claude-mem-lite 3.62.0 → 3.64.0

package/search-engine.mjs

@@ -6,13 +6,16 @@
 // module exists to eliminate.
 
 import {
-  OBS_BM25, TYPE_DECAY_CASE, TYPE_QUALITY_CASE,
+  OBS_BM25, TYPE_QUALITY_CASE,
   DEFAULT_DECAY_HALF_LIFE_MS,
   notLowSignalTitleClause, LOW_SIGNAL_TITLE,
   relaxFtsQueryToOr, debugLog, debugCatch, estimateTokens,
+  noisePenaltyClause,
 } from './utils.mjs';
+import { citeFactorClause } from './scoring-sql.mjs';
 import { getVocabulary, computeVector, vectorSearch, rrfMerge, vectorsEnabled } from './tfidf.mjs';
 import { extractPRFTerms, expandQueryByConcepts } from './search-scoring.mjs';
+import { liveObsFilterSql, recencyDecaySql } from './lib/inject-search-core.mjs';
 
 // Scoring expressions — full adds project boost + access bonus; simple is for
 // expansion paths where boost would over-amplify already-loose matches.
@@ -21,19 +24,37 @@ import { extractPRFTerms, expandQueryByConcepts } from './search-scoring.mjs';
 // exponent large-positive → EXP overflowed to +Infinity → score -Infinity → that row sorted
 // #1 for any match AND JSON.stringify emitted `"score": null` (numeric-contract break). A
 // future row now reads as age 0 = max (finite) recency, not Infinity.
+// M-3 (audit 2026-08-14): cite/noise behavior factors joined FULL_SCORE — they had
+// shipped for months on every AUTO surface (UPS / pre-tool-recall / hook-memory)
+// while the EXPLICIT surfaces (mem_search / CLI search) discarded the accumulated
+// citation + noise signal (the mirror image of "guards wired on the auto face,
+// missing on the explicit face"). Both factors are hard-bounded (cite ∈ [0.4, 3.0],
+// noise ∈ {0.2, 0.5, 1.0}), so they reorder, never dominate. algo-F6 note: the
+// access-count LN bonus below stays — noisePenalty uses access_count only inside a
+// ratio GUARD (never as a bonus) and citeFactor reads cited/uncited columns, so no
+// term is counted twice as a reward. Denoise A/B 2026-08-16: NEUTRAL (suite rows
+// carry zero cite/noise state); the behavioral pin lives in
+// tests/audit-fixes-20260816.test.mjs (M-3).
 const FULL_SCORE = `${OBS_BM25}
-  * (1.0 + EXP(-0.693 * MAX(0, ? - MAX(o.created_at_epoch, COALESCE(o.last_accessed_at, o.created_at_epoch))) / ${TYPE_DECAY_CASE}))
+  * ${recencyDecaySql({ tsExpr: 'MAX(o.created_at_epoch, COALESCE(o.last_accessed_at, o.created_at_epoch))' })}
   * ${TYPE_QUALITY_CASE}
   * (CASE WHEN ? IS NOT NULL AND o.project = ? THEN 2.0 ELSE 1.0 END)
   * (0.5 + 0.5 * COALESCE(o.importance, 1))
   * (1.0 + 0.1 * LN(1 + COALESCE(o.access_count, 0)))
-  * (1.0 + 0.3 * (o.lesson_learned IS NOT NULL AND o.lesson_learned NOT IN ('', 'none')))`;
+  * (1.0 + 0.3 * (o.lesson_learned IS NOT NULL AND o.lesson_learned NOT IN ('', 'none')))
+  * ${noisePenaltyClause('o')}
+  * ${citeFactorClause('o')}`;
 
+// D#121: noisePenalty joins SIMPLE (an entrenched-noise row demoted 0.2× on every
+// direct surface re-entered concept/PRF expansion at full magnitude); citeFactor
+// stays OUT deliberately — it can amplify 3×, and SIMPLE exists precisely to avoid
+// amplifying already-loose expansion matches. Noise only shrinks: safe direction.
 const SIMPLE_SCORE = `${OBS_BM25}
-  * (1.0 + EXP(-0.693 * MAX(0, ? - MAX(o.created_at_epoch, COALESCE(o.last_accessed_at, o.created_at_epoch))) / ${TYPE_DECAY_CASE}))
+  * ${recencyDecaySql({ tsExpr: 'MAX(o.created_at_epoch, COALESCE(o.last_accessed_at, o.created_at_epoch))' })}
   * ${TYPE_QUALITY_CASE}
   * (0.5 + 0.5 * COALESCE(o.importance, 1))
-  * (1.0 + 0.3 * (o.lesson_learned IS NOT NULL AND o.lesson_learned NOT IN ('', 'none')))`;
+  * (1.0 + 0.3 * (o.lesson_learned IS NOT NULL AND o.lesson_learned NOT IN ('', 'none')))
+  * ${noisePenaltyClause('o')}`;
 
