@yemi33/minions 0.1.2447 → 0.1.2449

package/engine/{stdio-timestamps.js → core/stdio-timestamps.js}

@@ -1,5 +1,5 @@
 /**
- * engine/stdio-timestamps.js — Prefix every console.log/warn/error/info line
+ * engine/core/stdio-timestamps.js — Prefix every console.log/warn/error/info line
  * with an ISO-8601 timestamp so dashboard-stdio.log and engine-stdio.log
  * become diagnosable to the second.
  *

package/engine/{untrusted-fence.js → core/untrusted-fence.js}

@@ -1,5 +1,5 @@
 /**
- * engine/untrusted-fence.js — F5 (W-mpeklod3000we69c).
+ * engine/core/untrusted-fence.js — F5 (W-mpeklod3000we69c).
  *
  * Wraps human-authored / external content in
  *   <UNTRUSTED-INPUT source="…">…</UNTRUSTED-INPUT>
@@ -7,7 +7,7 @@
  * `playbooks/shared-rules.md` and `prompts/cc-system.md` that teaches agents
  * to treat fenced content as data, not instructions.
  *
- * Zero dependencies beyond `engine/shared` (for the ENGINE_DEFAULTS byte cap).
+ * Zero dependencies beyond `engine/core/shared` (for the ENGINE_DEFAULTS byte cap).
  * Pure helpers — safe to call from poll-time, render-time, and consolidation
  * paths. Source attributes are sanitized so attacker-influenced parts
  * (PR comment author, file paths) cannot break out of the fence header.
@@ -33,7 +33,7 @@ const INNER_CLOSE_RE = /<\/UNTRUSTED-INPUT(?:\s[^>]*)?>/gi;
 
 function _shared() {
   // Late require — keep this module loadable in isolated test contexts that
-  // bust `engine/shared` from require.cache between runs.
+  // bust `engine/core/shared` from require.cache between runs.
   return require('./shared');
 }
 

package/engine/db/index.js

@@ -94,7 +94,7 @@ function _resolveDbPath() {
   const envHome = process.env.MINIONS_TEST_DIR || process.env.MINIONS_HOME;
   let minionsDir = envHome;
   if (!minionsDir) {
-    try { minionsDir = require('../shared').MINIONS_DIR; } catch { /* shared not loaded */ }
+    try { minionsDir = require('../core/shared').MINIONS_DIR; } catch { /* shared not loaded */ }
   }
   if (!minionsDir) throw new Error('engine/db: MINIONS_DIR not resolvable');
   const engineDir = path.join(minionsDir, 'engine');
@@ -263,4 +263,13 @@ function prepareCached(db, sql) {
   return stmt;
 }
 
-module.exports = { getDb, closeDb, withTransaction, prepareCached, cleanupRetiredJsonFiles };
+module.exports = {
+  getDb,
+  closeDb,
+  withTransaction,
+  prepareCached,
+  cleanupRetiredJsonFiles,
+  // Standalone read-only connections (backup verification) need the same
+  // ExperimentalWarning suppression that getDb() installs.
+  installSqliteWarningFilter: _installExperimentalWarningFilter,
+};

package/engine/db/migrations/002-dispatches.js

@@ -26,7 +26,7 @@ const fs = require('fs');
 function _resolveMinionsDir() {
   const envHome = process.env.MINIONS_TEST_DIR || process.env.MINIONS_HOME;
   if (envHome) return envHome;
-  try { return require('../../shared').MINIONS_DIR; } catch { return null; }
+  try { return require('../../core/shared').MINIONS_DIR; } catch { return null; }
 }
 
 function _toMs(v) {
@@ -102,8 +102,8 @@ module.exports = {
     // dispatch.json stays on disk as a dual-write mirror — every successful
     // mutateDispatch refreshes it from SQL via dispatch-store._mirrorJsonFromSql.
     // SQL is the source of truth; the file is a read-only derivative kept
-    // for backward compatibility with legacy direct-readers (engine/routing.js,
-    // engine/queries.js fallback, test infrastructure). Rollback path: if a
+    // for backward compatibility with legacy direct-readers (engine/orchestration/routing.js,
+    // engine/core/queries.js fallback, test infrastructure). Rollback path: if a
     // user pins back to a pre-Phase-1 release, dispatch.json already contains
     // the latest committed state (last mirror write), and the SQL table can
     // be discarded.

