nlm-memory 0.19.0 → 0.20.1

package/dist/core/ingest/reprocess.js

@@ -0,0 +1,275 @@
+/**
+ * reprocess: retroactive re-classification of prior sessions under a
+ * stronger configured lane.
+ *
+ * Selection: sessions with a non-empty body whose classifier_model is NULL,
+ * differs from the current lane model, or (when --min-confidence is given)
+ * whose stored confidence falls below the threshold even for the same model.
+ *
+ * Per session: classifyAdaptive on the stored body, then a full insertSession
+ * upsert (refreshes chunks + facts). A below-floor classification updates the
+ * session row (label, summary, markers, provenance) but preserves prior facts
+ * and their embeddings unchanged. It is counted in belowFloorOverwrites.
+ * Workstream binding (workstream_id) is NOT touched by the upsert.
+ *
+ * Resumable via a JSON state file (default ~/.nlm/reprocess.state). A lane
+ * change (different provider or model) invalidates the done-set.
+ *
+ * SQLite only. Pg variant deferred; file task against nlm#TODO in report.
+ */
+import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
+import { dirname, join } from "node:path";
+import { homedir } from "node:os";
+import { classifyAdaptive } from "../classifier/hierarchical-classify.js";
+import { extractFacts } from "../facts/extract-facts.js";
+const DEFAULT_STATE_PATH = join(homedir(), ".nlm", "reprocess.state");
+const SAVE_EVERY = 25;
+const CONFIDENCE_FLOOR = 0.4;
+function confidenceBand(conf) {
+    if (conf === null)
+        return "null";
+    if (conf < 0.4)
+        return "<0.4";
+    if (conf < 0.6)
+        return "0.4-0.6";
+    if (conf < 0.8)
+        return "0.6-0.8";
+    return ">=0.8";
+}
+function loadState(path, lane) {
+    if (!existsSync(path))
+        return new Set();
+    try {
+        const raw = JSON.parse(readFileSync(path, "utf8"));
+        if (raw.lane?.provider === lane.provider && raw.lane?.model === lane.model) {
+            return new Set(raw.done ?? []);
+        }
+        return new Set();
+    }
+    catch {
+        return new Set();
+    }
+}
+function saveState(path, done, lane) {
+    mkdirSync(dirname(path), { recursive: true });
+    writeFileSync(path, JSON.stringify({ done: [...done].sort(), lane }));
+}
+export function selectReprocessCandidates(db, model, minConfidence, opts) {
+    const params = [];
+    let classifierClause;
+    if (opts?.onlyNull) {
+        classifierClause = "classifier_model IS NULL";
+    }
+    else if (minConfidence !== undefined) {
+        classifierClause = "(classifier_model IS NULL OR classifier_model != ? OR classifier_confidence < ?)";
+        params.push(model, minConfidence);
+    }
+    else {
+        classifierClause = "(classifier_model IS NULL OR classifier_model != ?)";
+        params.push(model);
+    }
+    const excludeModels = opts?.excludeModels ?? [];
+    let excludeClause = "";
+    if (excludeModels.length > 0) {
+        const placeholders = excludeModels.map(() => "?").join(", ");
+        excludeClause = ` AND (classifier_model IS NULL OR classifier_model NOT IN (${placeholders}))`;
+        params.push(...excludeModels);
+    }
+    const sql = "SELECT id, runtime, runtime_session_id, started_at, ended_at, duration_min, " +
+        "label, summary, status, transcript_kind, transcript_path, " +
+        "transcript_offset, transcript_length, " +
+        "classifier_provider, classifier_model, classifier_confidence " +
+        "FROM sessions " +
+        "WHERE body IS NOT NULL AND length(body) > 0 " +
+        "AND " +
+        classifierClause +
+        excludeClause +
+        " " +
+        "ORDER BY started_at DESC";
+    return db.prepare(sql).all(...params);
+}
+export async function reprocess(deps, opts = {}) {
+    const { db, store, factStore, embedder, classifier, classifierDescriptor } = deps;