 // Shared column set for fetching an observation surfaced by the vector arm — used by BOTH
 // the RRF-merge branch (FTS also had results) and the FTS-empty fallback branch. Single
@@ -56,8 +77,7 @@ export function buildObsFtsQuery(scoring, { multiplier, withSnippet, withOffset,
     FROM observations_fts
     JOIN observations o ON observations_fts.rowid = o.id
     WHERE observations_fts MATCH ?
-      AND COALESCE(o.compressed_into, 0) = 0
-      AND o.superseded_at IS NULL
+      AND ${liveObsFilterSql('o')}
       AND (? IS NULL OR o.project = ?)
       AND (? IS NULL OR o.type = ?)
       AND (? IS NULL OR o.created_at_epoch >= ?)
@@ -108,8 +128,7 @@ export function countObsFtsMatches(db, { ftsQuery, args = {}, epochFrom = null,
       FROM observations_fts
       JOIN observations o ON observations_fts.rowid = o.id
       WHERE observations_fts MATCH ?
-        AND COALESCE(o.compressed_into, 0) = 0
-        AND o.superseded_at IS NULL
+        AND ${liveObsFilterSql('o')}
         AND (? IS NULL OR o.project = ?)
         AND (? IS NULL OR o.type = ?)
         AND (? IS NULL OR o.created_at_epoch >= ?)
@@ -294,15 +313,18 @@ function expandObsByConceptCo(db, ctx, now, existingIds, results, includeNoise =
 function expandObsByPRF(db, ctx, now, primaryCount, existingIds, results, includeNoise = false) {
   const { ftsQuery, args, epochFrom, epochTo, limit } = ctx;
   if (primaryCount < 3) return;
+  // effectiveFtsQuery = the query that actually matched (OR-relaxed when the strict
+  // AND missed and the fallback rescued rows — M-2). The strict query here returned
+  // zero top docs in that case, silently disabling PRF where it helps most.
+  const seedQuery = ctx.effectiveFtsQuery || ftsQuery;
   const topResults = db.prepare(`
     SELECT o.title, o.narrative FROM observations_fts
     JOIN observations o ON observations_fts.rowid = o.id
-    WHERE observations_fts MATCH ? AND COALESCE(o.compressed_into, 0) = 0
-      AND o.superseded_at IS NULL
+    WHERE observations_fts MATCH ? AND ${liveObsFilterSql('o')}
       AND (? IS NULL OR o.project = ?)
     ORDER BY ${OBS_BM25}
     LIMIT 8
-  `).all(ftsQuery, args.project ?? null, args.project ?? null);
+  `).all(seedQuery, args.project ?? null, args.project ?? null);
   const prfTerms = extractPRFTerms(topResults, ftsQuery);
   if (prfTerms.length === 0) return;
   const prfFts = prfTerms.map(t => `"${t.replace(/"/g, '""')}"`).join(' OR ');
@@ -365,10 +387,9 @@ export function findFtsAnchor(db, { ftsQuery, project = null, nowT = null, halfL
     JOIN observations o ON observations_fts.rowid = o.id
     WHERE observations_fts MATCH ?
       AND (? IS NULL OR o.project = ?)
-      AND COALESCE(o.compressed_into, 0) = 0
-      AND o.superseded_at IS NULL
+      AND ${liveObsFilterSql('o')}
     ORDER BY ${OBS_BM25}
-      * (1.0 + EXP(-0.693 * MAX(0, ? - o.created_at_epoch) / ${halfLifeMs}.0))
+      * ${recencyDecaySql({ tsExpr: 'o.created_at_epoch', halfLifeSql: `${halfLifeMs}.0` })}
     LIMIT 1
   `;
   const stmt = db.prepare(sql);
@@ -393,7 +414,7 @@ export function searchObservationsHybrid(db, ctx) {
 