package/engine/db/migrations/003-work-items.js

@@ -22,7 +22,7 @@ const fs = require('fs');
 function _resolveMinionsDir() {
   const envHome = process.env.MINIONS_TEST_DIR || process.env.MINIONS_HOME;
   if (envHome) return envHome;
-  try { return require('../../shared').MINIONS_DIR; } catch { return null; }
+  try { return require('../../core/shared').MINIONS_DIR; } catch { return null; }
 }
 
 function _toMs(v) {

package/engine/db/migrations/004-pull-requests.js

@@ -23,7 +23,7 @@ const fs = require('fs');
 function _resolveMinionsDir() {
   const envHome = process.env.MINIONS_TEST_DIR || process.env.MINIONS_HOME;
   if (envHome) return envHome;
-  try { return require('../../shared').MINIONS_DIR; } catch { return null; }
+  try { return require('../../core/shared').MINIONS_DIR; } catch { return null; }
 }
 
 function _toMs(v) {

package/engine/db/migrations/006-metrics.js

@@ -37,7 +37,7 @@ function _resolveMinionsDir() {
   // backfill its tables from MINIONS_HOME — cross-directory corruption.
   const envHome = process.env.MINIONS_TEST_DIR || process.env.MINIONS_HOME;
   if (envHome) return envHome;
-  try { return require('../../shared').MINIONS_DIR; } catch { return null; }
+  try { return require('../../core/shared').MINIONS_DIR; } catch { return null; }
 }
 
 const RESERVED_KEYS = new Map([

package/engine/db/migrations/007-watches.js

@@ -1,6 +1,6 @@
 // engine/db/migrations/007-watches.js
 //
-// Phase 6: move engine/watches.json into a `watches` table.
+// Phase 6: move engine/watches/index.json into a `watches` table.
 //
 // watches.json is an array of watch jobs polled every 3 ticks. Most
 // installs carry only a handful (operator-defined notifications, plan-
@@ -21,7 +21,7 @@ function _resolveMinionsDir() {
   // backfill its tables from MINIONS_HOME — cross-directory corruption.
   const envHome = process.env.MINIONS_TEST_DIR || process.env.MINIONS_HOME;
   if (envHome) return envHome;
-  try { return require('../../shared').MINIONS_DIR; } catch { return null; }
+  try { return require('../../core/shared').MINIONS_DIR; } catch { return null; }
 }
 
 function _toMs(v) {

package/engine/db/migrations/008-small-state.js

@@ -20,7 +20,7 @@ function _resolveMinionsDir() {
   // backfill its tables from MINIONS_HOME — cross-directory corruption.
   const envHome = process.env.MINIONS_TEST_DIR || process.env.MINIONS_HOME;
   if (envHome) return envHome;
-  try { return require('../../shared').MINIONS_DIR; } catch { return null; }
+  try { return require('../../core/shared').MINIONS_DIR; } catch { return null; }
 }
 
 function _toMs(v) {

package/engine/db/migrations/009-qa.js

@@ -15,7 +15,7 @@ const fs = require('fs');
 function _resolveMinionsDir() {
   const envHome = process.env.MINIONS_HOME || process.env.MINIONS_TEST_DIR;
   if (envHome) return envHome;
-  try { return require('../../shared').MINIONS_DIR; } catch { return null; }
+  try { return require('../../core/shared').MINIONS_DIR; } catch { return null; }
 }
 
 function _toMs(v) {

package/engine/db/migrations/010-pr-links.js

@@ -17,7 +17,7 @@ const fs = require('fs');
 function _resolveMinionsDir() {
   const envHome = process.env.MINIONS_HOME || process.env.MINIONS_TEST_DIR;
   if (envHome) return envHome;
-  try { return require('../../shared').MINIONS_DIR; } catch { return null; }
+  try { return require('../../core/shared').MINIONS_DIR; } catch { return null; }
 }
 
