sensorium-mcp 3.1.0-refactor.6 → 3.1.0-refactor.9

package/dist/data/memory/bootstrap.d.ts

@@ -46,6 +46,13 @@ export interface BootstrapContext {
     reflections: BootstrapReflection[];
 }
 export declare function getMemoryStatus(db: Database, threadId: number): MemoryStatus;
+/**
+ * Top topics, computed on demand over the active notes' keywords. This replaced
+ * the stored meta_topic_index aggregate (dropped in migration 29): the stored
+ * counters needed increment/decrement bookkeeping on every write, expiry and
+ * restore path, drifted whenever a path bypassed them, and fed nothing but
+ * this display. Aggregating a few thousand active notes takes milliseconds.
+ */
 export declare function getTopicIndex(db: Database): TopicEntry[];
 export declare function getBootstrapContext(db: Database, threadId: number, memorySourceThreadId?: number): BootstrapContext;
 export declare function getCompactRefreshNotes(db: Database, threadId: number): SemanticNote[];

package/dist/data/memory/bootstrap.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"bootstrap.d.ts","sourceRoot":"","sources":["../../../src/data/memory/bootstrap.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AAC5C,OAAO,EAAqB,KAAK,OAAO,EAAE,MAAM,eAAe,CAAC;AAChE,OAAO,EAIL,KAAK,YAAY,EAClB,MAAM,qBAAqB,CAAC;AAC7B,OAAO,EAAE,gBAAgB,EAAE,MAAM,gBAAgB,CAAC;AAQlD,eAAO,MAAM,gCAAgC,SAAU,CAAC;AACxD,eAAO,MAAM,yBAAyB,MAAM,CAAC;AAE7C,MAAM,WAAW,UAAU;IACzB,KAAK,EAAE,MAAM,CAAC;IACd,aAAa,EAAE,MAAM,CAAC;IACtB,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,aAAa,EAAE,MAAM,CAAC;IACtB,aAAa,EAAE,MAAM,CAAC;CACvB;AAED,MAAM,WAAW,YAAY;IAC3B,aAAa,EAAE,MAAM,CAAC;IACtB,sBAAsB,EAAE,MAAM,CAAC;IAC/B,kBAAkB,EAAE,MAAM,CAAC;IAC3B,oBAAoB,EAAE,MAAM,CAAC;IAC7B,iBAAiB,EAAE,MAAM,GAAG,IAAI,CAAC;IACjC,SAAS,EAAE,UAAU,EAAE,CAAC;IACxB,WAAW,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,mBAAmB;IAClC,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,GAAG,CAAC,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,mBAAmB;IAClC,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,gBAAgB;IAC/B,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,QAAQ,EAAE,MAAM,CAAC;IACjB,aAAa,EAAE,MAAM,CAAC;IACtB,oBAAoB,CAAC,EAAE,MAAM,CAAC;IAC9B,cAAc,EAAE,OAAO,EAAE,CAAC;IAC1B,UAAU,EAAE,YAAY,EAAE,CAAC;IAC3B,WAAW,EAAE,YAAY,EAAE,CAAC;IAC5B,YAAY,EAAE,YAAY,EAAE,CAAC;IAC7B,QAAQ,EAAE,UAAU,CAAC,OAAO,gBAAgB,CAAC,CAAC;IAC9C,UAAU,EAAE,mBAAmB,GAAG,IAAI,CAAC;IACvC,WAAW,EAAE,mBAAmB,EAAE,CAAC;CACpC;AAQD,wBAAgB,eAAe,CAAC,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,GAAG,YAAY,CAwC5E;AAED;;;;;;GAMG;AACH,wBAAgB,aAAa,CAAC,EAAE,EAAE,QAAQ,GAAG,UAAU,EAAE,CAmDxD;AAED,wBAAgB,mBAAmB,CACjC,EAAE,EAAE,QAAQ,EACZ,QAAQ,EAAE,MAAM,EAChB,oBAAoB,CAAC,EAAE,MAAM,GAC5B,gBAAgB,CAkFlB;AAED,wBAAgB,sBAAsB,CAAC,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,GAAG,YAAY,EAAE,CAMrF;AAED,wBAAgB,YAAY,CAC1B,EAAE,EAAE,QAAQ,EACZ,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,MAAM,GACd;IAAE,KAAK,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,OAAO,CAAA;CAAE,CAgDrC"}