+    const log = deps.log ?? ((m) => console.error(m));
+    const statePath = opts.statePath ?? DEFAULT_STATE_PATH;
+    const lane = {
+        provider: classifierDescriptor.provider,
+        model: classifierDescriptor.model,
+    };
+    const allCandidates = selectReprocessCandidates(db, classifierDescriptor.model, opts.minConfidence, {
+        ...(opts.onlyNull ? { onlyNull: true } : {}),
+        ...(opts.excludeModels ? { excludeModels: opts.excludeModels } : {}),
+    });
+    if (opts.dryRun) {
+        const groupMap = new Map();
+        for (const row of allCandidates) {
+            const key = `${row.classifier_provider ?? ""}\u0000${row.classifier_model ?? ""}\u0000${confidenceBand(row.classifier_confidence)}`;
+            const existing = groupMap.get(key);
+            if (existing) {
+                groupMap.set(key, { ...existing, count: existing.count + 1 });
+            }
+            else {
+                groupMap.set(key, {
+                    classifierProvider: row.classifier_provider,
+                    classifierModel: row.classifier_model,
+                    confidenceBand: confidenceBand(row.classifier_confidence),
+                    count: 1,
+                });
+            }
+        }
+        const cohort = [...groupMap.values()].sort((a, b) => b.count - a.count);
+        let stateNote;
+        if (existsSync(statePath)) {
+            const n = loadState(statePath, lane).size;
+            stateNote = `state file present, ${n} sessions already done, real run will skip them`;
+        }
+        return {
+            totalEligible: allCandidates.length,
+            processed: 0,
+            succeeded: 0,
+            failed: 0,
+            skippedAlreadyDone: 0,
+            limitSkipped: 0,
+            belowFloorOverwrites: 0,
+            meanConfidenceOld: null,
+            meanConfidenceNew: null,
+            cohort,
+            ...(stateNote !== undefined ? { stateNote } : {}),
+        };
+    }
+    if (deps.embeddingConfig && deps.embedderDescriptor) {
+        const stored = deps.embeddingConfig.getLane("prose");
+        if (stored) {
+            let dim = null;
+            try {
+                const result = await deps.embedder.embed("nlm probe", "query");
+                dim = result.vector.length;
+            }
+            catch {
+                // probe failure: pre-tracking tolerance, proceed
+            }
+            if (dim !== null) {
+                const mismatch = stored.provider !== deps.embedderDescriptor.provider ||
+                    stored.model !== deps.embedderDescriptor.model ||
+                    stored.dim !== dim;
+                if (mismatch && !opts.forceEmbed) {
+                    const msg = `reprocess: prose embedding lane mismatch: stored ${stored.provider}/${stored.model}@${stored.dim}` +
+                        ` vs runtime ${deps.embedderDescriptor.provider}/${deps.embedderDescriptor.model}@${dim}.` +
+                        ` Re-embedding under a mismatched lane writes mixed vectors. Run nlm embed-backfill first,` +
+                        ` or pass --force-embed to override.`;
+                    log(msg);
+                    throw new Error(msg);
+                }
+            }
+        }
+    }
+    const bodyStmt = db.prepare("SELECT body FROM sessions WHERE id = ?");
+    const done = loadState(statePath, lane);
+    const skippedByState = allCandidates.filter((r) => done.has(r.id)).length;
+    const candidates = allCandidates.filter((r) => !done.has(r.id));
+    const work = opts.limit !== undefined ? candidates.slice(0, opts.limit) : candidates;
+    const total = work.length;
+    let processed = 0;
+    let succeeded = 0;
+    let failed = 0;
+    let belowFloorOverwrites = 0;
+    let sumConfidenceOld = 0;
+    let countOld = 0;
+    let sumConfidenceNew = 0;