 function _readJsonOr(filePath, fallback) {

package/engine/db/migrations/011-remaining-state.js

@@ -15,7 +15,7 @@ const fs = require('fs');
 function _resolveMinionsDir() {
   const envHome = process.env.MINIONS_HOME || process.env.MINIONS_TEST_DIR;
   if (envHome) return envHome;
-  try { return require('../../shared').MINIONS_DIR; } catch { return null; }
+  try { return require('../../core/shared').MINIONS_DIR; } catch { return null; }
 }
 
 function _readJsonOr(filePath, fallback) {

package/engine/db/migrations/012-steering-deliveries.js

@@ -7,12 +7,12 @@
 // well-defined state machine (queued → live_kill | deferred →
 // re_spawning → delivered → acknowledged) instead of relying on the
 // stdout-timestamp heuristic alone for visibility. The legacy
-// heuristic ack (engine/steering.js#ackProcessedSteeringMessages) is
+// heuristic ack (engine/agents/steering.js#ackProcessedSteeringMessages) is
 // kept as a back-compat path for inbox files that predate this
 // migration (no `steerId:` in frontmatter, no row in this table).
 //
 // SQL-first per CLAUDE.md "New state goes into SQL first" — no JSON
-// sidecar; reads/writes go through engine/steering-store.js.
+// sidecar; reads/writes go through engine/persistence/steering-store.js.
 
 module.exports = {
   version: 12,

package/engine/db/migrations/013-backfill-broken-note-links.js

@@ -1,7 +1,7 @@
 // engine/db/migrations/013-backfill-broken-note-links.js
 //
 // No-op marker. The one-time repair of broken inbox note links was moved to an
-// idempotent engine-boot sweep (engine/cli.js → note-link-backfill.runNoteLink
+// idempotent engine-boot sweep (engine/operations/cli.js → note-link-backfill.runNoteLink
 // Backfill) because it must go through shared.mutateWorkItems to keep the SQL
 // store and its JSON mirror consistent — a raw in-migration UPDATE left the
 // mirror diverged and could be reverted by the store's resync. This migration

package/engine/db/migrations/014-pr-fix-target-prefs.js

@@ -4,7 +4,7 @@
 // execution-target choice per repo (optional)".
 //
 // Adds the `pr_fix_target_prefs` table — one row per repo scope — so the
-// execution-target choice surface (engine/pr-fix-target.js) can OPTIONALLY
+// execution-target choice surface (engine/providers/pr-fix-target.js) can OPTIONALLY
 // remember the user's pick (clone-keep | temp-clone | remote-patch) keyed by
 // canonical PR scope (github:owner/repo / ado:org/proj/repo). When a remembered
 // choice exists, a repeat fix on that repo routes straight to the executor
@@ -12,7 +12,7 @@
 // never clone silently). The choice is clearable/overridable.
 //
 // SQL-first per CLAUDE.md "New state goes into SQL first" — no JSON sidecar;
-// reads/writes go through engine/pr-fix-target-store.js.
+// reads/writes go through engine/persistence/pr-fix-target-store.js.
 
 module.exports = {
   version: 14,

package/engine/db/migrations/018-sql-only-cutover.js

@@ -6,12 +6,12 @@ module.exports = {
     let legacyPrdCount = 0;
     let importedPrdCount = 0;
     const minionsDir = process.env.MINIONS_TEST_DIR || process.env.MINIONS_HOME
-      || (() => { try { return require('../../shared').MINIONS_DIR; } catch { return null; } })();
+      || (() => { try { return require('../../core/shared').MINIONS_DIR; } catch { return null; } })();
     if (minionsDir) {
       const importDir = (dir, archived) => {
         let files = [];
         try { files = fs.readdirSync(dir).filter(f => f.endsWith('.json')); } catch { return; }
-        const { _upsertPrd } = require('../../prd-store');
+        const { _upsertPrd } = require('../../planning/prd-store');
         for (const filename of files) {
           legacyPrdCount++;
           const filePath = path.join(dir, filename);

