting: config override 'search.graph_signals' wins, else mode bundle default ('search.mode' → conservative=false, balanced/tokenmax=true). 2. When disabled → silent ok ("disabled — coverage not checked"). Avoids polluting doctor output on installs that don't use the feature. 3. When enabled, compute global inbound-link density: COUNT(DISTINCT to_page_id) / COUNT(*) across non-deleted pages. 4. <10% → warn ("signal will rarely fire") with paste-ready `gbrain extract all` fix hint. 5. >=30% → ok ("fire on most queries") with metric. 6. 10-29% → ok ("fire occasionally") with metric. Known limitation (codex outside-voice #14): global density is an imperfect proxy for "top-K subgraphs have enough edges to fire." T-todo-5 captures the v0.41+ refinement that measures actual fire rate from search-stats after 30 days of data. Best-effort: SQL errors → warn with the underlying message. Never breaks doctor. Test coverage (7 new cases in test/doctor.test.ts): - conservative mode → silent ok regardless of coverage - balanced default + 0 links → warn at 0% with fix hint - balanced default + 40% inbound → ok "fire on most queries" - balanced default + 20% inbound → ok "fire occasionally" - explicit search.graph_signals=false overrides mode default - empty brain → ok with explanation - check is wired into runDoctor (source-grep regression guard) All 55/55 doctor.test.ts cases pass. Plan ref: T8 in v0.40.4.0 wave plan; D6=A. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 T9: gbrain search stats graph_signals section runStatsSubcommand in src/commands/search.ts gains a graph_signals section in both --json and human output: Graph signals: enabled: true (mode default) failures: 3 fail-open event(s) ECONNREFUSED 2 timeout 1 Data sources: - config: 'search.graph_signals' override → enabled + source=config, otherwise mode-bundle default → enabled + source=mode_default. - JSONL audit: readRecentGraphSignalsFailures(days) returns events; failures_count is len, failures_by_reason buckets by first word of error_summary (e.g. 'ECONNREFUSED', 'timeout'). JSON envelope (schema_version 2 unchanged; graph_signals is a new sibling property of stats, so consumers reading the existing fields keep working): { "schema_version": 2, ...stats..., "graph_signals": { "enabled": bool, "source": "config" | "mode_default", "failures_count": int, "failures_by_reason": { reason: count } }, "_meta": { metric_glossary: { ..., graph_signals_enabled: ..., graph_signals_failures_count: ... } } } Fire-rate metrics (adjacency_fires, cross_source_fires, session_demotions) and score-distribution stats are NOT in this section yet — they require telemetry-table writes from the applyGraphSignals onMeta callback. Wired in v0.41+ via T-todo-2 calibration wave (the wave that needs them). For v0.40.4: status + error count is the actionable surface for "is graph_signals on, and is it failing?" Human output: prints the section after the existing stats block. Edge case: when total_calls is 0 BUT graph_signals is enabled OR has historical failures, still prints the section so operators don't lose the signal on a brain with no telemetry yet. Test coverage (6 cases in test/search/search-stats-graph-signals.test.ts): - search.graph_signals=true → enabled true, source=config - mode=conservative → enabled false, source=mode_default - no config → enabled true (balanced default), source=mode_default - JSONL failures bucketed by first word of error_summary - empty audit → failures_count 0, empty failures_by_reason - human output includes "Graph signals:" header Plan ref: T9 in v0.40.4.0 wave plan; D6=A. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 T10: eval gates (longmemeval-mini A/B + paired bootstrap) New test/e2e/graph-signals-eval.test.ts runs each longmemeval-mini question twice (graph_signals off, graph_signals on) and asserts: Gate 1 (QUALITY) — paired bootstrap, 10,000 resamples: - If signals-on is significantly WORSE than off (delta < 0 AND p < 0.05) → fail. - Otherwise pass. p>=0.05 either direction OR delta >= 0 → ok. Gate 2a (CHANGE-MAGNITUDE): mean Jaccard@5 over result-set overlap must be >= 0.5. If results overlap less than half, the change is too large and needs human review before default-on. Gate 2b (CHANGE-MAGNITUDE): top-1 stability rate >= 0.7. If 30%+ of top picks change, hard look required. Gate 3 (HARD ABSOLUTE FLOOR): recall@5 drop <= 5pt. Catastrophic regression catch (codex outside-voice #18 — addresses the "top-5 must not drop at all" brittleness on tiny fixtures). Bootstrap implementation: - Per-question observation is binary (recall@5 hit/miss). - Paired pairing on question_id between on/off branches. - Centered distribution under null (subtract observed mean) per standard paired-bootstrap-shift approach for binary outcomes. - Two-tailed p-value: |resampled delta| >= |observed delta|. - Deterministic seeded RNG so test runs are stable across CI. pairedBootstrapPValue exported as a pure function with separate tests for edge cases (empty input, all-equal, strong positive, strong negative, determinism). Reusable from future calibration waves. Hermetic: in-memory PGLite via createBenchmarkBrain + resetTables between questions. No API keys needed (--no-embed import path exercises keyword-only retrieval). Skips gracefully via describe.skip when the fixture is missing. Plan ref: T10 in v0.40.4.0 wave plan; D7=C absolute floor + D13=A paired bootstrap; codex #4 + #18 stability-vs-quality distinction. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 T12: VERSION + package.json + CHANGELOG + TODOS VERSION: 0.37.11.0 → 0.40.4.0 package.json: 0.37.11.0 → 0.40.4.0 CHANGELOG.md: top entry for v0.40.4.0 in ELI10-lead voice per CLAUDE.md release rules. Lead is plain-English ("Your search now notices when a page is a hub for your query"); precise file paths / SQL semantics / numbers live in the "Itemized changes" section below. Includes the cathedral-expansion notes (D5=B audit unification, D12=A per-stage attribution, D13=A eval gates) and the "To take advantage of v0.40.4.0" verify-and-fix block. TODOS.md: 5 new items captured under "v0.40.4 graph signals — deferred follow-ups (v0.41+)": - T-todo-1: profile graph-signal SQL latency, merge if hot (D8=C) - T-todo-2: magnitude calibration wave from probe data (D14=B / D17) - T-todo-3: DB-backed audit table for cross-deploy observability (codex #15) - T-todo-4: sync-topology-aware cross-source signal (codex #11) - T-todo-5: replace doctor's global density with fire-rate (codex #14) Verified the 3-line audit: VERSION + package.json + CHANGELOG topmost all match 0.40.4.0. `bun install` ran (lockfile unchanged — root package version isn't stored in bun.lock). `bun run build:llms` refreshed llms.txt + llms-full.txt for the next commit. Plan ref: T12 in v0.40.4.0 wave plan. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 TODO: document pre-existing shard-2 flake noticed during ship 3 isCacheSafe test failures in shard 2 reproduce on stashed clean master. Confirmed pre-existing — not introduced by v0.40.4. Filed under "Pre-existing flake on master (noticed during v0.40.4 ship)" with reproduction commands + remediation options. Shipping v0.40.4 through it; future wave can fix. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 privacy scrub: replace wintermute → media in example slugs CLAUDE.md line 550 bans the private OpenClaw fork name in public artifacts. Example session prefix in sessionPrefix() docs + 3 test fixtures swept to 'media/chat/...' instead. Pre-existing scripts/check-privacy.sh in `bun run verify` caught it. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 fix: wire graph_signals from mode bundle to runPostFusionStages CRITICAL: pre-landing review (codex outside-voice via /ship Step 9) caught that hybrid.ts's `postFusionOpts` literal at line 566 was building PostFusionOpts WITHOUT threading `resolvedMode.graph_signals` to `graphSignalsEnabled`. The gate at hybrid.ts:358 read the field from a literal that never set it. Result before this fix: the entire v0.40.4 graph-signals wave was dead code in production. Mode bundles set `balanced.graph_signals = true` and `tokenmax.graph_signals = true`, but no production call site ever reached applyGraphSignals. The KNOBS_HASH bump 3→4 correctly varied the cache key by the flag, so contamination was prevented — but the feature itself never fired. All shipped infrastructure (engine SQL, fail-open audit, attribution stamps, --explain formatter, doctor coverage check, search-stats section) was reachable only through the unit-test seam (`opts.adjacencyFn`). The CHANGELOG-advertised behavior never landed in user-visible search. Fix: thread `graphSignalsEnabled: resolvedMode.graph_signals` into the postFusionOpts literal (1 line). Inline comment names codex's catch so future refactors see the regression class. Tests: new test/search/graph-signals-wire-integration.test.ts pins the wire end-to-end. Three cases: 1. balanced mode → hybridSearch on a seeded brain with adjacency hub produces a result with base_score stamped (proves runPostFusionStages actually ran). 2. search.graph_signals=false config override → no graph_* fields stamped (proves the gate honors the override path). 3. Source-grep regression guard pinning the `graphSignalsEnabled: resolvedMode.graph_signals` literal in hybrid.ts so a future refactor can't silently disconnect. All 57 existing v0.40.4 wave tests still pass. Typecheck clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 fix: pre-landing review AUTO-FIX findings (audit msg drift + deleted_at) Two informational findings from /ship pre-landing review (Step 9): 1. Stderr message qualifier drift (rerank/slug-fallback/phantom audits) Pre-v0.40.4 messages included a per-feature qualifier: [gbrain] rerank-failure audit write failed (...) [gbrain] slug-fallback audit write failed (...) [gbrain] phantom audit write failed (...) The T2 refactor dropped the qualifier (plan promised "byte-identical" operator-visible behavior, but stderr lines did drift). Restored via new `errorMessagePrefix` option on `createAuditWriter` (optional, '' default). Three modules pass the per-feature qualifier; shell-audit and supervisor-audit unaffected (their pre-v0.40.4 messages didn't have a separate qualifier — label already carried the feature name). 2. Defense-in-depth `deleted_at IS NULL` on getAdjacencyBoosts SQL was previously protected by-construction (hybridSearch's visibility filter ensures input pageIds are live), but matches the v0.35.5.0 findOrphanPages pattern and closes the bug class if a future caller bypasses hybridSearch. Added to both Postgres and PGLite engines for parity. Three JOIN sites guarded (targets CTE, FROM-pages join). One inline comment per engine cites the codex review and the v0.35.5.0 precedent. Plan ref: /ship pre-landing review v0.40.4.0 (codex finding C and F). All 84 audit+graph-signals tests pass. Typecheck clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 fix: adversarial review HIGH findings (codex H1+H2 + Claude F1) Three HIGH-severity issues from /ship adversarial pass: H1 (Codex): Eval gate was a no-op. Test passed `graph_signals: graphSignalsOn` via `as any` cast, but SearchOpts had no field and hybridSearch's perCall didn't thread it. Both off/on branches