+    let countNew = 0;
+    for (let i = 0; i < work.length; i++) {
+        const row = work[i];
+        const sid = row.id;
+        const idx = i + 1;
+        const bodyRow = bodyStmt.get(sid);
+        if (!bodyRow?.body) {
+            failed++;
+            processed++;
+            log(`[reprocess] empty body ${sid}: skipping`);
+            opts.onProgress?.(idx, total, sid, "empty_body");
+            continue;
+        }
+        const body = bodyRow.body;
+        let classification;
+        try {
+            classification = await classifyAdaptive(body, classifier, {
+                ...(opts.classifyTimeoutMs ? { perCallTimeoutMs: opts.classifyTimeoutMs } : {}),
+            });
+        }
+        catch (e) {
+            failed++;
+            processed++;
+            log(`[reprocess] classify failed ${sid}: ${e instanceof Error ? e.message : String(e)}`);
+            opts.onProgress?.(idx, total, sid, "classify_failed");
+            continue;
+        }
+        if (row.classifier_confidence !== null) {
+            sumConfidenceOld += row.classifier_confidence;
+            countOld++;
+        }
+        sumConfidenceNew += classification.confidence;
+        countNew++;
+        const belowFloor = classification.confidence < CONFIDENCE_FLOOR;
+        if (belowFloor) {
+            belowFloorOverwrites++;
+            if (opts.verbose) {
+                log(`[reprocess] below-floor ${sid}: old=${row.classifier_confidence ?? "null"} new=${classification.confidence}`);
+            }
+        }
+        else if (opts.verbose) {
+            log(`[reprocess] ${sid}: old=${row.classifier_confidence ?? "null"} new=${classification.confidence}`);
+        }
+        const record = {
+            id: sid,
+            runtime: row.runtime,
+            runtimeSessionId: row.runtime_session_id,
+            startedAt: row.started_at,
+            endedAt: row.ended_at,
+            durationMin: row.duration_min,
+            label: classification.label,
+            summary: classification.summary,
+            body,
+            status: row.status,
+            transcriptKind: row.transcript_kind,
+            transcriptPath: row.transcript_path,
+            transcriptOffset: row.transcript_offset,
+            transcriptLength: row.transcript_length,
+            entities: classification.entities,
+            decisions: classification.decisions,
+            openQuestions: classification.open,
+            classifier: { ...classifierDescriptor, confidence: classification.confidence },
+        };
+        try {
+            const factSinkArg = belowFloor
+                ? null
+                : { factStore, facts: extractFacts(classification, sid, row.started_at) };
+            await store.insertSession(record, embedder, null, factSinkArg);
+            done.add(sid);
+            succeeded++;
+            processed++;
+            opts.onProgress?.(idx, total, sid, "ok");
+            if (succeeded % SAVE_EVERY === 0)
+                saveState(statePath, done, lane);
+        }
+        catch (e) {
+            failed++;
+            processed++;
+            log(`[reprocess] ingest failed ${sid}: ${e instanceof Error ? e.message : String(e)}`);
+            opts.onProgress?.(idx, total, sid, "ingest_failed");
+        }
+    }
+    saveState(statePath, done, lane);
+    const limitSkipped = opts.limit !== undefined ? candidates.length - work.length : 0;
+    return {
+        totalEligible: allCandidates.length,
+        processed,
+        succeeded,
+        failed,
+        skippedAlreadyDone: skippedByState,
+        limitSkipped,
+        belowFloorOverwrites,
+        meanConfidenceOld: countOld > 0 ? sumConfidenceOld / countOld : null,
+        meanConfidenceNew: countNew > 0 ? sumConfidenceNew / countNew : null,
+    };
+}
+//# sourceMappingURL=reprocess.js.map