package/dist/data/memory/bootstrap.js

@@ -3,7 +3,6 @@ import { homedir } from "node:os";
 import { join } from "node:path";
 import { getRecentEpisodes } from "./episodes.js";
 import { getTopSemanticNotes, getGuardrailNotes, getPinnedNotes, } from "./semantic-notes.js";
-import { decrementTopicIndexForKeywords } from "./topic-index.js";
 import { getVoiceBaseline } from "./voice-sig.js";
 import { parseJsonArray } from "./utils.js";
 import { getNarrativesForBootstrap } from "./narrative.js";
@@ -13,15 +12,6 @@ import { log } from "../../lib/logger.js";
 import { errorMessage } from "../../lib/utils.js";
 export const MAX_BOOTSTRAP_CONVERSATION_CHARS = 100_000;
 export const MAX_MESSAGE_CONTENT_CHARS = 500;
-function rowToTopicEntry(row) {
-    return {
-        topic: row.topic,
-        semanticCount: row.semantic_count,
-        lastUpdated: row.last_updated ?? null,
-        avgConfidence: row.avg_confidence,
-        totalAccesses: row.total_accesses,
-    };
-}
 export function getMemoryStatus(db, threadId) {
     const totalEpisodes = db.prepare(`SELECT COUNT(*) as cnt FROM episodes`).get().cnt;
     const unconsolidatedEpisodes = db.prepare(`SELECT COUNT(*) as cnt FROM episodes WHERE consolidated = 0`).get().cnt;
@@ -50,11 +40,54 @@ export function getMemoryStatus(db, threadId) {
         dbSizeBytes,
     };
 }
+/**
+ * Top topics, computed on demand over the active notes' keywords. This replaced
+ * the stored meta_topic_index aggregate (dropped in migration 29): the stored
+ * counters needed increment/decrement bookkeeping on every write, expiry and
+ * restore path, drifted whenever a path bypassed them, and fed nothing but
+ * this display. Aggregating a few thousand active notes takes milliseconds.
+ */
 export function getTopicIndex(db) {
     const rows = db
-        .prepare(`SELECT * FROM meta_topic_index ORDER BY total_accesses DESC, semantic_count DESC LIMIT 50`)
+        .prepare(`SELECT keywords, confidence, access_count, updated_at FROM semantic_notes
+       WHERE valid_to IS NULL AND superseded_by IS NULL`)
         .all();
-    return rows.map(rowToTopicEntry);
+    const agg = new Map();
+    for (const row of rows) {
+        const keywords = parseJsonArray(row.keywords);
+        const seen = new Set();
+        for (const kw of keywords) {
+            if (typeof kw !== "string")
+                continue;
+            const normalised = kw.toLowerCase().trim();
+            if (normalised.length <= 1 || seen.has(normalised))
+                continue;
+            seen.add(normalised);
+            const entry = agg.get(normalised) ?? {
+                count: 0,
+                confSum: 0,
+                accesses: 0,
+                lastUpdated: null,
+            };
+            entry.count += 1;
+            entry.confSum += row.confidence ?? 0.5;
+            entry.accesses += row.access_count ?? 0;
+            if (row.updated_at && (!entry.lastUpdated || row.updated_at > entry.lastUpdated)) {
+                entry.lastUpdated = row.updated_at;
+            }
+            agg.set(normalised, entry);
+        }
+    }
+    return [...agg.entries()]
+        .map(([topic, entry]) => ({
+        topic,
+        semanticCount: entry.count,
+        lastUpdated: entry.lastUpdated,
+        avgConfidence: entry.confSum / entry.count,
+        totalAccesses: entry.accesses,
+    }))
+        .sort((a, b) => b.totalAccesses - a.totalAccesses || b.semanticCount - a.semanticCount)
+        .slice(0, 50);
 }
 export function getBootstrapContext(db, threadId, memorySourceThreadId) {
     const queryThreadId = memorySourceThreadId ?? threadId;
@@ -151,11 +184,9 @@ export function forgetMemory(db, memoryId, _reason) {
             .get(memoryId);
         if (!existing)
             return { layer: "semantic", deleted: false };
-        const keywords = parseJsonArray(existing.keywords);
         db.transaction(() => {
             db.prepare(`DELETE FROM semantic_notes WHERE note_id = ?`).run(memoryId);
             db.prepare(`DELETE FROM note_embeddings WHERE note_id = ?`).run(memoryId);
-            decrementTopicIndexForKeywords(db, keywords);
         })();
         return { layer: "semantic", deleted: true };
     }
@@ -173,11 +204,9 @@ export function forgetMemory(db, memoryId, _reason) {
         .prepare(`SELECT note_id, keywords FROM semantic_notes WHERE note_id = ?`)
         .get(memoryId);
     if (noteRow) {
-        const keywords = parseJsonArray(noteRow.keywords);
         db.transaction(() => {
             db.prepare(`DELETE FROM semantic_notes WHERE note_id = ?`).run(memoryId);
             db.prepare(`DELETE FROM note_embeddings WHERE note_id = ?`).run(memoryId);
-            decrementTopicIndexForKeywords(db, keywords);
         })();
         return { layer: "semantic", deleted: true };
     }