   if (!ftsQuery) {
     const params = [];
-    const wheres = ['COALESCE(compressed_into, 0) = 0', 'superseded_at IS NULL'];
+    const wheres = [liveObsFilterSql('')];
     if (args.project) { wheres.push('project = ?'); params.push(args.project); }
     if (args.obs_type) { wheres.push('type = ?'); params.push(args.obs_type); }
     if (epochFrom !== null) { wheres.push('created_at_epoch >= ?'); params.push(epochFrom); }
@@ -428,17 +449,32 @@ export function searchObservationsHybrid(db, ctx) {
       try {
         const orRows = db.prepare(buildObsFtsQuery('full', { multiplier: 0.5, withSnippet: true, withOffset: true, includeNoise }))
           .all(...buildObsFtsParams({ now, projectBoost, ftsQuery: orQuery, args, epochFrom, epochTo, limit: perSourceLimit, offset: perSourceOffset }));
-        if (orRows.length > 0) ctx.orFallbackFired = true;
+        if (orRows.length > 0) {
+          ctx.orFallbackFired = true;
+          // M-2: PRF's top-doc probe re-queries FTS itself — with the strict-AND
+          // query it reads 0 docs in exactly the OR-rescue case, keeping PRF inert.
+          // Record the query that actually produced the evidence rows.
+          ctx.effectiveFtsQuery = orQuery;
+        }
         for (const r of orRows) results.push(ftsRowToResult(r, { snippet: true }));
       } catch (e) { debugCatch(e, 'searchObservationsHybrid-or-fallback'); }
     }
   }
 
-  // Two-phase query expansion (only when well below limit)
-  if (rows.length > 0 && results.length < Math.ceil(limit / 2)) {
+  // Two-phase query expansion (only when well below limit). Gate on results.length,
+  // NOT rows.length (M-2, audit 2026-08-14): `rows` is the strict-AND set only, so
+  // when strict-AND missed and the OR fallback rescued a few rows — exactly the
+  // vocab-mismatch shape where expansion helps most — the old gate read rows.length
+  // === 0 and skipped concept/PRF expansion entirely. PRF likewise seeds from the
+  // rescued rows now (they are the only relevance evidence available).
+  if (results.length > 0 && results.length < Math.ceil(limit / 2)) {
     const existingIds = new Set(results.map(r => r.id));
+    // D#122 ②: capture the PRIMARY count before concept expansion mutates
+    // `results` — PRF's >=3 gate is meant to read direct-match evidence, not
+    // rows the concept pass just added.
+    const primaryCount = results.length;
     expandObsByConceptCo(db, ctx, now, existingIds, results, includeNoise);
-    expandObsByPRF(db, ctx, now, rows.length, existingIds, results, includeNoise);
+    expandObsByPRF(db, ctx, now, primaryCount, existingIds, results, includeNoise);
   }
 
   // Vector search + RRF hybrid merge

package/search-scoring.mjs

@@ -165,8 +165,13 @@ export function extractPRFTerms(results, ftsQuery, limit = 3) {
   // "cach" returns zero rows, only "caching"/"cache" match). Emitting a bare stem would
   // silently match nothing and kill expansion recall. Track each stem's surface forms with
   // their occurrence counts and emit the most frequent (best-matchable) surface.
-  const stemDocCount = {};      // stem -> # of top docs it appears in (the >=2 bar)
-  const stemSurfaces = {};      // stem -> Map(surface -> total occurrences)
+  // Prototype-less: doc text tokenizes to arbitrary identifiers, and a stem that
+  // collides with an Object.prototype property ("constructor" — common in code
+  // narratives) made `stemSurfaces[stem] ||= new Map()` read the INHERITED function
+  // as truthy, skip the assignment, and crash on sm.get (surfaced 2026-08-16 when
+  // the M-2 gate fix first ran PRF over OR-rescued rows).
+  const stemDocCount = Object.create(null);   // stem -> # of top docs it appears in (the >=2 bar)
+  const stemSurfaces = Object.create(null);   // stem -> Map(surface -> total occurrences)
   const docCount = Math.min(results.length, 8);
   for (let i = 0; i < docCount; i++) {
     const r = results[i];