package/dist/core/ingest/reprocess.js.map

@@ -0,0 +1 @@
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package/dist/core/integrity/check-invariants.d.ts

@@ -13,8 +13,12 @@
  *       'replaces' edges (BFS, depth-capped at 100)
  *   I4  every session_edges endpoint exists in sessions
  *   I5  at most one active fact per (subject, predicate); every superseded_by
- *       references an existing facts.id
+ *       references an existing facts.id; superseded_by forms no cycle (I5c)
  *   I6  every non-null adapter_state.session_id references a sessions.id
+ *   I7  every fact_embeddings row has a live (active, non-retired) parent fact
+ *   I7b chunk-level ghost: every session_embedding_chunks row has a map entry
+ *       (I7b-1); every session_chunk_map row references an existing session
+ *       (I7b-2)
  */
 import type Database from "better-sqlite3";
 import type { Pool } from "pg";
@@ -36,6 +40,7 @@ export declare function runCheapChecksOnPg(pool: Pool): Promise<ReadonlyArray<Vi
 export interface FixReport {
     readonly deletedSelfLoops: number;
     readonly restoredToClosed: number;
+    readonly deletedGhostEmbeddings: number;
 }
 export declare function applyFixOnSqlite(db: Database.Database): FixReport;
 export declare function applyFixOnPg(pool: Pool): Promise<FixReport>;

package/dist/core/integrity/check-invariants.js

@@ -13,9 +13,29 @@
  *       'replaces' edges (BFS, depth-capped at 100)
  *   I4  every session_edges endpoint exists in sessions
  *   I5  at most one active fact per (subject, predicate); every superseded_by
- *       references an existing facts.id
+ *       references an existing facts.id; superseded_by forms no cycle (I5c)
  *   I6  every non-null adapter_state.session_id references a sessions.id
+ *   I7  every fact_embeddings row has a live (active, non-retired) parent fact
+ *   I7b chunk-level ghost: every session_embedding_chunks row has a map entry
+ *       (I7b-1); every session_chunk_map row references an existing session
+ *       (I7b-2)
  */
+// Multi-valued predicates legitimately hold parallel active facts (e.g.
+// nlm-memory|stack = TypeScript AND SQLite, both simultaneously true).
+// Force-superseding one copy would destroy a true fact, which is the
+// #351-bug-3 trap. I5a skips subject|predicate groups whose predicate is
+// in this set and instead reports them as an informational count under
+// the id "I5a-mv". Entries MUST be members of PREDICATE_VOCABULARY
+// (src/core/classifier/prompt.ts): predicates are coerced to that closed
+// vocab before facts are written, so any other token here is inert. Add
+// predicates only when parallelism is a domain invariant, not when the
+// classifier merely failed to supersede (#358).
+const MULTI_VALUED_PREDICATES = new Set([
+    "stack",
+    "integration",
+    "dependency",
+]);
+const MV_IN = [...MULTI_VALUED_PREDICATES].map((p) => `'${p}'`).join(", ");
 // ─── SQL strings (portable) ──────────────────────────────────────────────────
 const SQL_I1 = `
   SELECT from_session AS bad_id
@@ -58,10 +78,23 @@ const SQL_I4_MISSING_TO = `
 // One row per conflicting (subject, predicate) group — the count is the number
 // of conflicts to resolve, not the number of facts involved. MIN(id) keeps the
 // projection aggregate-only so PostgreSQL's GROUP BY strictness accepts it.
+// Multi-valued predicates are excluded here; they are counted by SQL_I5A_MULTI_VALUED.
 const SQL_I5_DUPLICATE_FACTS = `
   SELECT MIN(id) AS bad_id
   FROM facts
-  WHERE superseded_by IS NULL
+  WHERE superseded_by IS NULL AND retired_at IS NULL
+    AND predicate NOT IN (${MV_IN})
+  GROUP BY subject, predicate
+  HAVING COUNT(*) > 1
+  LIMIT 6
+`;
+// One row per (subject, predicate) group in the multi-valued exemption set that
+// holds more than one active fact. Count drives the informational I5a-mv report.