package/dist/data/memory/bootstrap.js.map

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package/dist/data/memory/consolidation.d.ts

@@ -1,4 +1,5 @@
 import type { Database } from "./schema.js";
+import { type ExpiryReason } from "./note-archival.js";
 export interface ConsolidationReport {
     episodesProcessed: number;
     notesCreated: number;
@@ -42,12 +43,16 @@ export declare function getActiveNoteContent(db: Database, noteId: string): {
     noteId: string;
     content: string;
 } | null;
-export declare function expireNote(db: Database, noteId: string, now: string): void;
+export declare function expireNote(db: Database, noteId: string, now: string, reason: Extract<ExpiryReason, "pruned" | "quality-gate">): void;
 export declare function mergeDuplicateNote(db: Database, keepId: string, expireId: string, now: string, mergedContent?: string): void;
 /**
- * Delete note_embeddings rows whose semantic_notes have been expired or superseded.
- * These embeddings are already invisible to embedding search (loadAllEmbeddings filters
- * them out) but they accumulate on disk over time. Safe to delete at any point.
+ * Delete note_embeddings rows only for notes that are gone entirely or
+ * permanently dead (superseded / merged / pruned). Vectors of archived,
+ * worker-cleanup and legacy-expired notes are deliberately KEPT: those notes
+ * are restorable, and this sweep destroying their vectors is what turned the
+ * 2026 archiving incident into a store-wide embedding outage (re-embedding is
+ * expensive to notice needing; ~6 KB/note of disk is not). Expired vectors are
+ * already invisible to search — loadAllEmbeddings filters on the live note.
  * Returns the number of rows deleted.
  */
 export declare function sweepOrphanedEmbeddings(db: Database): number;

package/dist/data/memory/consolidation.d.ts.map

@@ -1 +1 @@
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package/dist/data/memory/consolidation.js