package/engine/db/migrations/021-archived-work-items.js

@@ -4,7 +4,7 @@ const fs = require('fs');
 function _resolveMinionsDir() {
   const envHome = process.env.MINIONS_TEST_DIR || process.env.MINIONS_HOME;
   if (envHome) return envHome;
-  try { return require('../../shared').MINIONS_DIR; } catch { return null; }
+  try { return require('../../core/shared').MINIONS_DIR; } catch { return null; }
 }
 
 function _toMs(value) {

package/engine/db/migrations/022-global-cc-session.js

@@ -6,7 +6,7 @@ const CC_GLOBAL_SESSION_ID = '__global__';
 function _resolveMinionsDir() {
   const envHome = process.env.MINIONS_TEST_DIR || process.env.MINIONS_HOME;
   if (envHome) return envHome;
-  try { return require('../../shared').MINIONS_DIR; } catch { return null; }
+  try { return require('../../core/shared').MINIONS_DIR; } catch { return null; }
 }
 
 module.exports = {

package/engine/db/migrations/023-engine-state.js

@@ -6,7 +6,7 @@ const ENGINE_STATE_MARKER = 'engine_state';
 function _resolveMinionsDir() {
   const envHome = process.env.MINIONS_TEST_DIR || process.env.MINIONS_HOME;
   if (envHome) return envHome;
-  try { return require('../../shared').MINIONS_DIR; } catch { return null; }
+  try { return require('../../core/shared').MINIONS_DIR; } catch { return null; }
 }
 
 module.exports = {

package/engine/db/migrations/025-malformed-work-item-phantoms.js

@@ -1,4 +1,4 @@
-const { isMalformedPhantomWorkItem } = require('../../work-item-validation');
+const { isMalformedPhantomWorkItem } = require('../../planning/work-item-validation');
 
 module.exports = {
   version: 25,

package/engine/db/migrations/027-review-learning-lifecycle.js

@@ -20,7 +20,7 @@ function _parseObject(value) {
   }
 }
 
-// Mirror engine/review-learning.js#normalizeCanonicalPrId's space-compatible
+// Mirror engine/memory/review-learning.js#normalizeCanonicalPrId's space-compatible
 // contract so the quarantine accepts valid canonical IDs whose ADO
 // org/project/repo segments contain spaces (or %20) — createReviewFeedbackForAuthor
 // writes the raw canonical `pr.id`, and valid ADO scopes may contain spaces.

package/engine/db/migrations/029-repair-reused-versions.js

@@ -0,0 +1,20 @@
+// Versions 27 and 28 were previously used by retired mirror-hash migrations.
+// Existing databases therefore skipped the current review-learning and
+// cc-queued-message migrations even though fresh databases applied them.
+
+function _hasTable(db, table) {
+  return !!db.prepare(`
+    SELECT 1 FROM sqlite_master WHERE type='table' AND name=?
+  `).get(table);
+}
+
+module.exports = {
+  version: 29,
+  description: 'repair reused migration versions 27/28',
+  up(db) {
+    require('./027-review-learning-lifecycle').up(db);
+    if (!_hasTable(db, 'cc_queued_messages')) {
+      require('./028-cc-queued-messages').up(db);
+    }
+  },
+};