package/server.mjs

@@ -5,10 +5,10 @@
 import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
 import { ListToolsRequestSchema } from '@modelcontextprotocol/sdk/types.js';
-import { truncate, typeIcon, inferProject, scrubSecrets, fmtDate, debugLog, debugCatch, isPathConfined } from './utils.mjs';
+import { truncate, typeIcon, inferProject, fmtDate, debugLog, debugCatch, isPathConfined } from './utils.mjs';
 import { resolveProject as _resolveProjectShared } from './project-utils.mjs';
 import { ensureDbWithWalRecovery, DB_PATH, DB_DIR, REGISTRY_DB_PATH } from './schema.mjs';
-import { reRankWithContext, autoBoostIfNeeded, runIdleCleanup, buildServerInstructions } from './search-scoring.mjs';
+import { reRankWithContext, runIdleCleanup, buildServerInstructions } from './search-scoring.mjs';
 import { searchObservationsHybrid } from './search-engine.mjs';
 import { deepSearch, resolveDeepMode, shouldEscalateToDeep, autoDeepLlmReady } from './deep-search.mjs';
 import { selectCompressionCandidates, groupByProjectWeek, compressGroup } from './lib/compress-core.mjs';
@@ -22,9 +22,10 @@ import {
   OP_CAP, STALE_AGE_MS,
 } from './lib/maintain-core.mjs';
 import { snapshotDb } from './lib/db-backup.mjs';
-import { deleteObservations } from './lib/delete-core.mjs';
+import { deleteObservations, previewDeleteRows } from './lib/delete-core.mjs';
+import { fetchObsDetail, OBS_FIELDS, SESSION_DETAIL_FIELDS } from './lib/get-core.mjs';
+import { collectBrowseTiers, getActiveMemorySessionId, BROWSE_TIERS, BROWSE_TIER_LABELS } from './lib/browse-core.mjs';
 import { effectiveQuiet, RUNTIME_DIR } from './hook-shared.mjs';
-import { TIER_CASE_SQL, tierSqlParams } from './tier.mjs';
 import { computeStatsFeed } from './lib/stats-core.mjs';
 import { buildLessonNudge } from './lib/save-nudge.mjs';
 import { formatObsFieldValue, obsFieldLabel, formatPendingPurgeLine } from './cli/common.mjs';
@@ -45,11 +46,11 @@ function descriptionOf(name) {
 import { optimizePreview, optimizeRun } from './hook-optimize.mjs';
 import { join, sep } from 'path';
 import { homedir } from 'os';
-import { ensureRegistryDb, upsertResource } from './registry.mjs';
+import { ensureRegistryDb, upsertResource, collectRegistryStats, listResourcesRanked, formatRegistryListLine } from './registry.mjs';
 import { searchResources } from './registry-retriever.mjs';
 import { probeOtherSources as probeIdSources, bucketIdTokens, splitDeferredTokens } from './lib/id-routing.mjs';
 import { saveObservation } from './lib/save-observation.mjs';
-import { rebuildObservationDerived } from './lib/observation-write.mjs';
+import { applyObsUpdate } from './lib/observation-write.mjs';
 import { EXPORT_COLUMNS_SQL } from './lib/export-columns.mjs';
 import { recallByFile } from './lib/recall-core.mjs';
 import { fetchRecent } from './lib/recent-core.mjs';
@@ -599,8 +600,6 @@ server.registerTool(
       return { content: [{ type: 'text', text: 'No valid IDs provided.' }] };
     }
 
-    const OBS_FIELDS = ['id', 'type', 'title', 'subtitle', 'narrative', 'text', 'facts', 'concepts', 'lesson_learned', 'search_aliases', 'files_read', 'files_modified', 'project', 'created_at', 'memory_session_id', 'prompt_number', 'importance', 'related_ids', 'access_count', 'branch', 'superseded_at', 'superseded_by', 'last_accessed_at'];
-
     // `fields` filter only makes sense for obs rows; session/prompt ignore it.
     // Validate when obs is queried — throw on all-invalid, note on partial-invalid.
     let fieldsNote = '';
@@ -622,12 +621,8 @@ server.registerTool(
     const foundBySource = { obs: new Set(), session: new Set(), prompt: new Set(), event: new Set() };
 
     if (bySrc.obs.length > 0) {
-      const ph = bySrc.obs.map(() => '?').join(',');
-      try {
-        db.prepare(`UPDATE observations SET access_count = COALESCE(access_count, 0) + 1, last_accessed_at = ? WHERE id IN (${ph})`).run(Date.now(), ...bySrc.obs);
-        autoBoostIfNeeded(db, bySrc.obs);
-      } catch { /* non-critical: FTS5 trigger may fail on corrupted index */ }
-      const rows = db.prepare(`SELECT * FROM observations WHERE id IN (${ph}) ORDER BY created_at_epoch ASC`).all(...bySrc.obs);
+      // Access-bump + fetch via the shared get-core (P2-12) — single source with CLI get.
+      const rows = fetchObsDetail(db, bySrc.obs);
       const renderFields = obsFieldFilter || OBS_FIELDS;
       for (const row of rows) {
         foundBySource.obs.add(row.id);
@@ -650,7 +645,9 @@ server.registerTool(
     if (bySrc.session.length > 0) {
       const ph = bySrc.session.map(() => '?').join(',');
       const rows = db.prepare(`SELECT * FROM session_summaries WHERE id IN (${ph}) ORDER BY created_at_epoch ASC`).all(...bySrc.session);
-      const sessFields = ['id', 'request', 'investigated', 'learned', 'completed', 'next_steps', 'files_read', 'files_edited', 'notes', 'project', 'created_at', 'memory_session_id', 'prompt_number'];
+      // SESSION_DETAIL_FIELDS (get-core, P2-12): shared full set — adds remaining_items
+      // (searchable via FTS but previously unrendered on BOTH detail faces).
+      const sessFields = SESSION_DETAIL_FIELDS;
       for (const row of rows) {
         foundBySource.session.add(row.id);
         const lines = [`── S#${row.id} ──`];
@@ -765,21 +762,15 @@ server.registerTool(
     inputSchema: memDeleteSchema,
   },
   safeHandler(async (args) => {
-    const placeholders = args.ids.map(() => '?').join(',');
-    const rows = db.prepare(`
-      SELECT id, type, title, project FROM observations WHERE id IN (${placeholders})
-    `).all(...args.ids);
+    // Shared preview body (lib/delete-core, P2-12) — single source with CLI delete.
+    const { rows, lines: previewLines } = previewDeleteRows(db, args.ids);
 
