nlm-memory 0.9.1 → 0.10.0

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

@@ -0,0 +1,349 @@
+/**
+ * check-invariants — pure integrity check definitions.
+ *
+ * Each check returns a typed violation describing the problem. A clean
+ * database returns an empty violations array. The SQL strings are backend-
+ * agnostic where possible; per-backend runners at the bottom execute them.
+ *
+ * Checks:
+ *   I1  no self-loop edges in session_edges for any 'kind'
+ *   I2  status matches incoming edge kind: status='superseded' has an incoming
+ *       'supersedes' edge; status='replaced' has an incoming 'replaces' edge
+ *   I3  supersedence graph is acyclic over the union of 'supersedes' and
+ *       '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
+ *   I6  every non-null adapter_state.session_id references a sessions.id
+ */
+// ─── SQL strings (portable) ──────────────────────────────────────────────────
+const SQL_I1 = `
+  SELECT from_session AS bad_id
+  FROM session_edges
+  WHERE from_session = to_session
+  LIMIT 6
+`;
+const SQL_I2_ORPHANED = `
+  SELECT s.id AS bad_id
+  FROM sessions s
+  WHERE s.status = 'superseded'
+    AND NOT EXISTS (
+      SELECT 1 FROM session_edges e
+      WHERE e.to_session = s.id AND e.kind = 'supersedes'
+    )
+  LIMIT 6
+`;
+const SQL_I2_ORPHANED_REPLACED = `
+  SELECT s.id AS bad_id
+  FROM sessions s
+  WHERE s.status = 'replaced'
+    AND NOT EXISTS (
+      SELECT 1 FROM session_edges e
+      WHERE e.to_session = s.id AND e.kind = 'replaces'
+    )
+  LIMIT 6
+`;
+const SQL_I4_MISSING_FROM = `
+  SELECT e.from_session AS bad_id
+  FROM session_edges e
+  WHERE NOT EXISTS (SELECT 1 FROM sessions s WHERE s.id = e.from_session)
+  LIMIT 6
+`;
+const SQL_I4_MISSING_TO = `
+  SELECT e.to_session AS bad_id
+  FROM session_edges e
+  WHERE NOT EXISTS (SELECT 1 FROM sessions s WHERE s.id = e.to_session)
+  LIMIT 6
+`;
+// 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.
+const SQL_I5_DUPLICATE_FACTS = `
+  SELECT MIN(id) AS bad_id
+  FROM facts
+  WHERE superseded_by IS NULL
+  GROUP BY subject, predicate
+  HAVING COUNT(*) > 1
+  LIMIT 6
+`;
+const SQL_I5_DANGLING_SUPERSEDED_BY = `
+  SELECT f.id AS bad_id
+  FROM facts f
+  WHERE f.superseded_by IS NOT NULL
+    AND NOT EXISTS (SELECT 1 FROM facts f2 WHERE f2.id = f.superseded_by)
+  LIMIT 6
+`;
+const SQL_I6 = `
+  SELECT a.session_id AS bad_id
+  FROM adapter_state a
+  WHERE a.session_id IS NOT NULL
+    AND NOT EXISTS (SELECT 1 FROM sessions s WHERE s.id = a.session_id)
+  LIMIT 6
+`;
+const MAX_CYCLE_DEPTH = 100;
+export function detectCycles(loadEdges) {
+    const edges = loadEdges();
+    const children = new Map();
+    for (const { from_session, to_session } of edges) {
+        const list = children.get(from_session);
+        if (list)
+            list.push(to_session);
+        else
+            children.set(from_session, [to_session]);
+    }
+    const cycleNodes = [];
+    const visited = new Set();
+    for (const start of children.keys()) {
+        if (visited.has(start))
+            continue;
+        const queue = [{ node: start, depth: 0 }];
+        const inPath = new Set();
+        while (queue.length > 0) {
+            const item = queue.shift();
+            if (item.depth > MAX_CYCLE_DEPTH)
+                break;
+            if (inPath.has(item.node)) {
+                if (cycleNodes.length < 5)
+                    cycleNodes.push(item.node);
+                continue;
+            }
+            inPath.add(item.node);
+            visited.add(item.node);
+            for (const child of children.get(item.node) ?? []) {
+                queue.push({ node: child, depth: item.depth + 1 });
+            }
+        }
+    }
+    if (cycleNodes.length === 0)
+        return null;
+    return {
+        id: "I3",
+        description: "supersedence graph contains cycles",
+        count: cycleNodes.length,
+        sampleIds: cycleNodes.slice(0, 5),
+    };
+}
+// ─── SQLite runner ────────────────────────────────────────────────────────────