@@ -1,10 +1,14 @@
 import { cleanupOldSentMessages } from "./schema.js";
-import { archiveNotesForThread, getThreadIdsWithActiveNotes } from "./note-archival.js";
+import { archiveNotesForThread, getThreadIdsWithActiveNotes, } from "./note-archival.js";
 import { migrateInboundLinks } from "./semantic-notes.js";
 import { log } from "../../lib/logger.js";
 import { nowISO } from "./utils.js";
 import { getAllThreads } from "./thread-registry.js";
-const TERMINAL_THREAD_STATUSES = new Set(["archived", "expired", "exited"]);
+// "archived" is deliberately absent: the operator archives threads for tidiness,
+// not to declare their knowledge dead, so archiving must NOT expire a thread's
+// notes. Only "expired"/"exited" are genuinely terminal. Unarchiving restores the
+// notes via restoreNotesForThread (see note-archival.ts).
+const TERMINAL_THREAD_STATUSES = new Set(["expired", "exited"]);
 export function getUnconsolidatedThreadIds(db) {
     const rows = db
         .prepare(`SELECT DISTINCT e.thread_id
@@ -49,28 +53,36 @@ export function getActiveNoteContent(db, noteId) {
         return null;
     return { noteId: row.note_id, content: row.content };
 }
-export function expireNote(db, noteId, now) {
-    db.prepare(`UPDATE semantic_notes SET valid_to = ?, updated_at = ? WHERE note_id = ?`).run(now, now, noteId);
+export function expireNote(db, noteId, now, reason) {
+    db.prepare(`UPDATE semantic_notes SET valid_to = ?, updated_at = ?, expiry_reason = ? WHERE note_id = ?`).run(now, now, reason, noteId);
 }
 export function mergeDuplicateNote(db, keepId, expireId, now, mergedContent) {
     if (mergedContent) {
         db.prepare(`UPDATE semantic_notes SET content = ?, updated_at = ? WHERE note_id = ?`).run(mergedContent, now, keepId);
     }
-    db.prepare(`UPDATE semantic_notes SET valid_to = ?, superseded_by = ?, updated_at = ? WHERE note_id = ?`).run(now, keepId, now, expireId);
+    db.prepare(`UPDATE semantic_notes SET valid_to = ?, superseded_by = ?, updated_at = ?, expiry_reason = 'merged' WHERE note_id = ?`).run(now, keepId, now, expireId);
     // Repoint inbound causal links from the merged-away note to the kept note.
     migrateInboundLinks(db, expireId, keepId);
 }
 /**
- * Delete note_embeddings rows whose semantic_notes have been expired or superseded.
- * These embeddings are already invisible to embedding search (loadAllEmbeddings filters
- * them out) but they accumulate on disk over time. Safe to delete at any point.
+ * Delete note_embeddings rows only for notes that are gone entirely or
+ * permanently dead (superseded / merged / pruned). Vectors of archived,
+ * worker-cleanup and legacy-expired notes are deliberately KEPT: those notes
+ * are restorable, and this sweep destroying their vectors is what turned the
+ * 2026 archiving incident into a store-wide embedding outage (re-embedding is
+ * expensive to notice needing; ~6 KB/note of disk is not). Expired vectors are
+ * already invisible to search — loadAllEmbeddings filters on the live note.
  * Returns the number of rows deleted.
  */
 export function sweepOrphanedEmbeddings(db) {
     const result = db
-        .prepare(`DELETE FROM note_embeddings WHERE note_id NOT IN (
-       SELECT note_id FROM semantic_notes WHERE valid_to IS NULL AND superseded_by IS NULL
-     )`)
+        .prepare(`DELETE FROM note_embeddings WHERE
+       note_id NOT IN (SELECT note_id FROM semantic_notes)
+       OR note_id IN (
+         SELECT note_id FROM semantic_notes
+         WHERE valid_to IS NOT NULL
+           AND (superseded_by IS NOT NULL OR expiry_reason IN ('superseded','merged','pruned'))
+       )`)
         .run();
     if (result.changes > 0) {
         log.info(`[memory] Embedding sweep: removed ${result.changes} orphaned embedding(s)`);
@@ -87,7 +99,7 @@ export function sweepOrphanedNotes(db) {
     for (const threadId of threadIdsWithNotes) {
         const status = threadStatusMap.get(threadId);
         if (!status || TERMINAL_THREAD_STATUSES.has(status)) {
-            totalArchived += archiveNotesForThread(db, threadId);
+            totalArchived += archiveNotesForThread(db, threadId, "thread-terminal");
         }
     }
     if (totalArchived > 0) {

package/dist/data/memory/consolidation.js.map

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package/dist/data/memory/index.d.ts

@@ -5,7 +5,7 @@
  * a single path: `./data/memory/index.js`.
  *
  * Modules: utils, schema, episodes, semantic-notes, semantic-search,
- * note-embeddings, note-archival, topic-index, voice-sig, consolidation,
+ * note-embeddings, note-archival, voice-sig, consolidation,
  * reflection (+ gates, dedup, sources), narrative (+ lint,
  * resolutions, store, sources), topic-shift, synthesis, bootstrap,
  * thread-registry.
@@ -17,7 +17,6 @@ export * from "./semantic-notes.js";
 export * from "./semantic-search.js";
 export * from "./note-embeddings.js";
 export * from "./note-archival.js";
-export * from "./topic-index.js";
 export * from "./voice-sig.js";
 export * from "./consolidation.js";
 export * from "./reflection.js";

package/dist/data/memory/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/data/memory/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,cAAc,YAAY,CAAC;AAC3B,cAAc,aAAa,CAAC;AAC5B,cAAc,eAAe,CAAC;AAC9B,cAAc,qBAAqB,CAAC;AACpC,cAAc,sBAAsB,CAAC;AACrC,cAAc,sBAAsB,CAAC;AACrC,cAAc,oBAAoB,CAAC;AACnC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,oBAAoB,CAAC;AACnC,cAAc,iBAAiB,CAAC;AAChC,cAAc,uBAAuB,CAAC;AACtC,cAAc,uBAAuB,CAAC;AACtC,cAAc,yBAAyB,CAAC;AACxC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,qBAAqB,CAAC;AACpC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,sBAAsB,CAAC;AACrC,cAAc,wBAAwB,CAAC;AACvC,cAAc,kBAAkB,CAAC;AACjC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,gBAAgB,CAAC;AAC/B,cAAc,sBAAsB,CAAC"}

