sensorium-mcp 3.1.0-refactor.6 → 3.1.0-refactor.8

package/dist/data/memory/note-archival.js

@@ -2,37 +2,66 @@
  * Thread-scoped semantic note archival — bulk expiry when a thread is
  * archived or a disposable worker is cleaned up.
  */
-import { nowISO, parseJsonArray } from "./utils.js";
-import { decrementTopicIndexForKeywords } from "./topic-index.js";
+import { nowISO } from "./utils.js";
 import { log } from "../../lib/logger.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.
+ * Reasons restoreNotesForThread revives unconditionally: kills that archived a
+ * thread's knowledge rather than retiring it. `pruned`/`quality-gate`/
+ * `reflection-cap`/`superseded`/`merged` stay dead through unarchive — those
+ * notes were individually judged, not swept. `thread-terminal` also stays dead:
+ * terminal threads cannot be unarchived, so a terminal-swept note reappearing
+ * via some later unarchive would be a bug, not a restore.
  */
-export function archiveNotesForThread(db, threadId) {
+const RESTORABLE_EXPIRY_REASONS = [
+    "thread-archived",
+    "archived-legacy",
+    "worker-cleanup",
+];
+/**
+ * Expire all active semantic notes belonging to a given thread, recording why.
+ * Sets valid_to = NOW(). Returns the count of archived notes.
+ */
+export function archiveNotesForThread(db, threadId, reason) {
     const now = nowISO();
-    const activeNotes = db
-        .prepare(`SELECT note_id, keywords FROM semantic_notes
+    const result = db
+        .prepare(`UPDATE semantic_notes SET valid_to = ?, updated_at = ?, expiry_reason = ?
      WHERE thread_id = ? AND valid_to IS NULL`)
-        .all(threadId);
-    if (activeNotes.length === 0)
-        return 0;
-    const expireStmt = db.prepare(`UPDATE semantic_notes SET valid_to = ?, updated_at = ? WHERE note_id = ?`);
-    const notes = activeNotes.map((row) => ({
-        noteId: row.note_id,
-        keywords: parseJsonArray(row.keywords),
-    }));
-    db.transaction(() => {
-        for (const note of notes) {
-            expireStmt.run(now, now, note.noteId);
-            if (note.keywords.length > 0) {
-                decrementTopicIndexForKeywords(db, note.keywords);
-            }
-        }
-    })();
-    log.info(`[memory] Archived ${notes.length} semantic notes for thread ${threadId}`);
-    return notes.length;
+        .run(now, now, reason, threadId);
+    if (result.changes > 0) {
+        log.info(`[memory] Archived ${result.changes} semantic notes for thread ${threadId} (${reason})`);
+    }
+    return result.changes;
+}
+/**
+ * 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 function restoreNotesForThread(db, threadId, options) {
+    const now = nowISO();
+    const reasonPlaceholders = RESTORABLE_EXPIRY_REASONS.map(() => "?").join(",");
+    const unknownClause = options?.includeUnknownLegacy
+        ? ` OR expiry_reason = 'unknown-legacy' OR expiry_reason IS NULL`
+        : "";
+    const result = db
+        .prepare(`UPDATE semantic_notes SET valid_to = NULL, expiry_reason = NULL, updated_at = ?
+     WHERE thread_id = ? AND valid_to IS NOT NULL AND superseded_by IS NULL
+       AND (expiry_reason IN (${reasonPlaceholders})${unknownClause})`)
+        .run(now, threadId, ...RESTORABLE_EXPIRY_REASONS);
+    if (result.changes > 0) {
+        log.info(`[memory] Restored ${result.changes} semantic notes for thread ${threadId}`);
+    }
+    return result.changes;
 }
 /**
  * Find thread IDs that have active (non-expired) semantic notes.

package/dist/data/memory/note-archival.js.map

@@ -1 +1 @@
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package/dist/data/memory/reflection.d.ts.map

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

@@ -42,7 +42,7 @@ function enforceReflectionCap(db, threadId) {
     // Phase 1: Expire stale never-accessed reflections
     const staleResult = db
         .prepare(`UPDATE semantic_notes
-       SET valid_to = ?
+       SET valid_to = ?, expiry_reason = 'reflection-cap'
        WHERE valid_to IS NULL AND superseded_by IS NULL
          AND content LIKE '[REFLECTION]%'
          AND access_count = 0
@@ -70,7 +70,7 @@ function enforceReflectionCap(db, threadId) {
             .all(knowledgeThreadId, excess);
         if (toExpire.length > 0) {
             const now = nowISO();
-            const stmt = db.prepare(`UPDATE semantic_notes SET valid_to = ? WHERE note_id = ?`);
+            const stmt = db.prepare(`UPDATE semantic_notes SET valid_to = ?, expiry_reason = 'reflection-cap' WHERE note_id = ?`);
             db.transaction(() => {
                 for (const row of toExpire)
                     stmt.run(now, row.note_id);