+function sqliteRows(db, sql) {
+    return db
+        .prepare(sql)
+        .all()
+        .map((r) => r.bad_id);
+}
+function sqliteCount(db, sql) {
+    const countSql = `SELECT count(*) AS n FROM (${sql.replace(/LIMIT \d+/, "")})`;
+    return (db.prepare(countSql).get()?.n) ?? 0;
+}
+function buildViolation(id, description, samples, count) {
+    return { id, description, count, sampleIds: samples.slice(0, 5) };
+}
+export function runChecksOnSqlite(db) {
+    const violations = [];
+    // I1
+    const i1Samples = sqliteRows(db, SQL_I1);
+    if (i1Samples.length > 0) {
+        const count = sqliteCount(db, SQL_I1);
+        violations.push(buildViolation("I1", "self-loop edges in session_edges", i1Samples, count));
+    }
+    // I2
+    const i2Samples = sqliteRows(db, SQL_I2_ORPHANED);
+    if (i2Samples.length > 0) {
+        const count = sqliteCount(db, SQL_I2_ORPHANED);
+        violations.push(buildViolation("I2", "sessions marked superseded with no incoming supersedes edge", i2Samples, count));
+    }
+    const i2ReplacedSamples = sqliteRows(db, SQL_I2_ORPHANED_REPLACED);
+    if (i2ReplacedSamples.length > 0) {
+        const count = sqliteCount(db, SQL_I2_ORPHANED_REPLACED);
+        violations.push(buildViolation("I2r", "sessions marked replaced with no incoming replaces edge", i2ReplacedSamples, count));
+    }
+    // I3
+    const i3 = detectCycles(() => db
+        .prepare("SELECT from_session, to_session FROM session_edges WHERE kind IN ('supersedes', 'replaces')")
+        .all());
+    if (i3)
+        violations.push(i3);
+    // I4
+    const i4FromSamples = sqliteRows(db, SQL_I4_MISSING_FROM);
+    const i4ToSamples = sqliteRows(db, SQL_I4_MISSING_TO);
+    const i4All = [...new Set([...i4FromSamples, ...i4ToSamples])];
+    if (i4All.length > 0) {
+        const countFrom = sqliteCount(db, SQL_I4_MISSING_FROM);
+        const countTo = sqliteCount(db, SQL_I4_MISSING_TO);
+        violations.push(buildViolation("I4", "session_edges reference session ids not in sessions table", i4All, countFrom + countTo));
+    }
+    // I5
+    const i5DupSamples = sqliteRows(db, SQL_I5_DUPLICATE_FACTS);
+    if (i5DupSamples.length > 0) {
+        const count = sqliteCount(db, SQL_I5_DUPLICATE_FACTS);
+        violations.push(buildViolation("I5a", "multiple active facts for same (subject, predicate)", i5DupSamples, count));
+    }
+    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));
+    }
+    // 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));
+    }
+    return violations;
+}
+// ─── PostgreSQL runner ────────────────────────────────────────────────────────
+async function pgRows(pool, sql) {
+    const stripped = sql.replace(/LIMIT \d+/, "LIMIT 6");
+    const result = await pool.query(stripped);
+    return result.rows.map((r) => r.bad_id);
+}
+async function pgCount(pool, sql) {
+    const countSql = `SELECT count(*) AS n FROM (${sql.replace(/LIMIT \d+/, "")}) AS sub`;
+    const result = await pool.query(countSql);
+    return Number.parseInt(result.rows[0]?.n ?? "0", 10);
+}
+export async function runChecksOnPg(pool) {
+    const violations = [];
+    // I1
+    const i1Samples = await pgRows(pool, SQL_I1);
+    if (i1Samples.length > 0) {
+        const count = await pgCount(pool, SQL_I1);
+        violations.push(buildViolation("I1", "self-loop edges in session_edges", i1Samples, count));
+    }
+    // I2
+    const i2Samples = await pgRows(pool, SQL_I2_ORPHANED);
+    if (i2Samples.length > 0) {
+        const count = await pgCount(pool, SQL_I2_ORPHANED);
+        violations.push(buildViolation("I2", "sessions marked superseded with no incoming supersedes edge", i2Samples, count));
+    }
+    const i2ReplacedSamples = await pgRows(pool, SQL_I2_ORPHANED_REPLACED);
+    if (i2ReplacedSamples.length > 0) {
+        const count = await pgCount(pool, SQL_I2_ORPHANED_REPLACED);
+        violations.push(buildViolation("I2r", "sessions marked replaced with no incoming replaces edge", i2ReplacedSamples, count));
+    }