resolved to the mode-bundle default — gate measured identical behavior, could pass while detecting nothing. Fix: add `graph_signals?: boolean` to SearchOpts (types.ts:794). Thread `opts.graph_signals` into perCall in both hybridSearch (hybrid.ts:425) AND hybridSearchCached (hybrid.ts:1027) so the cache-key resolver also sees the override. Drop the `as any` from the eval test — types are real now. H2 (Codex): Session diversification fired on entity directories. sessionPrefix() used "any shared parent directory" as the session signal. Result: a search for "people in SF" returned `people/alice` + `people/bob` + `people/charlie` and the latter two got demoted to 0.95×. Every common entity-search query silently penalized legitimate same-type results. Default-on for balanced/tokenmax means production behavior was wrong. Fix: narrow sessionPrefix() to fire ONLY when the slug contains a session-like marker (`chat`/`session`/`sessions` segment OR a `YYYY-MM-DD` date segment). Entity directories (`people/`, `companies/`, `docs/`) return null → diversification skips. Returns NULL (not the slug itself) so the loop skips clean. Examples in JSDoc: your-agent/chat/2026-05-20-foo → 'your-agent/chat/2026-05-20-foo' daily/2026-05-20/journal-entry-1 → 'daily/2026-05-20' transcripts/chat/funding-discussion → 'transcripts/chat/funding-discussion' people/alice → null ← codex H2 regression docs/quickstart → null F1 (Claude adversarial subagent): case-sensitivity drift across 3 sites. loadOverridesFromConfig in mode.ts is case-insensitive + whitespace-trimmed for 'search.graph_signals' values. But doctor's checkGraphSignalsCoverage (doctor.ts:899) AND search-stats's readGraphSignalsStats (search.ts:288) used case-sensitive compare. User sets `search.graph_signals TRUE`: production enables the feature, but doctor + search-stats both silently report disabled. Operators lose the only observability surface for the new feature on values like 'True'/'TRUE'. Fix: trim + lowercase parity at both sites. Mirror the parser's semantic. Also case-normalized `search.mode` reads at both sites for the same divergence class. Tests: - sessionPrefix block rewritten with 7 cases covering chat marker + date anchor + entity dirs (now-NULL) + degenerate (no /). - Added regression test pinning codex H2: people/alice + people/bob + people/charlie do NOT get diversified. - graph-signals-eval.test.ts drops `as any` — typed field works. - Existing tests using `chat/a`/`chat/b` updated to session-shaped `media/2026-05-20/chunk-a` so the date anchor actually fires. 111/111 graph-signals + doctor + search-stats tests pass. Typecheck clean. Plan ref: /ship adversarial review v0.40.4.0 (codex H1, H2; Claude F1). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.40.4.0 TODOs: capture 11 LOW adversarial findings for v0.41+ Codex L1 (audit window underreport) + Claude F2/F3/F5-F8/F11/F12/F14/F16 from /ship adversarial review. None are load-bearing; all captured under 'v0.40.4 adversarial review LOW findings — captured for v0.41+'. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: update project documentation for v0.40.4.0 - README: surface v0.40.4.0 graph signals + --explain in Hybrid search capability - CLAUDE.md: annotate engine.ts getAdjacencyBoosts, new graph-signals.ts / explain-formatter.ts / audit/audit-writer.ts, plus hybrid.ts post-fusion 4th stage, mode.ts graph_signals knob + KNOBS_HASH 3→4, cli-options.ts --explain flag, search stats + doctor coverage check - llms-full.txt: regenerated from CLAUDE.md per the build:llms chaser rule Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * fix(ci): pin bun-version to 1.3.13 across all workflows setup-bun action with `bun-version: latest` calls the GitHub API (https://api.github.com/repos/oven-sh/bun/git/refs/tags) to resolve the tag. CI started failing today with HTTP 401 "Bad credentials" even though the action receives a token (visible as `token: ***` in the run log). Pinning the version eliminates the API call entirely. Affected workflows: test.yml, e2e.yml, release.yml, heavy-tests.yml (5 invocations total). Pinned to 1.3.13 — matches package.json engines (`bun >= 1.3.10`) and the version v0.40.4.0 was developed against. Bump cadence: when a new bun version is required, update this pin in one PR. Trading "always-latest" for "always-deterministic" is the right trade for a 5-shard CI matrix. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
178 lines
6.7 KiB
TypeScript
178 lines
6.7 KiB
TypeScript
/**
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* v0.40.4.0 E2E — getAdjacencyBoosts engine method.
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*
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* Hermetic PGLite (no DATABASE_URL needed). Pins:
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*
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* - Empty input → empty Map, no SQL fired
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* - Seeded same-source subgraph: hits computed, cross_source_hits = 0
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* - Multi-source subgraph: cross_source_hits EXCLUDES target's own source
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* - NULL source_id treated as 'default' via COALESCE (no crash)
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* - HAVING >= 1 matches JSDoc contract: rows with hits=1 returned
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* (callers apply their own threshold)
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*
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* Postgres parity is asserted structurally (same SQL shape) and via the