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

@@ -1 +1 @@
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package/dist/data/memory/schema-ddl.d.ts

@@ -1,4 +1,4 @@
 import type { Database } from "./db-types.js";
-export declare const SCHEMA_SQL = "\nCREATE TABLE IF NOT EXISTS episodes (\n  episode_id     TEXT PRIMARY KEY,\n  session_id     TEXT NOT NULL,\n  thread_id      INTEGER NOT NULL,\n  timestamp      TEXT NOT NULL,\n  type           TEXT NOT NULL CHECK(type IN ('operator_message','agent_action','system_event','operator_reaction')),\n  modality       TEXT NOT NULL CHECK(modality IN ('text','voice','photo','video_note','document','mixed','reaction')),\n  content        TEXT NOT NULL,\n  topic_tags     TEXT,\n  importance     REAL NOT NULL DEFAULT 0.5,\n  consolidated   INTEGER DEFAULT 0,\n  accessed_count INTEGER DEFAULT 0,\n  last_accessed  TEXT,\n  created_at     TEXT NOT NULL\n);\n\nCREATE INDEX IF NOT EXISTS idx_ep_thread_time ON episodes(thread_id, timestamp DESC);\nCREATE INDEX IF NOT EXISTS idx_ep_importance ON episodes(importance DESC);\nCREATE INDEX IF NOT EXISTS idx_ep_uncons ON episodes(consolidated) WHERE consolidated = 0;\n\nCREATE TABLE IF NOT EXISTS semantic_notes (\n  note_id         TEXT PRIMARY KEY,\n  type            TEXT NOT NULL CHECK(type IN ('fact','preference','pattern','entity','relationship')),\n  content         TEXT NOT NULL,\n  keywords        TEXT NOT NULL,\n  confidence      REAL NOT NULL DEFAULT 0.5,\n  source_episodes TEXT,\n  linked_notes    TEXT,\n  link_reasons    TEXT,\n  valid_from      TEXT NOT NULL,\n  valid_to        TEXT,\n  superseded_by   TEXT,\n  access_count    INTEGER DEFAULT 0,\n  last_accessed   TEXT,\n  priority        INTEGER NOT NULL DEFAULT 0,\n  thread_id       INTEGER,\n  is_guardrail    INTEGER NOT NULL DEFAULT 0,\n  pinned          INTEGER NOT NULL DEFAULT 0,\n  quality_score   INTEGER,\n  created_at      TEXT NOT NULL,\n  updated_at      TEXT NOT NULL\n);\n\nCREATE INDEX IF NOT EXISTS idx_sem_type ON semantic_notes(type);\nCREATE INDEX IF NOT EXISTS idx_sem_conf ON semantic_notes(confidence DESC);\nCREATE INDEX IF NOT EXISTS idx_sem_valid ON semantic_notes(valid_to) WHERE valid_to IS NULL;\nCREATE INDEX IF NOT EXISTS idx_sem_priority ON semantic_notes(priority DESC) WHERE valid_to IS NULL;\nCREATE INDEX IF NOT EXISTS idx_sem_thread ON semantic_notes(thread_id) WHERE valid_to IS NULL;\nCREATE INDEX IF NOT EXISTS idx_sem_guardrail ON semantic_notes(is_guardrail) WHERE is_guardrail = 1 AND valid_to IS NULL;\nCREATE INDEX IF NOT EXISTS idx_sem_pinned ON semantic_notes(pinned) WHERE pinned = 1 AND valid_to IS NULL;\n\nCREATE TABLE IF NOT EXISTS meta_topic_index (\n  topic            TEXT PRIMARY KEY,\n  semantic_count   INTEGER DEFAULT 0,\n  last_updated     TEXT,\n  avg_confidence   REAL DEFAULT 0.5,\n  total_accesses   INTEGER DEFAULT 0\n);\n\nCREATE TABLE IF NOT EXISTS meta_consolidation_log (\n  id                  INTEGER PRIMARY KEY AUTOINCREMENT,\n  run_at              TEXT NOT NULL,\n  episodes_processed  INTEGER,\n  notes_created       INTEGER,\n  duration_ms         INTEGER\n);\n\nCREATE TABLE IF NOT EXISTS voice_signatures (\n  id             INTEGER PRIMARY