+    // I3
+    const edgeResult = await pool.query("SELECT from_session, to_session FROM session_edges WHERE kind IN ('supersedes', 'replaces')");
+    const i3 = detectCycles(() => edgeResult.rows);
+    if (i3)
+        violations.push(i3);
+    // I4
+    const [i4FromSamples, i4ToSamples] = await Promise.all([
+        pgRows(pool, SQL_I4_MISSING_FROM),
+        pgRows(pool, SQL_I4_MISSING_TO),
+    ]);
+    const i4All = [...new Set([...i4FromSamples, ...i4ToSamples])];
+    if (i4All.length > 0) {
+        const [countFrom, countTo] = await Promise.all([
+            pgCount(pool, SQL_I4_MISSING_FROM),
+            pgCount(pool, SQL_I4_MISSING_TO),
+        ]);
+        violations.push(buildViolation("I4", "session_edges reference session ids not in sessions table", i4All, countFrom + countTo));
+    }
+    // I5
+    const [i5DupSamples, i5DangleSamples] = await Promise.all([
+        pgRows(pool, SQL_I5_DUPLICATE_FACTS),
+        pgRows(pool, SQL_I5_DANGLING_SUPERSEDED_BY),
+    ]);
+    if (i5DupSamples.length > 0) {
+        const count = await pgCount(pool, SQL_I5_DUPLICATE_FACTS);
+        violations.push(buildViolation("I5a", "multiple active facts for same (subject, predicate)", i5DupSamples, count));
+    }
+    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));
+    }
+    // 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));
+    }
+    return violations;
+}
+// ─── Cheap subset (I1 + I2 + I6) for scheduled watchdog ─────────────────────
+export function runCheapChecksOnSqlite(db) {
+    const violations = [];
+    const i1Samples = sqliteRows(db, SQL_I1);
+    if (i1Samples.length > 0) {
+        violations.push(buildViolation("I1", "self-loop edges in session_edges", i1Samples, sqliteCount(db, SQL_I1)));
+    }
+    const i2Samples = sqliteRows(db, SQL_I2_ORPHANED);
+    if (i2Samples.length > 0) {
+        violations.push(buildViolation("I2", "sessions marked superseded with no incoming supersedes edge", i2Samples, sqliteCount(db, SQL_I2_ORPHANED)));
+    }
+    const i2ReplacedSamples = sqliteRows(db, SQL_I2_ORPHANED_REPLACED);
+    if (i2ReplacedSamples.length > 0) {
+        violations.push(buildViolation("I2r", "sessions marked replaced with no incoming replaces edge", i2ReplacedSamples, sqliteCount(db, SQL_I2_ORPHANED_REPLACED)));
+    }
+    const i6Samples = sqliteRows(db, SQL_I6);
+    if (i6Samples.length > 0) {
+        violations.push(buildViolation("I6", "adapter_state.session_id references non-existent sessions.id", i6Samples, sqliteCount(db, SQL_I6)));
+    }
+    return violations;
+}
+export async function runCheapChecksOnPg(pool) {
+    const violations = [];
+    const [i1, i2, i2r, i6] = await Promise.all([
+        pgRows(pool, SQL_I1),
+        pgRows(pool, SQL_I2_ORPHANED),
+        pgRows(pool, SQL_I2_ORPHANED_REPLACED),
+        pgRows(pool, SQL_I6),
+    ]);
+    if (i1.length > 0) {
+        violations.push(buildViolation("I1", "self-loop edges in session_edges", i1, await pgCount(pool, SQL_I1)));
+    }
+    if (i2.length > 0) {
+        violations.push(buildViolation("I2", "sessions marked superseded with no incoming supersedes edge", i2, await pgCount(pool, SQL_I2_ORPHANED)));
+    }
+    if (i2r.length > 0) {
+        violations.push(buildViolation("I2r", "sessions marked replaced with no incoming replaces edge", i2r, await pgCount(pool, SQL_I2_ORPHANED_REPLACED)));
+    }
+    if (i6.length > 0) {
+        violations.push(buildViolation("I6", "adapter_state.session_id references non-existent sessions.id", i6, await pgCount(pool, SQL_I6)));
+    }
+    return violations;
+}
+export function applyFixOnSqlite(db) {
+    const deleteResult = db
+        .prepare("DELETE FROM session_edges WHERE from_session = to_session")
+        .run();
+    const updateSuperseded = db
+        .prepare(`
+      UPDATE sessions
+      SET status = 'closed', updated_at = datetime('now')
+      WHERE status = 'superseded'
+        AND id NOT IN (SELECT to_session FROM session_edges WHERE kind = 'supersedes')
+    `)