+const SQL_I5A_MULTI_VALUED = `
+  SELECT MIN(id) AS bad_id
+  FROM facts
+  WHERE superseded_by IS NULL AND retired_at IS NULL
+    AND predicate IN (${MV_IN})
   GROUP BY subject, predicate
   HAVING COUNT(*) > 1
   LIMIT 6
@@ -80,6 +113,67 @@ const SQL_I6 = `
     AND NOT EXISTS (SELECT 1 FROM sessions s WHERE s.id = a.session_id)
   LIMIT 6
 `;
+// An embedding row must have a live (active, non-retired) parent fact.
+// Superseded/retired facts leave the ANN index at write time (ingest collapse,
+// markSuperseded, retire, session cascade); a row here means a write path
+// skipped cleanup; the NLM #351 orphan class.
+//
+// SQLite: fact_embeddings is a vec0 virtual table; its shadow rowids table
+// (fact_embeddings_rowids, column: id) supports standard LEFT JOIN.
+const SQL_I7_GHOST_SQLITE = `
+  SELECT r.id AS bad_id
+  FROM fact_embeddings_rowids r
+  LEFT JOIN facts f ON f.id = r.id
+  WHERE f.id IS NULL OR f.superseded_by IS NOT NULL OR f.retired_at IS NOT NULL
+  LIMIT 6
+`;
+// PG: fact_embeddings is a regular table with fact_id as PK; the FK ON DELETE
+// CASCADE means f.id IS NULL cannot occur, but the condition is kept symmetric.
+const SQL_I7_GHOST_PG = `
+  SELECT fe.fact_id AS bad_id
+  FROM fact_embeddings fe
+  LEFT JOIN facts f ON f.id = fe.fact_id
+  WHERE f.id IS NULL OR f.superseded_by IS NOT NULL OR f.retired_at IS NOT NULL
+  LIMIT 6
+`;
+// I7b-1: chunk vectors with no map row (vec0 has no FK; interrupted deletes
+// orphan here). Uses the session_embedding_chunks_rowids shadow table for
+// full-scan access: vec0 tables do not support unfiltered SELECT without a
+// KNN predicate. For INTEGER PK vec0 tables the shadow column is chunk_id
+// (not id, which is null for non-text PKs).
+const SQL_I7B_1_GHOST_SQLITE = `
+  SELECT CAST(r.chunk_id AS TEXT) AS bad_id
+  FROM session_embedding_chunks_rowids r
+  LEFT JOIN session_chunk_map m ON m.chunk_id = r.chunk_id
+  WHERE m.chunk_id IS NULL
+  LIMIT 6
+`;
+// I7b-2: map rows pointing at missing sessions (SQLite; FK ON DELETE CASCADE
+// fires in normal operation but vec0 deletes are not atomic with the map).
+const SQL_I7B_2_ORPHAN_MAP_SQLITE = `
+  SELECT m.session_id AS bad_id
+  FROM session_chunk_map m
+  LEFT JOIN sessions s ON s.id = m.session_id
+  WHERE s.id IS NULL
+  LIMIT 6
+`;
+// PG: session_embedding_chunks.session_id and session_chunk_map both carry
+// FK ON DELETE CASCADE to sessions; both checks are FK-impossible in practice
+// and land as regression guards.
+const SQL_I7B_1_GHOST_PG = `
+  SELECT CAST(c.chunk_id AS TEXT) AS bad_id
+  FROM session_embedding_chunks c
+  LEFT JOIN session_chunk_map m ON m.chunk_id = c.chunk_id
+  WHERE m.chunk_id IS NULL
+  LIMIT 6
+`;
+const SQL_I7B_2_ORPHAN_MAP_PG = `
+  SELECT m.session_id AS bad_id
+  FROM session_chunk_map m
+  LEFT JOIN sessions s ON s.id = m.session_id
+  WHERE s.id IS NULL
+  LIMIT 6
+`;
 const MAX_CYCLE_DEPTH = 100;
 export function detectCycles(loadEdges) {
     const edges = loadEdges();
@@ -177,17 +271,48 @@ export function runChecksOnSqlite(db) {
         const count = sqliteCount(db, SQL_I5_DUPLICATE_FACTS);
         violations.push(buildViolation("I5a", "multiple active facts for same (subject, predicate)", i5DupSamples, count));
     }
+    // I5a-mv: informational count of multi-valued predicate groups (not violations).