KEY AUTOINCREMENT,\n  episode_id     TEXT NOT NULL,\n  emotion        TEXT,\n  arousal        REAL,\n  dominance      REAL,\n  valence        REAL,\n  speech_rate    REAL,\n  mean_pitch_hz  REAL,\n  pitch_std_hz   REAL,\n  jitter         REAL,\n  shimmer        REAL,\n  hnr_db         REAL,\n  audio_events   TEXT,\n  duration_sec   REAL,\n  created_at     TEXT NOT NULL\n);\n\nCREATE INDEX IF NOT EXISTS idx_voice_ep ON voice_signatures(episode_id);\nCREATE INDEX IF NOT EXISTS idx_voice_time ON voice_signatures(created_at DESC);\n\nCREATE TABLE IF NOT EXISTS note_embeddings (\n  note_id    TEXT PRIMARY KEY,\n  embedding  BLOB NOT NULL,\n  model      TEXT NOT NULL DEFAULT 'text-embedding-3-small',\n  created_at TEXT NOT NULL\n);\n\nCREATE INDEX IF NOT EXISTS idx_emb_note ON note_embeddings(note_id);\n\nCREATE TABLE IF NOT EXISTS sent_messages (\n  message_id INTEGER PRIMARY KEY,\n  thread_id  INTEGER NOT NULL,\n  created_at TEXT DEFAULT (datetime('now'))\n);\n\nCREATE INDEX IF NOT EXISTS idx_sent_messages_thread ON sent_messages(thread_id);\n\nCREATE TABLE IF NOT EXISTS topic_registry (\n  chat_id       TEXT NOT NULL,\n  name          TEXT NOT NULL COLLATE NOCASE,\n  thread_id     INTEGER NOT NULL,\n  registered_at TEXT NOT NULL DEFAULT (datetime('now')),\n  PRIMARY KEY (chat_id, name)\n);\n\nCREATE TABLE IF NOT EXISTS temporal_narratives (\n  id INTEGER PRIMARY KEY AUTOINCREMENT,\n  thread_id INTEGER NOT NULL,\n  resolution TEXT NOT NULL CHECK(resolution IN ('day', 'week', 'month', 'quarter', 'half_year')),\n  period_start TEXT NOT NULL,\n  period_end TEXT NOT NULL,\n  narrative TEXT NOT NULL,\n  source_episode_count INTEGER NOT NULL DEFAULT 0,\n  source_note_count INTEGER NOT NULL DEFAULT 0,\n  model TEXT,\n  created_at TEXT NOT NULL DEFAULT (datetime('now')),\n  UNIQUE(thread_id, resolution, period_start)\n);\nCREATE INDEX IF NOT EXISTS idx_narrative_thread_res ON temporal_narratives(thread_id, resolution, created_at DESC);\n\nCREATE TABLE IF NOT EXISTS thread_registry (\n  id              INTEGER PRIMARY KEY AUTOINCREMENT,\n  thread_id       INTEGER NOT NULL UNIQUE,\n  name            TEXT NOT NULL,\n  type            TEXT NOT NULL CHECK(type IN ('root','daily','branch','worker')),\n  root_thread_id  INTEGER,\n  badge           TEXT NOT NULL DEFAULT 'root',\n  client          TEXT DEFAULT 'claude',\n  max_retries     INTEGER DEFAULT 5,\n  cooldown_ms     INTEGER DEFAULT 300000,\n  keep_alive      INTEGER DEFAULT 0,\n  created_at      TEXT NOT NULL,\n  last_active_at  TEXT,\n  session_reset_at TEXT,\n  clean_shutdown  INTEGER NOT NULL DEFAULT 1,\n  status          TEXT NOT NULL DEFAULT 'active' CHECK(status IN ('active','archived','expired','exited')),\n  daily_rotation  INTEGER NOT NULL DEFAULT 0,\n  autonomous_mode INTEGER NOT NULL DEFAULT 0,\n  telegram_topic_id INTEGER,\n  identity_prompt TEXT,\n  working_directory TEXT,\n  pid INTEGER,\n  archived_at TEXT,\n  summary TEXT\n);\nCREATE INDEX IF NOT EXISTS idx_thread_reg_type ON thread_registry(type);\nCREATE INDEX IF NOT EXISTS idx_thread_reg_root ON thread_registry(root_thread_id);\nCREATE INDEX IF NOT EXISTS idx_thread_reg_status ON thread_registry(status);\n\nCREATE TABLE IF NOT EXISTS schema_version (\n  version     INTEGER PRIMARY KEY,\n  applied_at  TEXT NOT NULL\n);\n";