+        .run();
+    const updateReplaced = db
+        .prepare(`
+      UPDATE sessions
+      SET status = 'closed', updated_at = datetime('now')
+      WHERE status = 'replaced'
+        AND id NOT IN (SELECT to_session FROM session_edges WHERE kind = 'replaces')
+    `)
+        .run();
+    return {
+        deletedSelfLoops: deleteResult.changes,
+        restoredToClosed: updateSuperseded.changes + updateReplaced.changes,
+    };
+}
+export async function applyFixOnPg(pool) {
+    const deleteResult = await pool.query("DELETE FROM session_edges WHERE from_session = to_session");
+    const updateSuperseded = await pool.query(`
+    UPDATE sessions
+    SET status = 'closed', updated_at = NOW()
+    WHERE status = 'superseded'
+      AND id NOT IN (SELECT to_session FROM session_edges WHERE kind = 'supersedes')
+  `);
+    const updateReplaced = await pool.query(`
+    UPDATE sessions
+    SET status = 'closed', updated_at = NOW()
+    WHERE status = 'replaced'
+      AND id NOT IN (SELECT to_session FROM session_edges WHERE kind = 'replaces')
+  `);
+    return {
+        deletedSelfLoops: deleteResult.rowCount ?? 0,
+        restoredToClosed: (updateSuperseded.rowCount ?? 0) + (updateReplaced.rowCount ?? 0),
+    };
+}
+//# sourceMappingURL=check-invariants.js.map

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

@@ -0,0 +1 @@
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package/dist/core/scheduler/scan-once.d.ts

@@ -33,4 +33,7 @@ export declare function recordClassified(db: Database.Database, adapterName: str
 export declare function recordFailed(db: Database.Database, adapterName: string, sourcePath: string): void;
 export declare function getFileSize(sourcePath: string): number | null;
 export declare function scanOncePg(adapter: TranscriptAdapter, idleMinutes: number, pool: Pool, now?: number): Promise<ScanResult[]>;
-export declare function recordFailedPg(pool: Pool, adapterName: string, sourcePath: string, fileSize: number | null): Promise<void>;
+export declare function recordClassifiedPg(pool: Pool, adapterName: string, sourcePath: string, sessionId: string): Promise<void>;
+export declare function recordSkippedLowConfidence(db: Database.Database, adapterName: string, sourcePath: string): void;
+export declare function recordSkippedLowConfidencePg(pool: Pool, adapterName: string, sourcePath: string): Promise<void>;
+export declare function recordFailedPg(pool: Pool, adapterName: string, sourcePath: string, fileSize: number | null): Promise<number>;

package/dist/core/scheduler/scan-once.js

@@ -42,7 +42,6 @@ export async function scanOnce(adapter, idleMinutes, db, now = Date.now()) {
         if (age < idleMs)
             continue;
         const prior = byPath.get(path);
-        let supersedes = null;
         if (prior) {
             const sizeUnchanged = (prior.file_size ?? 0) === st.size;
             if (sizeUnchanged) {
@@ -54,11 +53,11 @@ export async function scanOnce(adapter, idleMinutes, db, now = Date.now()) {
             if (prior.failure_count >= MAX_CLASSIFY_FAILURES) {
                 db.prepare("UPDATE adapter_state SET failure_count = 0 WHERE adapter_name = ? AND source_path = ?").run(adapter.name, path);
             }
-            supersedes = prior.session_id;
         }
         const chunk = await adapter.parseSession(path);
         if (!chunk)
             continue;
+        const supersedes = prior?.session_id && prior.session_id !== chunk.id ? prior.session_id : null;
         out.push({ chunk, supersedes });
     }
     return out;
@@ -109,9 +108,15 @@ export async function scanOncePg(adapter, idleMinutes, pool, now = Date.now()) {
     const idleMs = idleMinutes * 60 * 1000;
     const stateRows = await pool.query(`SELECT source_path, file_size, session_id, COALESCE(failure_count, 0) AS failure_count
      FROM adapter_state WHERE adapter_name = $1`, [adapter.name]);
+    // pg returns BIGINT (file_size) as a string; coerce to number so the
+    // unchanged-size check compares against statSync's numeric size.