+    const i5aMvCount = sqliteCount(db, SQL_I5A_MULTI_VALUED);
+    if (i5aMvCount > 0) {
+        violations.push(buildViolation("I5a-mv", `multi-valued predicate groups exempted from I5a (${[...MULTI_VALUED_PREDICATES].join(", ")})`, [], i5aMvCount));
+    }
     const i5DangleSamples = sqliteRows(db, SQL_I5_DANGLING_SUPERSEDED_BY);
     if (i5DangleSamples.length > 0) {
         const count = sqliteCount(db, SQL_I5_DANGLING_SUPERSEDED_BY);
         violations.push(buildViolation("I5b", "facts.superseded_by references non-existent facts.id", i5DangleSamples, count));
     }
+    // I5c — facts.superseded_by is a functional graph; a cycle traps every fact in
+    // it as recall-ineligible forever (both copies have a non-null superseded_by).
+    const i5cCycle = detectCycles(() => db
+        .prepare("SELECT id AS from_session, superseded_by AS to_session FROM facts WHERE superseded_by IS NOT NULL")
+        .all());
+    if (i5cCycle) {
+        violations.push({ ...i5cCycle, id: "I5c", description: "facts.superseded_by forms a cycle" });
+    }
     // I6
     const i6Samples = sqliteRows(db, SQL_I6);
     if (i6Samples.length > 0) {
         const count = sqliteCount(db, SQL_I6);
         violations.push(buildViolation("I6", "adapter_state.session_id references non-existent sessions.id", i6Samples, count));
     }
+    // I7
+    const i7Samples = sqliteRows(db, SQL_I7_GHOST_SQLITE);
+    if (i7Samples.length > 0) {
+        const count = sqliteCount(db, SQL_I7_GHOST_SQLITE);
+        violations.push(buildViolation("I7", "fact embedding without a live parent fact", i7Samples, count));
+    }
+    // I7b-1
+    const i7b1Samples = sqliteRows(db, SQL_I7B_1_GHOST_SQLITE);
+    if (i7b1Samples.length > 0) {
+        const count = sqliteCount(db, SQL_I7B_1_GHOST_SQLITE);
+        violations.push(buildViolation("I7b-1", "chunk embedding without a map entry", i7b1Samples, count));
+    }
+    // I7b-2
+    const i7b2Samples = sqliteRows(db, SQL_I7B_2_ORPHAN_MAP_SQLITE);
+    if (i7b2Samples.length > 0) {
+        const count = sqliteCount(db, SQL_I7B_2_ORPHAN_MAP_SQLITE);
+        violations.push(buildViolation("I7b-2", "session_chunk_map references non-existent session", i7b2Samples, count));
+    }
     return violations;
 }
 // ─── PostgreSQL runner ────────────────────────────────────────────────────────
@@ -247,16 +372,45 @@ export async function runChecksOnPg(pool) {
         const count = await pgCount(pool, SQL_I5_DUPLICATE_FACTS);
         violations.push(buildViolation("I5a", "multiple active facts for same (subject, predicate)", i5DupSamples, count));
     }
+    // I5a-mv: informational count of multi-valued predicate groups (not violations).
+    const i5aMvCount = await pgCount(pool, SQL_I5A_MULTI_VALUED);
+    if (i5aMvCount > 0) {
+        violations.push(buildViolation("I5a-mv", `multi-valued predicate groups exempted from I5a (${[...MULTI_VALUED_PREDICATES].join(", ")})`, [], i5aMvCount));
+    }
     if (i5DangleSamples.length > 0) {
         const count = await pgCount(pool, SQL_I5_DANGLING_SUPERSEDED_BY);
         violations.push(buildViolation("I5b", "facts.superseded_by references non-existent facts.id", i5DangleSamples, count));
     }
+    // I5c — fact supersedence cycle (see SQLite runner).