+export declare const SCHEMA_SQL = "\nCREATE TABLE IF NOT EXISTS episodes (\n  episode_id     TEXT PRIMARY KEY,\n  session_id     TEXT NOT NULL,\n  thread_id      INTEGER NOT NULL,\n  timestamp      TEXT NOT NULL,\n  type           TEXT NOT NULL CHECK(type IN ('operator_message','agent_action','system_event','operator_reaction')),\n  modality       TEXT NOT NULL CHECK(modality IN ('text','voice','photo','video_note','document','mixed','reaction')),\n  content        TEXT NOT NULL,\n  topic_tags     TEXT,\n  importance     REAL NOT NULL DEFAULT 0.5,\n  consolidated   INTEGER DEFAULT 0,\n  accessed_count INTEGER DEFAULT 0,\n  last_accessed  TEXT,\n  created_at     TEXT NOT NULL\n);\n\nCREATE INDEX IF NOT EXISTS idx_ep_thread_time ON episodes(thread_id, timestamp DESC);\nCREATE INDEX IF NOT EXISTS idx_ep_importance ON episodes(importance DESC);\nCREATE INDEX IF NOT EXISTS idx_ep_uncons ON episodes(consolidated) WHERE consolidated = 0;\n\nCREATE TABLE IF NOT EXISTS semantic_notes (\n  note_id         TEXT PRIMARY KEY,\n  type            TEXT NOT NULL CHECK(type IN ('fact','preference','pattern','entity','relationship')),\n  content         TEXT NOT NULL,\n  keywords        TEXT NOT NULL,\n  confidence      REAL NOT NULL DEFAULT 0.5,\n  source_episodes TEXT,\n  linked_notes    TEXT,\n  link_reasons    TEXT,\n  valid_from      TEXT NOT NULL,\n  valid_to        TEXT,\n  superseded_by   TEXT,\n  access_count    INTEGER DEFAULT 0,\n  last_accessed   TEXT,\n  priority        INTEGER NOT NULL DEFAULT 0,\n  thread_id       INTEGER,\n  is_guardrail    INTEGER NOT NULL DEFAULT 0,\n  pinned          INTEGER NOT NULL DEFAULT 0,\n  quality_score   INTEGER,\n  expiry_reason   TEXT,\n  created_at      TEXT NOT NULL,\n  updated_at      TEXT NOT NULL\n);\n\nCREATE INDEX IF NOT EXISTS idx_sem_type ON semantic_notes(type);\nCREATE INDEX IF NOT EXISTS idx_sem_conf ON semantic_notes(confidence DESC);\nCREATE INDEX IF NOT EXISTS idx_sem_valid ON semantic_notes(valid_to) WHERE valid_to IS NULL;\nCREATE INDEX IF NOT EXISTS idx_sem_priority ON semantic_notes(priority DESC) WHERE valid_to IS NULL;\nCREATE INDEX IF NOT EXISTS idx_sem_thread ON semantic_notes(thread_id) WHERE valid_to IS NULL;\nCREATE INDEX IF NOT EXISTS idx_sem_guardrail ON semantic_notes(is_guardrail) WHERE is_guardrail = 1 AND valid_to IS NULL;\nCREATE INDEX IF NOT EXISTS idx_sem_pinned ON semantic_notes(pinned) WHERE pinned = 1 AND valid_to IS NULL;\nCREATE INDEX IF NOT EXISTS idx_sem_expiry_reason ON semantic_notes(thread_id, expiry_reason) WHERE valid_to IS NOT NULL;\n\nCREATE TABLE IF NOT EXISTS meta_consolidation_log (\n  id                  INTEGER PRIMARY KEY AUTOINCREMENT,\n  run_at              TEXT NOT NULL,\n  episodes_processed  INTEGER,\n  notes_created       INTEGER,\n  duration_ms         INTEGER\n);\n\nCREATE TABLE IF NOT EXISTS voice_signatures (\n  id             INTEGER PRIMARY KEY AUTOINCREMENT,\n  episode_id     TEXT NOT NULL,\n  emotion        TEXT,\n  arousal        REAL,\n  dominance      REAL,\n  valence        REAL,\n  speech_rate    REAL,\n  mean_pitch_hz  REAL,\n  pitch_std_hz   