     if (rows.length === 0) {
       return { content: [{ type: 'text', text: 'No observations found for given IDs.' }] };
     }
 
     if (!args.confirm) {
-      // Preview mode
-      const lines = [`Preview: ${rows.length} observation(s) will be deleted:\n`];
-      for (const r of rows) {
-        lines.push(`  #${r.id} [${r.type}] ${truncate(r.title || '(untitled)', 80)} | ${r.project}`);
-      }
+      const lines = [`Preview: ${rows.length} observation(s) will be deleted:\n`, ...previewLines];
       lines.push(`\nCall mem_delete(ids=[...], confirm=true) to execute.`);
       return { content: [{ type: 'text', text: lines.join('\n') }] };
     }
@@ -1162,32 +1153,22 @@ server.registerTool(
       const staleAge = Date.now() - STALE_AGE_MS;
       const mctx = { projectFilter, baseParams, staleAge, opCap: OP_CAP };
 
-      // T2-P0-A: purge_stale is the only DELETE in this handler. Require confirm=true;
-      // a first call without confirm returns a dry-run preview so callers know the blast radius.
-      const purgeRequested = ops.includes('purge_stale');
-      if (purgeRequested && args.confirm !== true) {
-        const retainDays = args.retain_days ?? 30;
-        const retainCutoff = Date.now() - retainDays * 86400000;
-        const previewRow = purgeStalePreview(db, mctx, retainCutoff);
-        const lines = [
-          'purge_stale preview (confirm=false):',
-          `  Candidates (pending-purge, older than ${retainDays}d): ${previewRow.candidates}`,
-        ];
-        if (previewRow.candidates > 0) {
-          lines.push(`  Oldest: ${new Date(previewRow.oldest).toISOString().slice(0, 10)}`);
-          lines.push(`  Newest: ${new Date(previewRow.newest).toISOString().slice(0, 10)}`);
-        }
-        lines.push('');
-        lines.push('Nothing was deleted. To execute, re-run with confirm=true:');
-        lines.push(`  mem_maintain(action="execute", operations=${JSON.stringify(ops)}, confirm=true${args.retain_days ? `, retain_days=${args.retain_days}` : ''}${args.project ? `, project="${args.project}"` : ''})`);
-        return { content: [{ type: 'text', text: lines.join('\n') }] };
-      }
+      // T2-P0-A: purge_stale is the only op gated on confirm=true — cleanupBroken also
+      // hard-deletes (broken rows only) but always ran unconfirmed on both surfaces, and
+      // the pre-transaction snapshot above covers it. An unconfirmed call gets a dry-run
+      // preview of the purge INSTEAD OF the purge.
+      // M-7 (audit 2026-08-14): preview-instead-of-early-return — the old
+      // `return`-on-unconfirmed skipped EVERY requested op, while the CLI twin ran the
+      // non-destructive ones (cleanup/decay/boost) and previewed only the purge. Same
+      // op list, two different amounts of work done, both reporting success. Aligned
+      // to the CLI semantics (the safer surface changed less: nothing destructive
+      // runs unconfirmed on either surface now or before).
+      const purgeConfirmed = args.confirm === true;
 
       // MED-2: snapshot the DB before the irreversible cleanup/purge hard-deletes —
       // only when rows will actually be removed, and OUTSIDE the transaction below
-      // (VACUUM cannot run inside one). purge_stale is already confirmed by here (the
-      // preview branch returned above otherwise). Best-effort; snapshotDb never throws.
-      if (hardDeleteCandidateCount(db, mctx, { cleanup: ops.includes('cleanup'), purge: ops.includes('purge_stale') }) > 0) {
+      // (VACUUM cannot run inside one). Best-effort; snapshotDb never throws.
+      if (hardDeleteCandidateCount(db, mctx, { cleanup: ops.includes('cleanup'), purge: ops.includes('purge_stale') && purgeConfirmed }) > 0) {
         snapshotDb(db, { tag: 'pre-maintain' });
       }
 