package/engine/db/migrations/031-pr-author-identity.js

@@ -0,0 +1,137 @@
+// engine/db/migrations/031-pr-author-identity.js
+//
+// W-mscibegy005e8b74: separate PR author identity from Minions agent attribution.
+//
+// Historically `pr.agent` was overloaded: GitHub/ADO provider sync overwrote it
+// with the platform author login (`agent === 'human'` → login/displayName),
+// while orchestration and routing use `pr.agent` as the *Minions* agent that
+// created/owns the automated work. That conflated two distinct identities.
+//
+// This migration:
+//   1. Adds an `author` projection column (typed label; canonical structured
+//      identity lives in the `data` JSON under `author`).
+//   2. Backfills, FAIL-CLOSED, by un-overloading historical rows: a row whose
+//      `agent` is a human login (i.e. not the 'human' sentinel, not a configured
+//      Minions agent id, not a temp-* ephemeral, not 'unknown'/'unassigned') has
+//      that login moved into `author` and `agent` reset to 'human'. When the set
+//      of configured agent ids cannot be resolved, the destructive move is
+//      SKIPPED entirely so a real agent row (e.g. 'dallas') is never mistaken for
+//      a human login. Rows that already carry a structured `data.author` just get
+//      the label projected into the new column.
+//
+// Rows whose identity cannot be established are left untouched: `author` stays
+// NULL and renders as "Unknown" rather than silently falling back to the agent.
+
+const path = require('path');
+const fs = require('fs');
+
+function _resolveMinionsDir() {
+  const envHome = process.env.MINIONS_TEST_DIR || process.env.MINIONS_HOME;
+  if (envHome) return envHome;
+  try { return require('../../core/shared').MINIONS_DIR; } catch { return null; }
+}
+
+// Resolve the set of configured Minions agent ids from config.json. Returns null
+// (not an empty set) when the config is unavailable/unreadable so the caller can
+// distinguish "no agents configured" from "cannot tell" and fail closed.
+function _resolveConfiguredAgentIds(minionsDir) {
+  if (!minionsDir) return null;
+  try {
+    const raw = fs.readFileSync(path.join(minionsDir, 'config.json'), 'utf8');
+    const cfg = JSON.parse(raw);
+    if (!cfg || typeof cfg !== 'object' || !cfg.agents || typeof cfg.agents !== 'object') {
+      return new Set();
+    }
+    const ids = new Set();
+    for (const key of Object.keys(cfg.agents)) {
+      if (key) ids.add(String(key).toLowerCase());
+    }
+    return ids;
+  } catch {
+    return null;
+  }
+}
+
+const _NON_HUMAN_AGENTS = new Set(['human', 'unknown', 'unassigned', '', 'none', 'null']);
+
+// Does this legacy `agent` value look like a human login wrongly stored in agent?
+function _looksLikeHumanLogin(agent, configuredAgentIds) {
+  if (!agent || typeof agent !== 'string') return false;
+  const norm = agent.trim().toLowerCase();
+  if (_NON_HUMAN_AGENTS.has(norm)) return false;
+  if (norm.startsWith('temp-')) return false;           // ephemeral Minions agent
+  if (configuredAgentIds && configuredAgentIds.has(norm)) return false; // real agent
+  return true;
+}
+
+function _authorLabel(author) {
+  if (!author || typeof author !== 'object') return null;
+  const label = author.displayName || author.login || author.id || '';
+  const s = String(label).trim();
+  return s ? s.slice(0, 200) : null;
+}
+
+function _hasTable(db, table) {
+  return !!db.prepare(`
+    SELECT 1 FROM sqlite_master WHERE type='table' AND name=?
+  `).get(table);
+}
+
+module.exports = {
+  version: 31,
+  description: 'pull_requests.author — separate PR author identity from pr.agent (W-mscibegy005e8b74)',
+  up(db) {
+    // The pull_requests table is created by migration 004, so a real database
+    // always has it by the time this runs. Synthetic databases (e.g. hand-built
+    // version-26 fixtures that only create the tables under test) may not — a DB
+    // with no pull_requests table has no PR identities to migrate, so skip.
+    if (!_hasTable(db, 'pull_requests')) return;
+
+    db.exec(`
+      ALTER TABLE pull_requests ADD COLUMN author TEXT;
+      CREATE INDEX IF NOT EXISTS idx_pr_author ON pull_requests(author);
+    `);
+
+    const minionsDir = _resolveMinionsDir();
+    const configuredAgentIds = _resolveConfiguredAgentIds(minionsDir);
+    // FAIL-CLOSED: if we cannot resolve configured agent ids, do not perform the
+    // destructive agent→author move (real agent rows would be corrupted). We can
+    // still safely project already-structured authors into the column below.
+    const canUnoverload = configuredAgentIds != null;
+
+    const rows = db.prepare('SELECT scope, id, agent, data FROM pull_requests').all();
+    const update = db.prepare('UPDATE pull_requests SET agent = ?, author = ?, data = ? WHERE scope = ? AND id = ?');
+
+    let unoverloaded = 0;
+    let projected = 0;
+
+    for (const row of rows) {
+      let record;
+      try { record = JSON.parse(row.data); }
+      catch { continue; }
+      if (!record || typeof record !== 'object') continue;
+
+      // Case 1: already-structured author on the record — project label only.
+      if (record.author && typeof record.author === 'object') {
+        const label = _authorLabel(record.author);
+        if (label) {
+          update.run(record.agent || row.agent || null, label, JSON.stringify(record), row.scope, row.id);
+          projected += 1;
+        }
+        continue;
+      }
+
+      // Case 2: legacy overloaded agent — un-overload into author.
+      if (canUnoverload && _looksLikeHumanLogin(row.agent, configuredAgentIds)) {
+        const login = String(row.agent).trim().slice(0, 200);
+        record.author = { login };
+        record.agent = 'human';
+        update.run('human', login, JSON.stringify(record), row.scope, row.id);
+        unoverloaded += 1;
+      }
+    }
+
+    // eslint-disable-next-line no-console
+    console.log(`[db-migrate] v31: author column added; un-overloaded ${unoverloaded} legacy agent→author row(s), projected ${projected} structured author(s)${canUnoverload ? '' : ' (agent→author move SKIPPED: configured agent ids unavailable)'}`);
+  },
+};