REAL,\n  jitter         REAL,\n  shimmer        REAL,\n  hnr_db         REAL,\n  audio_events   TEXT,\n  duration_sec   REAL,\n  created_at     TEXT NOT NULL\n);\n\nCREATE INDEX IF NOT EXISTS idx_voice_ep ON voice_signatures(episode_id);\nCREATE INDEX IF NOT EXISTS idx_voice_time ON voice_signatures(created_at DESC);\n\nCREATE TABLE IF NOT EXISTS note_embeddings (\n  note_id    TEXT PRIMARY KEY,\n  embedding  BLOB NOT NULL,\n  model      TEXT NOT NULL DEFAULT 'text-embedding-3-small',\n  created_at TEXT NOT NULL\n);\n\nCREATE INDEX IF NOT EXISTS idx_emb_note ON note_embeddings(note_id);\n\nCREATE TABLE IF NOT EXISTS sent_messages (\n  message_id INTEGER PRIMARY KEY,\n  thread_id  INTEGER NOT NULL,\n  created_at TEXT DEFAULT (datetime('now'))\n);\n\nCREATE INDEX IF NOT EXISTS idx_sent_messages_thread ON sent_messages(thread_id);\n\nCREATE TABLE IF NOT EXISTS topic_registry (\n  chat_id       TEXT NOT NULL,\n  name          TEXT NOT NULL COLLATE NOCASE,\n  thread_id     INTEGER NOT NULL,\n  registered_at TEXT NOT NULL DEFAULT (datetime('now')),\n  PRIMARY KEY (chat_id, name)\n);\n\nCREATE TABLE IF NOT EXISTS temporal_narratives (\n  id INTEGER PRIMARY KEY AUTOINCREMENT,\n  thread_id INTEGER NOT NULL,\n  resolution TEXT NOT NULL CHECK(resolution IN ('day', 'week', 'month', 'quarter', 'half_year')),\n  period_start TEXT NOT NULL,\n  period_end TEXT NOT NULL,\n  narrative TEXT NOT NULL,\n  source_episode_count INTEGER NOT NULL DEFAULT 0,\n  source_note_count INTEGER NOT NULL DEFAULT 0,\n  model TEXT,\n  created_at TEXT NOT NULL DEFAULT (datetime('now')),\n  UNIQUE(thread_id, resolution, period_start)\n);\nCREATE INDEX IF NOT EXISTS idx_narrative_thread_res ON temporal_narratives(thread_id, resolution, created_at DESC);\n\nCREATE TABLE IF NOT EXISTS thread_registry (\n  id              INTEGER PRIMARY KEY AUTOINCREMENT,\n  thread_id       INTEGER NOT NULL UNIQUE,\n  name            TEXT NOT NULL,\n  type            TEXT NOT NULL CHECK(type IN ('root','daily','branch','worker')),\n  root_thread_id  INTEGER,\n  badge           TEXT NOT NULL DEFAULT 'root',\n  client          TEXT DEFAULT 'claude',\n  max_retries     INTEGER DEFAULT 5,\n  cooldown_ms     INTEGER DEFAULT 300000,\n  keep_alive      INTEGER DEFAULT 0,\n  created_at      TEXT NOT NULL,\n  last_active_at  TEXT,\n  session_reset_at TEXT,\n  clean_shutdown  INTEGER NOT NULL DEFAULT 1,\n  status          TEXT NOT NULL DEFAULT 'active' CHECK(status IN ('active','archived','expired','exited')),\n  daily_rotation  INTEGER NOT NULL DEFAULT 0,\n  autonomous_mode INTEGER NOT NULL DEFAULT 0,\n  telegram_topic_id INTEGER,\n  identity_prompt TEXT,\n  working_directory TEXT,\n  pid INTEGER,\n  archived_at TEXT,\n  summary TEXT\n);\nCREATE INDEX IF NOT EXISTS idx_thread_reg_type ON thread_registry(type);\nCREATE INDEX IF NOT EXISTS idx_thread_reg_root ON thread_registry(root_thread_id);\nCREATE INDEX IF NOT EXISTS idx_thread_reg_status ON thread_registry(status);\n\nCREATE TABLE IF NOT EXISTS schema_version (\n  version     INTEGER PRIMARY KEY,\n  applied_at  TEXT NOT NULL\n);\n";
 export declare function cleanupOldSentMessages(db: Database): void;
 //# sourceMappingURL=schema-ddl.d.ts.map