+    const factEdges = await pool.query("SELECT id AS from_session, superseded_by AS to_session FROM facts WHERE superseded_by IS NOT NULL");
+    const i5cCycle = detectCycles(() => factEdges.rows);
+    if (i5cCycle) {
+        violations.push({ ...i5cCycle, id: "I5c", description: "facts.superseded_by forms a cycle" });
+    }
     // I6
     const i6Samples = await pgRows(pool, SQL_I6);
     if (i6Samples.length > 0) {
         const count = await pgCount(pool, SQL_I6);
         violations.push(buildViolation("I6", "adapter_state.session_id references non-existent sessions.id", i6Samples, count));
     }
+    // I7
+    const i7Samples = await pgRows(pool, SQL_I7_GHOST_PG);
+    if (i7Samples.length > 0) {
+        const count = await pgCount(pool, SQL_I7_GHOST_PG);
+        violations.push(buildViolation("I7", "fact embedding without a live parent fact", i7Samples, count));
+    }
+    // I7b-1
+    const i7b1Samples = await pgRows(pool, SQL_I7B_1_GHOST_PG);
+    if (i7b1Samples.length > 0) {
+        const count = await pgCount(pool, SQL_I7B_1_GHOST_PG);
+        violations.push(buildViolation("I7b-1", "chunk embedding without a map entry", i7b1Samples, count));
+    }
+    // I7b-2
+    const i7b2Samples = await pgRows(pool, SQL_I7B_2_ORPHAN_MAP_PG);
+    if (i7b2Samples.length > 0) {
+        const count = await pgCount(pool, SQL_I7B_2_ORPHAN_MAP_PG);
+        violations.push(buildViolation("I7b-2", "session_chunk_map references non-existent session", i7b2Samples, count));
+    }
     return violations;
 }
 // ─── Cheap subset (I1 + I2 + I6) for scheduled watchdog ─────────────────────
@@ -278,15 +432,33 @@ export function runCheapChecksOnSqlite(db) {
     if (i6Samples.length > 0) {
         violations.push(buildViolation("I6", "adapter_state.session_id references non-existent sessions.id", i6Samples, sqliteCount(db, SQL_I6)));
     }
+    // I7: LEFT JOIN over fact_embeddings is index-only; within the cheap budget.
+    const i7Samples = sqliteRows(db, SQL_I7_GHOST_SQLITE);
+    if (i7Samples.length > 0) {
+        violations.push(buildViolation("I7", "fact embedding without a live parent fact", i7Samples, sqliteCount(db, SQL_I7_GHOST_SQLITE)));
+    }
+    // I7b-1
+    const i7b1CheapSamples = sqliteRows(db, SQL_I7B_1_GHOST_SQLITE);
+    if (i7b1CheapSamples.length > 0) {
+        violations.push(buildViolation("I7b-1", "chunk embedding without a map entry", i7b1CheapSamples, sqliteCount(db, SQL_I7B_1_GHOST_SQLITE)));
+    }
+    // I7b-2
+    const i7b2CheapSamples = sqliteRows(db, SQL_I7B_2_ORPHAN_MAP_SQLITE);
+    if (i7b2CheapSamples.length > 0) {
+        violations.push(buildViolation("I7b-2", "session_chunk_map references non-existent session", i7b2CheapSamples, sqliteCount(db, SQL_I7B_2_ORPHAN_MAP_SQLITE)));
+    }
     return violations;
 }
 export async function runCheapChecksOnPg(pool) {
     const violations = [];
-    const [i1, i2, i2r, i6] = await Promise.all([
+    const [i1, i2, i2r, i6, i7, i7b1, i7b2] = await Promise.all([
         pgRows(pool, SQL_I1),