package/engine/{consolidation.js → memory/consolidation.js}

@@ -1,5 +1,5 @@
 /**
- * engine/consolidation.js — Inbox note consolidation for Minions engine.
+ * engine/memory/consolidation.js — Inbox note consolidation for Minions engine.
  * Extracted from engine.js: LLM-powered and regex fallback consolidation,
  * knowledge base classification, inbox archival.
  */
@@ -7,14 +7,14 @@
 const fs = require('fs');
 const path = require('path');
 const crypto = require('crypto');
-const shared = require('./shared');
+const shared = require('../core/shared');
 const { safeRead, safeWrite,
   classifyInboxItem, KB_CATEGORIES, log, ts, dateStamp } = shared;
-const { callLLM, trackEngineUsage } = require('./llm');
-const queries = require('./queries');
+const { callLLM, trackEngineUsage } = require('../agents/llm');
+const queries = require('../core/queries');
 const { getInboxFiles, getNotes, INBOX_DIR, ENGINE_DIR,
   NOTES_PATH, KNOWLEDGE_DIR, ARCHIVE_DIR } = queries;
-const { wrapUntrusted, buildSource } = require('./untrusted-fence');
+const { wrapUntrusted, buildSource } = require('../core/untrusted-fence');
 const reviewLearning = require('./review-learning');
 const memoryStore = require('./memory-store');
 
@@ -141,7 +141,7 @@ const AGENT_MEMORY_RECONCILE_MIN_RETAIN_RATIO = 0.30;
 const AGENT_MEMORY_RECONCILE_SIGNAL_RE = /\b(invalid|rejected|rejection|incorrect|wrong|does not exist|never existed|stale|superseded?|_failureClass|invalid_managed_spawn)\b|(^|\n)\s*(\*\*)?reason:/i;
 
 // W-mq07b8do000nc86a — Sliding-window persistent memory defaults. These
-// mirror the engine.agentMemory* tunables in ENGINE_DEFAULTS (engine/shared.js)
+// mirror the engine.agentMemory* tunables in ENGINE_DEFAULTS (engine/core/shared.js)
 // and are exported so callers that synthesize a one-off prune (tests,
 // migrations) can opt into the same shape without re-importing shared.
 const AGENT_MEMORY_MAX_ENTRIES_DEFAULT = 300;

package/engine/{kb-sweep-runner.js → memory/kb-sweep-runner.js}

@@ -1,6 +1,6 @@
 #!/usr/bin/env node
 /**
- * engine/kb-sweep-runner.js — Detached entrypoint for the KB sweep.
+ * engine/memory/kb-sweep-runner.js — Detached entrypoint for the KB sweep.
  *
  * Spawned by dashboard.js `handleKnowledgeSweep` with `{ detached: true,
  * stdio: ['ignore', logFd, logFd] }` so the sweep survives dashboard /
@@ -48,7 +48,7 @@ const dryRun = cliDryRun || body.dryRun === true;
 