package/dist/data/memory/schema-ddl.d.ts.map

@@ -1 +1 @@
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package/dist/data/memory/schema-ddl.js

@@ -40,6 +40,7 @@ CREATE TABLE IF NOT EXISTS semantic_notes (
   is_guardrail    INTEGER NOT NULL DEFAULT 0,
   pinned          INTEGER NOT NULL DEFAULT 0,
   quality_score   INTEGER,
+  expiry_reason   TEXT,
   created_at      TEXT NOT NULL,
   updated_at      TEXT NOT NULL
 );
@@ -51,14 +52,7 @@ CREATE INDEX IF NOT EXISTS idx_sem_priority ON semantic_notes(priority DESC) WHE
 CREATE INDEX IF NOT EXISTS idx_sem_thread ON semantic_notes(thread_id) WHERE valid_to IS NULL;
 CREATE INDEX IF NOT EXISTS idx_sem_guardrail ON semantic_notes(is_guardrail) WHERE is_guardrail = 1 AND valid_to IS NULL;
 CREATE INDEX IF NOT EXISTS idx_sem_pinned ON semantic_notes(pinned) WHERE pinned = 1 AND valid_to IS NULL;
-
-CREATE TABLE IF NOT EXISTS meta_topic_index (
-  topic            TEXT PRIMARY KEY,
-  semantic_count   INTEGER DEFAULT 0,
-  last_updated     TEXT,
-  avg_confidence   REAL DEFAULT 0.5,
-  total_accesses   INTEGER DEFAULT 0
-);
+CREATE INDEX IF NOT EXISTS idx_sem_expiry_reason ON semantic_notes(thread_id, expiry_reason) WHERE valid_to IS NOT NULL;
 
 CREATE TABLE IF NOT EXISTS meta_consolidation_log (
   id                  INTEGER PRIMARY KEY AUTOINCREMENT,

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package/dist/data/memory/semantic-notes.d.ts.map

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package/dist/data/memory/semantic-notes.js

@@ -3,7 +3,6 @@
  * (save, read, update, supersede, link migration).
  */
 import { generateId, nowISO, jsonOrNull, parseJsonArray, parseJsonObject } from "./utils.js";
-import { updateTopicIndexForKeywords } from "./topic-index.js";
 import { log } from "../../lib/logger.js";
 // ─── Constants ───────────────────────────────────────────────────────────────
 /** Maximum guardrail notes returned by getGuardrailNotes. */
@@ -154,8 +153,6 @@ export function saveSemanticNote(db, note) {
     db.prepare(`INSERT INTO semantic_notes
        (note_id, type, content, keywords, confidence, priority, thread_id, is_guardrail, pinned, source_episodes, linked_notes, link_reasons, valid_from, access_count, quality_score, created_at, updated_at)
      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, 0, ?, ?, ?)`).run(id, note.type, note.content, JSON.stringify(note.keywords), Math.max(0, Math.min(1, note.confidence ?? 0.5)), Math.max(0, Math.min(2, note.priority ?? 0)), note.threadId ?? null, note.isGuardrail ? 1 : 0, note.pinned ? 1 : 0, jsonOrNull(note.sourceEpisodes), jsonOrNull(note.linkedNotes), note.linkReasons ? JSON.stringify(note.linkReasons) : null, now, qualityScore, now, now);
-    // Update topic index for each keyword
-    updateTopicIndexForKeywords(db, note.keywords);
     return id;
 }
 export function getTopSemanticNotes(db, options) {
@@ -290,7 +287,7 @@ export function supersedeNote(db, oldNoteId, newNote) {
         sourceEpisodes: newNote.sourceEpisodes,
     });
     const now = nowISO();
-    db.prepare(`UPDATE semantic_notes SET superseded_by = ?, valid_to = ?, updated_at = ? WHERE note_id = ?`).run(newId, now, now, oldNoteId);
+    db.prepare(`UPDATE semantic_notes SET superseded_by = ?, valid_to = ?, updated_at = ?, expiry_reason = 'superseded' WHERE note_id = ?`).run(newId, now, now, oldNoteId);
     // The supersession relationship is already recorded by superseded_by above.
     // Repoint any inbound causal links from the now-expired note to its successor
     // so they stay live for the bootstrap consumer.

package/dist/data/memory/semantic-notes.js.map

@@ -1 +1 @@
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package/dist/data/memory/thread-registry.d.ts.map

@@ -1 +1 @@
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package/dist/data/memory/thread-registry.js

@@ -5,6 +5,7 @@
  * (root, daily, branch, worker) with their configuration and status.
  */
 import { nowISO } from "./utils.js";
+import { restoreNotesForThread } from "./note-archival.js";
 export class ThreadRepository {
     registerThread(db, entry) {
         return registerThread(db, entry);
@@ -211,10 +212,25 @@ export function archiveThread(db, threadId) {
     return result.changes > 0;
 }
 export function unarchiveThread(db, threadId) {
-    const result = db
-        .prepare(`UPDATE thread_registry SET status = 'active', keep_alive = 1, archived_at = NULL WHERE thread_id = ? AND status = 'archived'`)
-        .run(threadId);
-    return result.changes > 0;
+    // The status flip and the note restore must be atomic. If restore threw after
+    // the status was already committed as 'active', the WHERE status = 'archived'
+    // guard below would never match again, so a retry could not re-run restore and
+    // the notes would be stranded expired forever. Wrapping both in one
+    // transaction rolls the status change back on any restore failure.
+    return db.transaction(() => {
+        const result = db
+            .prepare(`UPDATE thread_registry SET status = 'active', keep_alive = 1, archived_at = NULL WHERE thread_id = ? AND status = 'archived'`)
+            .run(threadId);
+        if (result.changes === 0)
+            return false;
+        // Archiving expired this thread's notes (historically, before "archived" was
+        // removed from TERMINAL_THREAD_STATUSES). Restore them so the reactivated
+        // thread gets its memory back — the missing half of the archive symmetry.
+        // includeUnknownLegacy: for a thread that was archived, the historical
+        // sweep is the overwhelmingly likely killer of its unlabeled tombstones.
+        restoreNotesForThread(db, threadId, { includeUnknownLegacy: true });
+        return true;
+    })();
 }
 export function getArchivedThreads(db) {
     const rows = db