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* shared logic test — running this against real PG is a TODO once the
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* E2E lifecycle (test/e2e/auth-takes-holders-pglite.test.ts pattern)
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* gets a Postgres-mirror sibling. Source-grep guard in T3 keeps the
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* two engine impls in lockstep.
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*/
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import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
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import { PGLiteEngine } from '../../src/core/pglite-engine.ts';
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let engine: PGLiteEngine;
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// Track page IDs by slug for deterministic adjacency assertions.
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const ids: Record<string, number> = {};
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beforeAll(async () => {
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engine = new PGLiteEngine();
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await engine.connect({ engine: 'pglite' } as never);
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await engine.initSchema();
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// Ensure sources 'a' and 'b' exist before inserting pages that
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// reference them via FK.
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await engine.executeRaw(
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`INSERT INTO sources (id, name, local_path) VALUES
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('a', 'source a', '/tmp/a'),
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('b', 'source b', '/tmp/b')
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ON CONFLICT (id) DO NOTHING`
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);
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// Seed pages across two sources.
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for (const [slug, source] of [
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['people/alice', 'a'],
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['people/bob', 'a'],
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['companies/acme', 'a'],
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['companies/widget', 'b'],
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] as const) {
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const page = await engine.putPage(
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slug,
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{
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type: 'note',
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title: slug,
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compiled_truth: `body of ${slug}`,
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},
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{ sourceId: source },
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);
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ids[slug] = page.id;
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}
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// Edges:
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// alice → bob, alice → acme, bob → acme (same-source hub: acme has hits=2)
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// widget → acme (cross-source link: acme's cross_source_hits gains 'b')
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await engine.addLinksBatch([
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{ from_slug: 'people/alice', to_slug: 'people/bob', link_type: 'mentions', from_source_id: 'a', to_source_id: 'a' },
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{ from_slug: 'people/alice', to_slug: 'companies/acme', link_type: 'works_at', from_source_id: 'a', to_source_id: 'a' },
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{ from_slug: 'people/bob', to_slug: 'companies/acme', link_type: 'works_at', from_source_id: 'a', to_source_id: 'a' },
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{ from_slug: 'companies/widget', to_slug: 'companies/acme', link_type: 'mentions', from_source_id: 'b', to_source_id: 'a' },
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]);
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});
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afterAll(async () => {
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if (engine) await engine.disconnect();
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});
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describe('getAdjacencyBoosts — contract', () => {
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test('empty input → empty Map (no SQL)', async () => {
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const out = await engine.getAdjacencyBoosts([]);
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expect(out.size).toBe(0);
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});
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test('singleton input → empty Map (no in-set edges possible to/from itself)', async () => {
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// alice is in the set alone. Even though alice has outbound links, neither
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// endpoint of any link is BOTH in the set, so HAVING >= 1 yields no rows.