package/dist/data/memory/index.js

@@ -5,7 +5,7 @@
  * a single path: `./data/memory/index.js`.
  *
  * Modules: utils, schema, episodes, semantic-notes, semantic-search,
- * note-embeddings, note-archival, topic-index, voice-sig, consolidation,
+ * note-embeddings, note-archival, voice-sig, consolidation,
  * reflection (+ gates, dedup, sources), narrative (+ lint,
  * resolutions, store, sources), topic-shift, synthesis, bootstrap,
  * thread-registry.
@@ -17,7 +17,6 @@ export * from "./semantic-notes.js";
 export * from "./semantic-search.js";
 export * from "./note-embeddings.js";
 export * from "./note-archival.js";
-export * from "./topic-index.js";
 export * from "./voice-sig.js";
 export * from "./consolidation.js";
 export * from "./reflection.js";

package/dist/data/memory/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/data/memory/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,cAAc,YAAY,CAAC;AAC3B,cAAc,aAAa,CAAC;AAC5B,cAAc,eAAe,CAAC;AAC9B,cAAc,qBAAqB,CAAC;AACpC,cAAc,sBAAsB,CAAC;AACrC,cAAc,sBAAsB,CAAC;AACrC,cAAc,oBAAoB,CAAC;AACnC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,oBAAoB,CAAC;AACnC,cAAc,iBAAiB,CAAC;AAChC,cAAc,uBAAuB,CAAC;AACtC,cAAc,uBAAuB,CAAC;AACtC,cAAc,yBAAyB,CAAC;AACxC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,qBAAqB,CAAC;AACpC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,sBAAsB,CAAC;AACrC,cAAc,wBAAwB,CAAC;AACvC,cAAc,kBAAkB,CAAC;AACjC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,gBAAgB,CAAC;AAC/B,cAAc,sBAAsB,CAAC"}

package/dist/data/memory/migration-runner.d.ts

@@ -1,5 +1,28 @@
 import type { Database } from "./db-types.js";
-export declare const SCHEMA_VERSION = 27;
+export declare const SCHEMA_VERSION = 29;
 export declare function rebuildThreadRegistryWithExitedStatus(db: Database, existingColumns: string[]): void;
+/**
+ * Label pre-column tombstones (valid_to set, expiry_reason NULL) with the most
+ * that can be *proven* about who expired them — measured on the 2026-07-26
+ * incident DB, but every rule below is derived from writer code, not from that
+ * one dataset:
+ *
+ * 1. `superseded_by IS NOT NULL` → 'superseded'. Structural.
+ * 2. Bulk clusters (≥10 rows, same thread, byte-identical valid_to — the
+ *    signature of a single-nowISO() loop):
+ *    - on a dead/archived/unregistered thread, only archiveNotesForThread ever
+ *      produced that → 'archived-legacy';
+ *    - on a live thread the sweep never ran; if the cluster is 100%
+ *      '[REFLECTION]%' rows it can only be enforceReflectionCap's buffer trim
+ *      → 'reflection-cap' (e.g. the predicted 635-row trim of restored
+ *      reflections on thread 1327 at 2026-07-26T01:02:55);
+ *    - a mixed cluster on a live thread is ambiguous → falls through to 3.
+ * 3. Everything else → 'unknown-legacy'. Pruning singles, gate kills and
+ *    small sweeps are indistinguishable after the fact; no guess is recorded
+ *    as fact. These stay dead unless their thread is explicitly unarchived.
+ *
+ * Exported for tests; idempotent (only touches expiry_reason IS NULL rows).
+ */
+export declare function backfillExpiryReasons(db: Database): void;
 export declare function runMigrations(db: Database): void;
 //# sourceMappingURL=migration-runner.d.ts.map

package/dist/data/memory/migration-runner.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"migration-runner.d.ts","sourceRoot":"","sources":["../../../src/data/memory/migration-runner.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAE9C,eAAO,MAAM,cAAc,KAAK,CAAC;AAkBjC,wBAAgB,qCAAqC,CACnD,EAAE,EAAE,QAAQ,EACZ,eAAe,EAAE,MAAM,EAAE,GACxB,IAAI,CA0DN;AAicD;;;;;;;;;;;;;;;;;;;;;GAqBG;AACH,wBAAgB,qBAAqB,CAAC,EAAE,EAAE,QAAQ,GAAG,IAAI,CAyDxD;AAED,wBAAgB,aAAa,CAAC,EAAE,EAAE,QAAQ,GAAG,IAAI,CAsBhD"}