package/dist/data/memory/thread-registry.js.map

@@ -1 +1 @@
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package/dist/services/background-runner.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"background-runner.d.ts","sourceRoot":"","sources":["../../src/services/background-runner.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,yBAAyB,CAAC;AAC5D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,eAAe,CAAC;AAGpD,OAAO,KAAK,EAAE,sBAAsB,EAAE,MAAM,+BAA+B,CAAC;AAW5E,UAAU,oBAAoB;IAC5B,WAAW,EAAE,MAAM,UAAU,CAAC,OAAO,YAAY,CAAC,CAAC;IACnD,QAAQ,EAAE,cAAc,CAAC;IACzB,MAAM,EAAE,MAAM,CAAC;IACf,eAAe,EAAE,sBAAsB,CAAC;IACxC,GAAG,EAAE;QACH,IAAI,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;QAC5B,IAAI,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;QAC5B,KAAK,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;KAC9B,CAAC;CACH;AAED,qBAAa,mBAAmB;IAIlB,OAAO,CAAC,QAAQ,CAAC,IAAI;IAHjC,OAAO,CAAC,SAAS,CAAwC;IACzD,OAAO,CAAC,oBAAoB,CAAuB;gBAEtB,IAAI,EAAE,oBAAoB;IAEvD,KAAK,IAAI,IAAI;IA0Bb,IAAI,IAAI,IAAI;YAOE,gBAAgB;YA4BhB,kBAAkB;YA0ClB,qBAAqB;CAqCpC"}

package/dist/services/background-runner.js

@@ -2,7 +2,7 @@ import { rotateAllDailySessions } from "./daily-session.js";
 import { cleanupExpiredWorkers } from "./worker-cleanup.service.js";
 import { errorMessage } from "../lib/utils.js";
 import { getAllThreads } from "../data/memory/thread-registry.js";
-import { isThreadRunning, spawnedThreads } from "./process.service.js";
+import { isThreadRunning, spawnedThreads, sweepOrphanDescendants } from "./process.service.js";
 import { decommissionWorker } from "./worker-cleanup.service.js";
 import { hasRunToday } from "../data/daily-marker.js";
 const DAILY_ROTATION_INTERVAL_MS = 5 * 60_000;
@@ -50,6 +50,16 @@ export class BackgroundJobRunner {
         catch (err) {
             this.deps.log.error(`Expired worker cleanup error: ${errorMessage(err)}`);
         }
+        // Piggyback the orphan-descendant sweep on the same cadence and (single)
+        // process snapshot budget — no new timer. It records lineage for live threads
+        // and logs (or, behind ORPHAN_SWEEP_KILL, reaps) grandchildren whose middle
+        // parent died on its own. Failures here must not affect worker cleanup.
+        try {
+            await sweepOrphanDescendants();
+        }
+        catch (err) {
+            this.deps.log.error(`Orphan-descendant sweep error: ${errorMessage(err)}`);
+        }
     }
     async runDeadWorkerSweep() {
         try {