     const stateMap = new Map(stateRows.rows.map((r) => [
         r.source_path,
-        { fileSize: r.file_size, sessionId: r.session_id, failureCount: r.failure_count },
+        {
+            fileSize: r.file_size === null ? null : Number(r.file_size),
+            sessionId: r.session_id,
+            failureCount: r.failure_count,
+        },
     ]));
     const paths = await adapter.discover();
     const results = [];
@@ -140,25 +145,59 @@ export async function scanOncePg(adapter, idleMinutes, pool, now = Date.now()) {
         const chunk = await adapter.parseSession(sourcePath);
         if (!chunk)
             continue;
-        const prior = stateMap.get(sourcePath);
-        const supersedes = prior?.sessionId !== chunk.id ? (prior?.sessionId ?? null) : null;
+        const supersedes = state?.sessionId && state.sessionId !== chunk.id ? state.sessionId : null;
         results.push({ chunk, supersedes });
-        await pool.query(`INSERT INTO adapter_state (adapter_name, source_path, last_offset, file_size, session_id, failure_count)
-       VALUES ($1, $2, 0, $3, $4, 0)
-       ON CONFLICT (adapter_name, source_path) DO UPDATE SET
-         file_size = EXCLUDED.file_size,
-         session_id = EXCLUDED.session_id,
-         failure_count = 0,
-         last_processed_at = NOW()`, [adapter.name, sourcePath, getFileSize(sourcePath), chunk.id]);
     }
     return results;
 }
+export async function recordClassifiedPg(pool, adapterName, sourcePath, sessionId) {
+    const size = getFileSize(sourcePath);
+    if (size === null)
+        return;
+    await pool.query(`INSERT INTO adapter_state (adapter_name, source_path, last_offset, file_size, session_id, failure_count, last_processed_at)
+     VALUES ($1, $2, 0, $3, $4, 0, NOW())
+     ON CONFLICT (adapter_name, source_path) DO UPDATE SET
+       file_size = EXCLUDED.file_size,
+       session_id = EXCLUDED.session_id,
+       failure_count = 0,
+       last_processed_at = NOW()`, [adapterName, sourcePath, size, sessionId]);
+}
+export function recordSkippedLowConfidence(db, adapterName, sourcePath) {
+    let size = 0;
+    try {
+        size = statSync(sourcePath).size;
+    }
+    catch {
+        return;
+    }
+    db.prepare(`INSERT INTO adapter_state
+       (adapter_name, source_path, last_offset, file_size, session_id, failure_count, last_processed_at)
+     VALUES (?, ?, ?, ?, NULL, 0, datetime('now'))
+     ON CONFLICT(adapter_name, source_path) DO UPDATE SET
+       last_offset = excluded.last_offset,
+       file_size = excluded.file_size,
+       failure_count = 0,
+       last_processed_at = excluded.last_processed_at`).run(adapterName, sourcePath, size, size);
+}
+export async function recordSkippedLowConfidencePg(pool, adapterName, sourcePath) {
+    const size = getFileSize(sourcePath);
+    if (size === null)
+        return;
+    await pool.query(`INSERT INTO adapter_state (adapter_name, source_path, last_offset, file_size, session_id, failure_count, last_processed_at)
+     VALUES ($1, $2, 0, $3, NULL, 0, NOW())
+     ON CONFLICT (adapter_name, source_path) DO UPDATE SET
+       file_size = EXCLUDED.file_size,
+       failure_count = 0,
+       last_processed_at = NOW()`, [adapterName, sourcePath, size]);
+}
 export async function recordFailedPg(pool, adapterName, sourcePath, fileSize) {
-    await pool.query(`INSERT INTO adapter_state (adapter_name, source_path, last_offset, failure_count, file_size)
+    const res = await pool.query(`INSERT INTO adapter_state (adapter_name, source_path, last_offset, failure_count, file_size)
      VALUES ($1, $2, 0, 1, $3)
      ON CONFLICT (adapter_name, source_path) DO UPDATE SET