@@ -1201,8 +1182,25 @@ server.registerTool(
         if (ops.includes('purge_stale')) {
           const retainDays = args.retain_days ?? 30;
           const retainCutoff = Date.now() - retainDays * 86400000;
-          const purged = purgeStale(db, mctx, retainCutoff);
-          results.push(`Purged ${purged} stale observations (retained last ${retainDays} days)` + (purged >= OP_CAP ? ' (cap reached, re-run for more)' : ''));
+          if (!purgeConfirmed) {
+            // Dry-run preview (parity with CLI `maintain` without --confirm): the other
+            // requested non-destructive ops still run below.
+            const previewRow = purgeStalePreview(db, mctx, retainCutoff);
+            const lines = [
+              'purge_stale preview (confirm=false):',
+              `  Candidates (pending-purge, older than ${retainDays}d): ${previewRow.candidates}`,
+            ];
+            if (previewRow.candidates > 0) {
+              lines.push(`  Oldest: ${new Date(previewRow.oldest).toISOString().slice(0, 10)}`);
+              lines.push(`  Newest: ${new Date(previewRow.newest).toISOString().slice(0, 10)}`);
+            }
+            lines.push('  Nothing was deleted. To delete, re-run with confirm=true:');
+            lines.push(`  mem_maintain(action="execute", operations=${JSON.stringify(ops)}, confirm=true${args.retain_days ? `, retain_days=${args.retain_days}` : ''}${args.project ? `, project="${args.project}"` : ''})`);
+            results.push(lines.join('\n'));
+          } else {
+            const purged = purgeStale(db, mctx, retainCutoff);
+            results.push(`Purged ${purged} stale observations (retained last ${retainDays} days)` + (purged >= OP_CAP ? ' (cap reached, re-run for more)' : ''));
+          }
         }
 
         if (ops.includes('cleanup')) {
@@ -1418,51 +1416,27 @@ server.registerTool(
     }
 
     if (action === 'list') {
-      const typeFilter = args.type;
-      const where = typeFilter ? 'WHERE type = ? AND status = ?' : 'WHERE status = ?';
-      const params = typeFilter ? [typeFilter, 'active'] : ['active'];
-      // T3-P2-A: order by adoption then recommendation (CLI parity), and coalesce NULL counts
-      // so the output shows "adopt:0" rather than the jarring "adopt:null".
-      const resources = rdb.prepare(`
-        SELECT name, type, invocation_name, recommend_count, adopt_count, capability_summary
-        FROM resources ${where}
-        ORDER BY COALESCE(adopt_count, 0) DESC, COALESCE(recommend_count, 0) DESC, type, name
-      `).all(...params);
-
+      // Shared ranked query + row line (registry.mjs, P2-12) — single source with CLI list.
+      const resources = listResourcesRanked(rdb, { type: args.type });
       if (resources.length === 0) return { content: [{ type: 'text', text: 'No resources found.' }] };
-
-      const lines = resources.map(r =>
-        `${r.type === 'skill' ? 'S' : 'A'} ${r.name}${r.invocation_name ? ` (${r.invocation_name})` : ''} — rec:${r.recommend_count ?? 0} adopt:${r.adopt_count ?? 0} — ${truncate(r.capability_summary || '', 80)}`
-      );
+      const lines = resources.map(formatRegistryListLine);
       return { content: [{ type: 'text', text: `Resources (${resources.length}):\n${lines.join('\n')}` }] };
     }
 
     if (action === 'stats') {
-      const total = rdb.prepare('SELECT COUNT(*) as c FROM resources WHERE status = ?').get('active');
-      const byType = rdb.prepare('SELECT type, COUNT(*) as c FROM resources WHERE status = ? GROUP BY type').all('active');
-      const topAdopted = rdb.prepare(`
-        SELECT name, type, adopt_count, recommend_count
-        FROM resources WHERE status = ? AND adopt_count > 0
-        ORDER BY adopt_count DESC LIMIT 10
-      `).all('active');
-      const zeroAdopt = rdb.prepare(`
-        SELECT COUNT(*) as c FROM resources
-        WHERE status = ? AND recommend_count > 0 AND adopt_count = 0
-      `).get('active');
-      const userAdded = rdb.prepare(`
-        SELECT COUNT(*) as c FROM resources WHERE status = ? AND source = 'user'
-      `).get('active');
-
+      // Shared collection (registry.mjs collectRegistryStats, P2-12) — single
+      // source with the CLI registry stats action.
+      const s = collectRegistryStats(rdb);
       const lines = [
         `Registry Stats:`,
-        `  Total active: ${total.c}`,
-        ...byType.map(t => `  ${t.type}: ${t.c}`),
-        `  User-added: ${userAdded.c}`,
-        `  Zero adoption (recommended but never adopted): ${zeroAdopt.c}`,
+        `  Total active: ${s.total}`,
+        ...s.byType.map(t => `  ${t.type}: ${t.c}`),
+        `  User-added: ${s.userAdded}`,
+        `  Zero adoption (recommended but never adopted): ${s.zeroAdopt}`,
       ];
-      if (topAdopted.length > 0) {
+      if (s.topAdopted.length > 0) {
         lines.push('', 'Top adopted:');
-        for (const r of topAdopted) {
+        for (const r of s.topAdopted) {
           lines.push(`  ${r.name} (${r.type}): ${r.adopt_count}/${r.recommend_count}`);
         }
       }
@@ -1689,26 +1663,15 @@ server.registerTool(
     const obs = db.prepare('SELECT id, title FROM observations WHERE id = ?').get(args.id);
     if (!obs) return { content: [{ type: 'text', text: `Observation #${args.id} not found` }], isError: true };
 