         pgRows(pool, SQL_I2_ORPHANED),
         pgRows(pool, SQL_I2_ORPHANED_REPLACED),
         pgRows(pool, SQL_I6),
+        pgRows(pool, SQL_I7_GHOST_PG),
+        pgRows(pool, SQL_I7B_1_GHOST_PG),
+        pgRows(pool, SQL_I7B_2_ORPHAN_MAP_PG),
     ]);
     if (i1.length > 0) {
         violations.push(buildViolation("I1", "self-loop edges in session_edges", i1, await pgCount(pool, SQL_I1)));
@@ -300,6 +472,15 @@ export async function runCheapChecksOnPg(pool) {
     if (i6.length > 0) {
         violations.push(buildViolation("I6", "adapter_state.session_id references non-existent sessions.id", i6, await pgCount(pool, SQL_I6)));
     }
+    if (i7.length > 0) {
+        violations.push(buildViolation("I7", "fact embedding without a live parent fact", i7, await pgCount(pool, SQL_I7_GHOST_PG)));
+    }
+    if (i7b1.length > 0) {
+        violations.push(buildViolation("I7b-1", "chunk embedding without a map entry", i7b1, await pgCount(pool, SQL_I7B_1_GHOST_PG)));
+    }
+    if (i7b2.length > 0) {
+        violations.push(buildViolation("I7b-2", "session_chunk_map references non-existent session", i7b2, await pgCount(pool, SQL_I7B_2_ORPHAN_MAP_PG)));
+    }
     return violations;
 }
 export function applyFixOnSqlite(db) {
@@ -322,9 +503,24 @@ export function applyFixOnSqlite(db) {
         AND id NOT IN (SELECT to_session FROM session_edges WHERE kind = 'replaces')
     `)
         .run();
+    // I7 fix: vec0 only supports single-value DELETE, so loop over bad fact_ids.
+    const ghostIds = db
+        .prepare(`
+      SELECT r.id AS bad_id
+      FROM fact_embeddings_rowids r
+      LEFT JOIN facts f ON f.id = r.id
+      WHERE f.id IS NULL OR f.superseded_by IS NOT NULL OR f.retired_at IS NOT NULL
+    `)
+        .all();
+    const delGhostEmb = db.prepare("DELETE FROM fact_embeddings WHERE fact_id = ?");
+    let deletedGhostEmbeddings = 0;
+    for (const { bad_id } of ghostIds) {
+        deletedGhostEmbeddings += delGhostEmb.run(bad_id).changes;
+    }
     return {
         deletedSelfLoops: deleteResult.changes,
         restoredToClosed: updateSuperseded.changes + updateReplaced.changes,
+        deletedGhostEmbeddings,
     };
 }
 export async function applyFixOnPg(pool) {
@@ -340,10 +536,20 @@ export async function applyFixOnPg(pool) {
     SET status = 'closed', updated_at = NOW()
     WHERE status = 'replaced'
       AND id NOT IN (SELECT to_session FROM session_edges WHERE kind = 'replaces')
+  `);
+    const ghostEmbResult = await pool.query(`
+    DELETE FROM fact_embeddings
+    WHERE fact_id IN (
+      SELECT fe.fact_id
+      FROM fact_embeddings fe
+      LEFT JOIN facts f ON f.id = fe.fact_id
+      WHERE f.id IS NULL OR f.superseded_by IS NOT NULL OR f.retired_at IS NOT NULL
+    )
   `);
     return {
         deletedSelfLoops: deleteResult.rowCount ?? 0,
         restoredToClosed: (updateSuperseded.rowCount ?? 0) + (updateReplaced.rowCount ?? 0),
+        deletedGhostEmbeddings: ghostEmbResult.rowCount ?? 0,
     };
 }
 //# sourceMappingURL=check-invariants.js.map