        failure_count = adapter_state.failure_count + 1,
        file_size = $3,
-       last_processed_at = NOW()`, [adapterName, sourcePath, fileSize]);
+       last_processed_at = NOW()
+     RETURNING failure_count`, [adapterName, sourcePath, fileSize]);
+    return res.rows[0]?.failure_count ?? 1;
 }
 //# sourceMappingURL=scan-once.js.map

package/dist/core/scheduler/scan-once.js.map

@@ -1 +1 @@
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package/dist/core/scheduler/scheduler.js

@@ -16,14 +16,45 @@
  * Confidence floor of 0.3 mirrors Python: classifier outputs below that
  * are skipped rather than persisted as low-quality noise.
  */
+import { readFileSync, writeFileSync, mkdirSync } from "node:fs";
+import { dirname, join } from "node:path";
+import { homedir } from "node:os";
 import { extractFacts } from "../facts/extract-facts.js";
 import { normalizeSignal } from "../signals/ingest-signal.js";
-import { MAX_CLASSIFY_FAILURES, getFileSize, recordClassified, recordFailed, recordFailedPg, scanOnce, scanOncePg } from "./scan-once.js";
+import { MAX_CLASSIFY_FAILURES, getFileSize, recordClassified, recordClassifiedPg, recordFailed, recordFailedPg, recordSkippedLowConfidence, recordSkippedLowConfidencePg, scanOnce, scanOncePg } from "./scan-once.js";
+import { runCheapChecksOnSqlite } from "../integrity/check-invariants.js";
 const DEFAULT_INTERVAL_MS = 30 * 60 * 1000; // 30 min, matches Python default
 const DEFAULT_CLASSIFY_TIMEOUT_MS = 120_000;
 const DEFAULT_CONFIDENCE_FLOOR = 0.3;
 const DEFAULT_IDLE_MINUTES = 15;
 const BODY_CAP = 200_000;
+const INTEGRITY_CHECK_INTERVAL_MS = 24 * 60 * 60 * 1000; // 24h
+function integrityCheckCachePath() {
+    return process.env["NLM_INTEGRITY_CACHE"] ?? join(homedir(), ".nlm", "integrity-check.json");
+}
+function shouldRunIntegrityCheck(now) {
+    try {
+        const raw = readFileSync(integrityCheckCachePath(), "utf8");
+        const parsed = JSON.parse(raw);
+        if (typeof parsed.checkedAt === "string") {
+            return now - Date.parse(parsed.checkedAt) >= INTEGRITY_CHECK_INTERVAL_MS;
+        }
+    }
+    catch {
+        // cache missing or corrupt — run the check
+    }
+    return true;
+}
+function markIntegrityCheckRan(now) {
+    try {
+        const path = integrityCheckCachePath();
+        mkdirSync(dirname(path), { recursive: true });
+        writeFileSync(path, JSON.stringify({ checkedAt: new Date(now).toISOString() }, null, 2), "utf8");
+    }
+    catch {
+        // cache write failure is non-fatal
+    }
+}
 export class ScanScheduler {
     opts;
     stopped = true;
@@ -70,8 +101,21 @@ export class ScanScheduler {
         let classifyFailures = 0;
         let storageFailures = 0;
         let chunksSeen = 0;
+        const now = Date.now();
+        const _pgPool = this.opts.store.pgPool?.();
+        if (!_pgPool && shouldRunIntegrityCheck(now)) {
+            try {
+                const violations = runCheapChecksOnSqlite(this.opts.store.rawDb());
+                markIntegrityCheckRan(now);
+                for (const v of violations) {
+                    this.opts.logger(`[integrity] FAIL ${v.id} count=${v.count} ${v.description}  run \`nlm doctor\` to inspect or \`nlm doctor --fix\` to repair`);
+                }
+            }
+            catch (e) {
+                this.opts.logger(`[integrity] check error: ${e instanceof Error ? e.message : String(e)}`);
+            }
+        }
         for (const adapter of this.opts.adapters) {
-            const _pgPool = this.opts.store.pgPool?.();
             let results;
             try {
                 results = _pgPool