-    const updates = [];
-    const params = [];
-    for (const [key, col] of [['title','title'],['narrative','narrative'],['type','type'],['importance','importance'],['lesson_learned','lesson_learned'],['concepts','concepts']]) {
-      if (args[key] !== undefined) {
-        updates.push(`${col} = ?`);
-        params.push(typeof args[key] === 'string' ? scrubSecrets(args[key]) : args[key]);
-      }
-    }
-    if (updates.length === 0) return { content: [{ type: 'text', text: 'No fields to update' }], isError: true };
-
-    params.push(args.id);
-
-    // Atomic: update fields + rebuild derived columns (FTS text + vector) via the
-    // shared core — single source with CLI cmdUpdate (lib/observation-write.mjs).
-    db.transaction(() => {
-      db.prepare(`UPDATE observations SET ${updates.join(', ')} WHERE id = ?`).run(...params);
-      rebuildObservationDerived(db, args.id);
-    })();
+    // Shared mutation (lib/observation-write applyObsUpdate, P2-12): scrub + UPDATE +
+    // derived-column rebuild in one transaction — single source with CLI cmdUpdate.
+    const updatedCols = applyObsUpdate(db, args.id, {
+      title: args.title, narrative: args.narrative, type: args.type,
+      importance: args.importance, lesson_learned: args.lesson_learned, concepts: args.concepts,
+    });
+    if (updatedCols.length === 0) return { content: [{ type: 'text', text: 'No fields to update' }], isError: true };
 
-    return { content: [{ type: 'text', text: `Updated observation #${args.id}: ${updates.map(u => u.split(' =')[0]).join(', ')}` }] };
+    return { content: [{ type: 'text', text: `Updated observation #${args.id}: ${updatedCols.join(', ')}` }] };
   })
 );
 
@@ -1862,33 +1825,18 @@ server.registerTool(
     const limit = args.limit ?? (tierFilter ? 20 : 5);
     const now = Date.now();
 
-    // Get active session for tier classification
-    const activeSession = db.prepare(
-      "SELECT memory_session_id FROM sdk_sessions WHERE project = ? AND status = 'active' ORDER BY started_at_epoch DESC LIMIT 1"
-    ).get(project);
-
-    const ctx = { now, currentProject: project, currentSessionId: activeSession?.memory_session_id ?? '' };
-    const params = tierSqlParams(ctx);
-
-    const tiers = ['working', 'active', 'archive'];
-    const tierLabels = { working: '🔴 Working Memory', active: '🟡 Active Memory', archive: '🔵 Archive' };
-    const showTiers = tierFilter ? [tierFilter] : tiers;
+    // Shared collection (lib/browse-core, P2-12) — single source with CLI browse.
+    const { showTiers, tierData, tierCounts, grandTotal } = collectBrowseTiers(db, {
+      project, tierFilter, limit, now,
+      currentSessionId: getActiveMemorySessionId(db, project),
+    });
+    const tiers = BROWSE_TIERS;
+    const tierLabels = BROWSE_TIER_LABELS;
 
     const lines = [`Memory Dashboard (${project})\n`];
-    let grandTotal = 0;
-    const tierCounts = {};
 
     for (const tier of showTiers) {
-      const countRow = db.prepare(`
-        SELECT COUNT(*) as c FROM (
-          SELECT ${TIER_CASE_SQL} as tier FROM observations
-          WHERE project = ? AND COALESCE(compressed_into, 0) = 0 AND superseded_at IS NULL
-        ) WHERE tier = ?
-      `).get(...params, project, tier);
-      const count = countRow?.c ?? 0;
-      tierCounts[tier] = count;
-      grandTotal += count;
-
+      const { count, rows } = tierData[tier];
       lines.push(`${tierLabels[tier]} (${count})`);
 
       if (tier === 'archive' && !tierFilter) {
@@ -1898,16 +1846,6 @@ server.registerTool(
 