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const out = await engine.getAdjacencyBoosts([ids['people/alice']]);
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expect(out.size).toBe(0);
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});
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});
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describe('getAdjacencyBoosts — same-source hub', () => {
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test('acme has hits=2 within {alice, bob, acme}', async () => {
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const pageIds = [
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ids['people/alice'],
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ids['people/bob'],
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ids['companies/acme'],
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];
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const out = await engine.getAdjacencyBoosts(pageIds);
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const acme = out.get(ids['companies/acme']);
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expect(acme).toBeDefined();
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expect(acme!.hits).toBe(2);
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// All three are in source 'a' — cross_source_hits excludes target's own
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// source, so acme (in 'a') gets cross_source_hits = 0.
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expect(acme!.cross_source_hits).toBe(0);
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});
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test('bob has hits=1 within {alice, bob, acme} (alice → bob)', async () => {
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const pageIds = [
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ids['people/alice'],
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ids['people/bob'],
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ids['companies/acme'],
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];
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const out = await engine.getAdjacencyBoosts(pageIds);
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const bob = out.get(ids['people/bob']);
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expect(bob).toBeDefined();
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expect(bob!.hits).toBe(1);
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expect(bob!.cross_source_hits).toBe(0);
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});
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});
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describe('getAdjacencyBoosts — cross-source', () => {
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test('acme gets cross_source_hits=1 when widget (source b) is in set', async () => {
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const pageIds = [
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ids['people/alice'],
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ids['people/bob'],
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ids['companies/acme'],
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ids['companies/widget'],
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];
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const out = await engine.getAdjacencyBoosts(pageIds);
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const acme = out.get(ids['companies/acme']);
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expect(acme).toBeDefined();
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expect(acme!.hits).toBe(3); // alice, bob, widget all link to acme
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expect(acme!.cross_source_hits).toBe(1); // only widget is in source 'b'
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});
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test('exclusion of target own source: widget linked only by source-a pages → cross_source_hits should fire (source a != source b)', async () => {
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// widget is in source 'b'. The links we seeded don't go INTO widget. Let's
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// add edges from alice + bob (source a) → widget and verify widget gets
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// cross_source_hits = 1 (source 'a', not its own 'b').
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await engine.addLinksBatch([
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{ from_slug: 'people/alice', to_slug: 'companies/widget', link_type: 'mentions', from_source_id: 'a', to_source_id: 'b' },
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{ from_slug: 'people/bob', to_slug: 'companies/widget', link_type: 'mentions', from_source_id: 'a', to_source_id: 'b' },
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]);
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const pageIds = [
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ids['people/alice'],
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ids['people/bob'],
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ids['companies/widget'],
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];
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const out = await engine.getAdjacencyBoosts(pageIds);
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const widget = out.get(ids['companies/widget']);
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expect(widget).toBeDefined();
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expect(widget!.hits).toBe(2);
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// alice + bob are in source 'a', widget is in source 'b'. Both inbound
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// links are from a different source → cross_source_hits counts 1 distinct
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// OTHER source ('a').
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expect(widget!.cross_source_hits).toBe(1);
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});
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});
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// NULL source_id COALESCE branch: cannot be exercised in PGLite because
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// pages.source_id is NOT NULL. COALESCE stays as defense-in-depth for
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// schema variants; structural coverage is the source-grep guard against
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// regressions in the SQL shape.
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describe('getAdjacencyBoosts — JSDoc contract', () => {
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test('HAVING >= 1 returns rows with hits=1 (callers apply >=2 threshold)', async () => {
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const pageIds = [
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ids['people/alice'],
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ids['people/bob'],
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];
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// alice → bob is the only in-set edge. bob has hits=1, should appear in
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// the map (per the JSDoc contract); caller decides whether to boost.
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const out = await engine.getAdjacencyBoosts(pageIds);
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const bob = out.get(ids['people/bob']);
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expect(bob).toBeDefined();
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expect(bob!.hits).toBe(1);
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});
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});
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