package/dist/data/memory/migration-runner.js

@@ -4,7 +4,7 @@ import { join } from "node:path";
 import { log } from "../../lib/logger.js";
 import { errorMessage } from "../../lib/utils.js";
 import { nowISO } from "./utils.js";
-export const SCHEMA_VERSION = 27;
+export const SCHEMA_VERSION = 29;
 function isDuplicateColumnError(err, columnName) {
     const message = errorMessage(err).toLowerCase();
     return message.includes(`duplicate column name: ${columnName}`.toLowerCase());
@@ -495,7 +495,91 @@ const MIGRATIONS = {
         }
         log.info("[migration-27] Added clean_shutdown column to thread_registry (default clean)");
     },
+    28: (db) => {
+        // Expiry provenance: record WHY a note's valid_to was set, so unarchive can
+        // tell an archive-kill (restore it) from a pruning/gate/cap retirement
+        // (leave it dead). See ExpiryReason in note-archival.ts for the writer
+        // matrix; backfillExpiryReasons labels the pre-column tombstones.
+        try {
+            db.exec(`ALTER TABLE semantic_notes ADD COLUMN expiry_reason TEXT`);
+        }
+        catch (err) {
+            if (!isDuplicateColumnError(err, "expiry_reason"))
+                throw err;
+        }
+        db.exec(`CREATE INDEX IF NOT EXISTS idx_sem_expiry_reason ON semantic_notes(thread_id, expiry_reason) WHERE valid_to IS NOT NULL`);
+        backfillExpiryReasons(db);
+        log.info("[migration-28] Added expiry_reason column to semantic_notes");
+    },
+    29: (db) => {
+        // The topic index is now computed on demand from active notes
+        // (getTopicIndex in bootstrap.ts); the stored aggregate and its
+        // increment/decrement bookkeeping drifted repeatedly and fed only
+        // display surfaces. Dropping the table is safe: nothing reads it.
+        db.exec(`DROP TABLE IF EXISTS meta_topic_index`);
+        log.info("[migration-29] Dropped meta_topic_index (topics are computed on demand)");
+    },
 };
+/**
+ * Label pre-column tombstones (valid_to set, expiry_reason NULL) with the most
+ * that can be *proven* about who expired them — measured on the 2026-07-26
+ * incident DB, but every rule below is derived from writer code, not from that
+ * one dataset:
+ *
+ * 1. `superseded_by IS NOT NULL` → 'superseded'. Structural.
+ * 2. Bulk clusters (≥10 rows, same thread, byte-identical valid_to — the
+ *    signature of a single-nowISO() loop):
+ *    - on a dead/archived/unregistered thread, only archiveNotesForThread ever
+ *      produced that → 'archived-legacy';
+ *    - on a live thread the sweep never ran; if the cluster is 100%
+ *      '[REFLECTION]%' rows it can only be enforceReflectionCap's buffer trim
+ *      → 'reflection-cap' (e.g. the predicted 635-row trim of restored
+ *      reflections on thread 1327 at 2026-07-26T01:02:55);
+ *    - a mixed cluster on a live thread is ambiguous → falls through to 3.
+ * 3. Everything else → 'unknown-legacy'. Pruning singles, gate kills and
+ *    small sweeps are indistinguishable after the fact; no guess is recorded
+ *    as fact. These stay dead unless their thread is explicitly unarchived.
+ *
+ * Exported for tests; idempotent (only touches expiry_reason IS NULL rows).
+ */
+export function backfillExpiryReasons(db) {
+    const superseded = db
+        .prepare(`UPDATE semantic_notes SET expiry_reason = 'superseded'
+       WHERE valid_to IS NOT NULL AND expiry_reason IS NULL AND superseded_by IS NOT NULL`)
+        .run().changes;
+    const clusters = db
+        .prepare(`SELECT sn.thread_id AS threadId, sn.valid_to AS validTo, COUNT(*) AS total,
+              SUM(CASE WHEN sn.content LIKE '[REFLECTION]%' THEN 1 ELSE 0 END) AS reflections,
+              tr.status AS threadStatus
+         FROM semantic_notes sn
+         LEFT JOIN thread_registry tr ON tr.thread_id = sn.thread_id
+        WHERE sn.valid_to IS NOT NULL AND sn.expiry_reason IS NULL
+        GROUP BY sn.thread_id, sn.valid_to
+       HAVING COUNT(*) >= 10`)
+        .all();
+    const labelCluster = db.prepare(`UPDATE semantic_notes SET expiry_reason = ?
+     WHERE thread_id IS ? AND valid_to = ? AND expiry_reason IS NULL`);
+    let archivedLegacy = 0;
+    let reflectionCap = 0;
+    for (const cluster of clusters) {
+        const threadIsLive = cluster.threadStatus !== null &&
+            !["archived", "expired", "exited"].includes(cluster.threadStatus);
+        if (!threadIsLive) {
+            archivedLegacy += labelCluster.run("archived-legacy", cluster.threadId, cluster.validTo)
+                .changes;
+        }
+        else if (cluster.reflections === cluster.total) {
+            reflectionCap += labelCluster.run("reflection-cap", cluster.threadId, cluster.validTo)
+                .changes;
+        }
+        // live thread, mixed content: ambiguous — falls through to unknown-legacy.
+    }
+    const unknown = db
+        .prepare(`UPDATE semantic_notes SET expiry_reason = 'unknown-legacy'
+       WHERE valid_to IS NOT NULL AND expiry_reason IS NULL`)
+        .run().changes;
+    log.info(`[migration-28] Expiry-reason backfill: ${superseded} superseded, ${archivedLegacy} archived-legacy, ${reflectionCap} reflection-cap, ${unknown} unknown-legacy`);
+}
 export function runMigrations(db) {
     const currentVersion = getCurrentSchemaVersion(db);
     log.info(`[memory] Current schema version: ${currentVersion}, target: ${SCHEMA_VERSION}`);