       if (count === 0) { lines.push(''); continue; }
 
-      const rows = db.prepare(`
-        SELECT * FROM (
-          SELECT id, type, title, created_at, created_at_epoch, ${TIER_CASE_SQL} as tier
-          FROM observations
-          WHERE project = ? AND COALESCE(compressed_into, 0) = 0 AND superseded_at IS NULL
-        ) WHERE tier = ?
-        ORDER BY created_at_epoch DESC
-        LIMIT ?
-      `).all(...params, project, tier, limit);
-
       for (const r of rows) {
         lines.push(`  #${r.id} ${typeIcon(r.type)} [${r.type}] ${truncate(r.title || '(untitled)', 80)} | ${fmtDate(r.created_at)}`);
       }

package/source-files.mjs

@@ -119,6 +119,20 @@ export const SOURCE_FILES = [
   // colliding with the scripts/ directory rename in installExtractedRelease
   // — see the SWITCHABLE_PATHS loop in hook-update.mjs.
   'lib/mem-override.mjs',
+  // D#120: injected-ids marker file-name derivation, shared by hook.mjs +
+  // scripts/user-prompt-search.js + scripts/pre-tool-recall.js. Under lib/ for
+  // the same scripts-dir-rename reason as mem-override.mjs above.
+  'lib/injected-ids.mjs',
+  // P2-11: injection-side shared SQL core (live-row filter / clamped decay /
+  // injection relevance chain). Statically imported by hook.mjs, hook-memory.mjs,
+  // search-engine.mjs AND the standalone hook scripts — missing it from the
+  // manifest kills every retrieval surface on auto-update.
+  'lib/inject-search-core.mjs',
+  // P2-12 twin cores: get/browse shared data collection for the CLI/MCP pairs
+  // (update lives in observation-write, delete-preview in delete-core, registry
+  // stats/list in registry.mjs — all already listed).
+  'lib/get-core.mjs',
+  'lib/browse-core.mjs',
   // v2.61 dedup refactor: shared "save one observation" pipeline used by both
   // mem-cli.mjs::cmdSave and server.mjs::mem_save. Statically imported from both
   // entry points; missing it from the manifest broke MCP saves on auto-update.
@@ -264,9 +278,37 @@ const LAUNCHER_SCRIPT_FILES = [
   'binding-probe-cli.mjs',
 ];
 
+// Plugin/marketplace DECLARATION files (audit 2026-08-14 P-2). Not executable
+// themselves, but they NAME what gets executed: hooks/hooks.json declares the
+// command lines Claude Code runs on every hook fire, .mcp.json declares the MCP
+// server launch command, plugin.json/marketplace.json steer the install source,
+// commands/*.md are model-visible skill bodies, registry/preinstalled.json seeds
+// the resource registry. All ship in the tarball; none were signed — the same
+// shape as the two closed RCE gaps (hook scripts v3.40, launch.mjs v3.42): a
+// release published without the signing key could swap hooks.json to point a
+// hook event at an arbitrary command while every signed hash still matched.
+// Additive: buildReleaseManifest skips entries absent at sign time, and
+// verifyReleaseFiles needs no change to enforce whatever the manifest carries.
+const PLUGIN_DECLARATION_FILES = [
+  'hooks/hooks.json',
+  '.mcp.json',
+  '.claude-plugin/plugin.json',
+  '.claude-plugin/marketplace.json',
+  'registry/preinstalled.json',
+  'commands/mem.md',
+  'commands/memory.md',
+  'commands/update.md',
+  'commands/tools.md',
+  'commands/adopt.md',
+  'commands/unadopt.md',
+  'commands/lesson.md',
+  'commands/bug.md',
+];
+
 // The complete set of files the release signature MUST cover: every runtime .mjs
 // (SOURCE_FILES) PLUS the executable hook scripts (copyReleaseIntoStaging installs these
-// into the live dir and they run on every hook fire) PLUS the launcher/setup scripts.
+// into the live dir and they run on every hook fire) PLUS the launcher/setup scripts
+// PLUS the plugin declaration files above.
 // HOOK_SCRIPT_FILES were historically NOT in the signed manifest, so an attacker able to
 // PUBLISH a release — but without the signing key — could swap a hook script (e.g.
 // post-tool-use.sh / hook-launcher.mjs) while every SOURCE_FILES hash still matched, and
@@ -278,4 +320,5 @@ export const RELEASE_SIGNED_FILES = [
   ...SOURCE_FILES,
   ...HOOK_SCRIPT_FILES.map(name => `scripts/${name}`),
   ...LAUNCHER_SCRIPT_FILES.map(name => `scripts/${name}`),
+  ...PLUGIN_DECLARATION_FILES,
 ];