@@ -92,23 +136,29 @@ export class ScanScheduler {
                 catch (e) {
                     classifyFailures += 1;
                     const reason = e instanceof TimeoutError ? "timed out" : `error: ${e instanceof Error ? e.message : String(e)}`;
+                    let count;
                     if (_pgPool) {
-                        void recordFailedPg(_pgPool, adapter.name, chunk.sourcePath, getFileSize(chunk.sourcePath));
+                        count = await recordFailedPg(_pgPool, adapter.name, chunk.sourcePath, getFileSize(chunk.sourcePath));
                     }
                     else {
                         recordFailed(this.opts.store.rawDb(), adapter.name, chunk.sourcePath);
-                    }
-                    const count = _pgPool
-                        ? 1
-                        : (this.opts.store.rawDb()
+                        count = this.opts.store.rawDb()
                             .prepare("SELECT COALESCE(failure_count, 0) AS failure_count FROM adapter_state WHERE adapter_name = ? AND source_path = ?")
-                            .get(adapter.name, chunk.sourcePath)?.failure_count ?? 1);
+                            .get(adapter.name, chunk.sourcePath)?.failure_count ?? 1;
+                    }
                     const ceiling = count >= MAX_CLASSIFY_FAILURES ? ` (failure ${count}/${MAX_CLASSIFY_FAILURES} — will skip until file grows)` : ` (failure ${count}/${MAX_CLASSIFY_FAILURES})`;
                     this.opts.logger(`[scheduler] classifier ${reason} for ${chunk.id}${ceiling}`);
                     continue;
                 }
                 if (classification.confidence < this.opts.confidenceFloor) {
                     skippedLowConfidence += 1;
+                    if (_pgPool) {
+                        await recordSkippedLowConfidencePg(_pgPool, adapter.name, chunk.sourcePath);
+                    }
+                    else {
+                        recordSkippedLowConfidence(this.opts.store.rawDb(), adapter.name, chunk.sourcePath);
+                    }
+                    this.opts.logger(`[scheduler] low-confidence (${classification.confidence} < ${this.opts.confidenceFloor}) for ${chunk.id} - skipping until file grows`);
                     continue;
                 }
                 const record = {
@@ -137,8 +187,11 @@ export class ScanScheduler {
                     }
                     : null;
                 try {
-                    await this.opts.store.insertSession(record, this.opts.embedder, supersedes, factSink);
-                    if (!_pgPool) {
+                    await this.opts.store.insertSession(record, this.opts.embedder, supersedes ? { priorSessionId: supersedes, kind: "replaces" } : null, factSink);
+                    if (_pgPool) {
+                        await recordClassifiedPg(_pgPool, adapter.name, chunk.sourcePath, chunk.id);
+                    }
+                    else {
                         recordClassified(this.opts.store.rawDb(), adapter.name, chunk.sourcePath, chunk.id);
                     }
                     inserted += 1;
@@ -146,7 +199,7 @@ export class ScanScheduler {
                 catch (e) {
                     storageFailures += 1;
                     if (_pgPool) {
-                        void recordFailedPg(_pgPool, adapter.name, chunk.sourcePath, getFileSize(chunk.sourcePath));
+                        await recordFailedPg(_pgPool, adapter.name, chunk.sourcePath, getFileSize(chunk.sourcePath));
                     }
                     else {
                         recordFailed(this.opts.store.rawDb(), adapter.name, chunk.sourcePath);