package/dist/services/background-runner.js.map

@@ -1 +1 @@
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package/dist/services/consolidation.service.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"consolidation.service.d.ts","sourceRoot":"","sources":["../../src/services/consolidation.service.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,0BAA0B,CAAC;AASzD,OAAO,EAEL,KAAK,mBAAmB,EAOzB,MAAM,iCAAiC,CAAC;AAqEzC,wBAAsB,0BAA0B,CAC9C,EAAE,EAAE,QAAQ,EACZ,OAAO,CAAC,EAAE;IAAE,oBAAoB,CAAC,EAAE,MAAM,CAAC;IAAC,MAAM,CAAC,EAAE,OAAO,CAAA;CAAE,GAC5D,OAAO,CAAC,mBAAmB,CAAC,CAqF9B;AAED,wBAAsB,2BAA2B,CAC/C,EAAE,EAAE,QAAQ,EACZ,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE;IAAE,WAAW,CAAC,EAAE,MAAM,CAAC;IAAC,MAAM,CAAC,EAAE,OAAO,CAAC;IAAC,SAAS,CAAC,EAAE,OAAO,CAAA;CAAE,GACxE,OAAO,CAAC,mBAAmB,CAAC,CAyf9B"}
+{"version":3,"file":"consolidation.service.d.ts","sourceRoot":"","sources":["../../src/services/consolidation.service.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,0BAA0B,CAAC;AAQzD,OAAO,EAEL,KAAK,mBAAmB,EAOzB,MAAM,iCAAiC,CAAC;AAqEzC,wBAAsB,0BAA0B,CAC9C,EAAE,EAAE,QAAQ,EACZ,OAAO,CAAC,EAAE;IAAE,oBAAoB,CAAC,EAAE,MAAM,CAAC;IAAC,MAAM,CAAC,EAAE,OAAO,CAAA;CAAE,GAC5D,OAAO,CAAC,mBAAmB,CAAC,CA8E9B;AAED,wBAAsB,2BAA2B,CAC/C,EAAE,EAAE,QAAQ,EACZ,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE;IAAE,WAAW,CAAC,EAAE,MAAM,CAAC;IAAC,MAAM,CAAC,EAAE,OAAO,CAAC;IAAC,SAAS,CAAC,EAAE,OAAO,CAAA;CAAE,GACxE,OAAO,CAAC,mBAAmB,CAAC,CA8e9B"}

package/dist/services/consolidation.service.js

@@ -1,7 +1,6 @@
 import { getUnconsolidatedEpisodes, markConsolidated } from "../data/memory/episodes.js";
 import { saveSemanticNote, supersedeNote, updateSemanticNote, } from "../data/memory/semantic-notes.js";
 import { searchByEmbedding, saveNoteEmbedding } from "../data/memory/note-embeddings.js";
-import { rebuildTopicIndex } from "../data/memory/topic-index.js";
 import { cleanupConsolidationHousekeeping, getUnconsolidatedThreadIds, hasActiveNote, expireNote, logConsolidation, sweepOrphanedNotes, sweepOrphanedEmbeddings, } from "../data/memory/consolidation.js";
 import { passesStructuralGate, passesQualityGate, parseReflectionFields, } from "../data/memory/reflection-gates.js";
 import { buildExtractionPrompt, buildSupersedePrompt, buildLinkingPrompt, } from "./consolidation-prompts.js";
@@ -97,13 +96,6 @@ export async function runConsolidationAllThreads(db, options) {
         catch (err) {
             log.warn(`[memory] Orphan embeddings sweep failed: ${errorMessage(err)}`);
         }
-        try {
-            const topicCount = rebuildTopicIndex(db);
-            allDetails.push(`Topic index rebuilt: ${topicCount} topics`);
-        }
-        catch (err) {
-            log.warn(`[memory] Topic index rebuild failed: ${errorMessage(err)}`);
-        }
         return {
             episodesProcessed: totalProcessed,
             notesCreated: totalNotes,
@@ -480,13 +472,13 @@ export async function runIntelligentConsolidation(db, threadId, options) {
                     // expiring historical notes is a separate, backed-up cleanup step, not this sweep.
                     const structural = passesStructuralGate(fields, { requireAnchor: false });
                     if (!structural.pass) {
-                        expireNote(db, row.note_id, nowStr);
+                        expireNote(db, row.note_id, nowStr, "quality-gate");
                         expiredReflections++;
                         continue;
                     }
                     const quality = passesQualityGate(row.content, row.confidence);
                     if (!quality.pass) {
-                        expireNote(db, row.note_id, nowStr);
+                        expireNote(db, row.note_id, nowStr, "quality-gate");
                         expiredReflections++;
                     }
                 }
@@ -498,17 +490,6 @@ export async function runIntelligentConsolidation(db, threadId, options) {
                 log.warn(`[consolidation] Reflection quality gate cleanup failed: ${errorMessage(err)}`);
             }
         }
-        // Keep meta_topic_index accurate on the hot path (drive-handler / daily-session).
-        // Skipped when running inside runConsolidationAllThreads (_skipLock), which rebuilds
-        // once after its pruning/sweep phase to avoid N redundant per-thread rebuilds.
-        if (!skipLock && !dryRun) {
-            try {
-                rebuildTopicIndex(db);
-            }
-            catch (err) {
-                log.warn(`[memory] Topic index rebuild failed: ${errorMessage(err)}`);
-            }
-        }
         return {
             episodesProcessed: episodes.length,
             notesCreated,