 // Lazy-require AFTER args are parsed so a malformed body-file doesn't drag in
 // the whole sweep stack before we've reported the failure.
-const queries = require('./queries');
+const queries = require('../core/queries');
 const { runKbSweep } = require('./kb-sweep');
 
 function cleanupBodyFile() {

package/engine/{kb-sweep.js → memory/kb-sweep.js}

@@ -1,5 +1,5 @@
 /**
- * engine/kb-sweep.js — Knowledge base sweep: dedup, compress, normalize.
+ * engine/memory/kb-sweep.js — Knowledge base sweep: dedup, compress, normalize.
  *
  * Replaces the inline sweep that lived in dashboard.js. Three passes:
  *   1. Hash-based dedup    — cheap, catches cross-batch duplicates
@@ -12,8 +12,8 @@
 const fs = require('fs');
 const path = require('path');
 const crypto = require('crypto');
-const shared = require('./shared');
-const queries = require('./queries');
+const shared = require('../core/shared');
+const queries = require('../core/queries');
 const { safeRead, safeReadOrNull, safeWrite, safeJson, safeUnlink, log, ts } = shared;
 const { MINIONS_DIR, ENGINE_DIR } = queries;
 
@@ -533,6 +533,7 @@ If nothing to do: { "duplicates": [], "reclassify": [], "remove": [] }`;
     try {
       result = await callLLM(prompt, 'Output only JSON.', {
         timeout: 120000, label: 'kb-sweep', model: 'haiku', maxTurns: 1, direct: true,
+        disableTools: true,
         engineConfig: opts.engineConfig,
       });
       trackEngineUsage('kb-sweep', result.usage);
@@ -650,6 +651,7 @@ ${body}`;
       try {
         const result = await callLLM(REWRITE_PROMPT(c.entry, c.body), 'Output ONLY the template body.', {
           timeout: 120000, label: 'kb-rewrite', model: 'haiku', maxTurns: 1, direct: true,
+          disableTools: true,
           engineConfig: opts.engineConfig,
         });
         trackEngineUsage('kb-rewrite', result.usage);
@@ -814,7 +816,7 @@ function readSweepLiveness(opts = {}) {
 /**
  * One-shot boot-time reconciliation for `engine/kb-sweep-state.json`.
  *
- * Mirrors the worktree-pool / keep-process boot reconcilers in `engine/cli.js`:
+ * Mirrors the worktree-pool / keep-process boot reconcilers in `engine/operations/cli.js`:
  * after an engine restart we may inherit a stale `in-flight`/`starting` record
  * whose runner has long since died (or — for legacy state files — never
  * recorded a pid). Without proactive cleanup the record sits there clogging
@@ -952,7 +954,7 @@ async function runKbSweep(opts = {}) {
 }
 
 async function _runKbSweepImpl(opts = {}) {
-  const { callLLM, trackEngineUsage } = require('./llm');
+  const { callLLM, trackEngineUsage } = require('../agents/llm');
   const summary = {
     ok: true,
     entriesBefore: 0,
@@ -1104,7 +1106,7 @@ async function _runKbSweepImpl(opts = {}) {
 }
 
 /**
- * Spawn the KB sweep runner (`engine/kb-sweep-runner.js`) as a detached child.
+ * Spawn the KB sweep runner (`engine/memory/kb-sweep-runner.js`) as a detached child.
  * Shared between dashboard's POST /api/knowledge/sweep handler and the engine
  * tick's auto-sweep phase. Performs the same synchronous "starting" → "in-flight"
  * CAS dance the dashboard handler used to do inline.
@@ -1152,7 +1154,7 @@ function spawnSweepRunnerDetached(opts = {}) {
   const logFn = typeof opts.log === 'function'
     ? opts.log
     : (level, msg) => { (level === 'error' ? console.error : console.log)(`[kb-sweep] ${msg}`); };
-  const cwd = opts.cwd || require('./queries').MINIONS_DIR;
+  const cwd = opts.cwd || require('../core/queries').MINIONS_DIR;
   const startedAt = Date.now();
   const sweepToken = `${startedAt}-${Math.random().toString(36).slice(2, 8)}`;
   const observed = readSweepLiveness({ now: startedAt });