package/dist/data/memory/migration-runner.js.map

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package/dist/data/memory/note-archival.d.ts

@@ -4,11 +4,36 @@
  */
 import type { Database } from "./schema.js";
 /**
- * Expire all active semantic notes belonging to a given thread.
- * Sets valid_to = NOW() and decrements the topic index for each note's keywords.
- * Returns the count of archived notes.
+ * Why a note's valid_to was set. Every live writer that expires a note records
+ * one, so restoreNotesForThread can tell a reversible archive-kill from a
+ * deliberate retirement (the fix for dd47ea9's known limitation). The two
+ * `*-legacy` values are written only by the migration-28 backfill over rows
+ * that predate the column; live code never writes them.
  */
-export declare function archiveNotesForThread(db: Database, threadId: number): number;
+export type ExpiryReason = "thread-terminal" | "thread-archived" | "worker-cleanup" | "pruned" | "quality-gate" | "reflection-cap" | "superseded" | "merged" | "archived-legacy" | "unknown-legacy";
+/**
+ * Expire all active semantic notes belonging to a given thread, recording why.
+ * Sets valid_to = NOW(). Returns the count of archived notes.
+ */
+export declare function archiveNotesForThread(db: Database, threadId: number, reason: Extract<ExpiryReason, "thread-terminal" | "worker-cleanup">): number;
+/**
+ * Restore notes previously expired by archiving a thread — the mirror of
+ * archiveNotesForThread. Clears valid_to (and expiry_reason) for the thread's
+ * restorable expired notes.
+ *
+ * Only notes whose expiry_reason marks an archive-kill are resurrected (see
+ * RESTORABLE_EXPIRY_REASONS); a note that was pruned, gate-expired, cap-trimmed
+ * or superseded stays dead. `unknown-legacy` (and NULL, which can only mean a
+ * pre-column binary wrote the expiry) is included only when the caller asserts
+ * the thread is being unarchived (`includeUnknownLegacy`) — for a thread that
+ * was archived, the historical sweep is the overwhelmingly likely killer, so a
+ * few wrongly-revived pruning singles are an accepted, disclosed cost.
+ *
+ * Returns the count of restored notes.
+ */
+export declare function restoreNotesForThread(db: Database, threadId: number, options?: {
+    includeUnknownLegacy?: boolean;
+}): number;
 /**
  * Find thread IDs that have active (non-expired) semantic notes.
  * Returns distinct thread IDs (excluding null/global notes).

package/dist/data/memory/note-archival.d.ts.map

@@ -1 +1 @@
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