monomind 2.0.3 → 2.1.0

package/packages/@monomind/cli/.claude/helpers/handlers/gates-handler.cjs

@@ -32,8 +32,13 @@ const SECRET_PATTERNS = [
   /(?:api[_-]?key|apikey)\s*[:=]\s*['"][^'"]{8,}['"]/gi,
   /(?:secret|password|passwd|pwd)\s*[:=]\s*['"][^'"]{8,}['"]/gi,
   /(?:token|bearer)\s*[:=]\s*['"][^'"]{10,}['"]/gi,
+  // Unquoted variants — env-style KEY equals value with no surrounding
+  // quotes (the single most common real leak pattern; the quoted patterns
+  // above never match a bare assignment in a shell export or .env file).
+  /(?:api[_-]?key|apikey|token|secret|password|passwd|pwd)\s*[:=]\s*[^\s'"]{8,}/gi,
   /-----BEGIN (?:RSA |EC |DSA )?PRIVATE KEY-----/g,
-  /sk-[a-zA-Z0-9]{20,}/g,
+  /sk-ant-[a-zA-Z0-9_-]{20,}/g,
+  /sk-[a-zA-Z0-9_-]{20,}/g,
   /ghp_[a-zA-Z0-9]{36}/g,
   /npm_[a-zA-Z0-9]{36}/g,
   /AKIA[0-9A-Z]{16}/g,
@@ -92,11 +97,14 @@ function handlePreBash(hCtx) {
 
   var result = checkDestructive(cmd);
   if (result.triggered) {
-    // Output block decision and set exit code 2 — both required by Claude Code PreToolUse protocol
-    console.log(JSON.stringify({
+    // Set exit code 2 to block, and write the reason to STDERR — per Claude
+    // Code's PreToolUse hook protocol, stdout JSON is only parsed when exit
+    // code is 0; at exit code 2 the caller reads the block reason from
+    // stderr instead, so putting it on stdout here would make it invisible.
+    process.stderr.write(JSON.stringify({
       decision: 'block',
       reason: '[gates] ' + result.reason,
-    }));
+    }) + '\n');
     process.exitCode = 2;
   }
 }
@@ -120,11 +128,12 @@ function handlePreWrite(hCtx) {
 
   var result = checkSecrets(content);
   if (result.triggered) {
-    // Output block decision and set exit code 2 — both required by Claude Code PreToolUse protocol
-    console.log(JSON.stringify({
+    // Set exit code 2 to block, and write the reason to STDERR — see the
+    // matching comment in handlePreBash for why stdout is the wrong stream.
+    process.stderr.write(JSON.stringify({
       decision: 'block',
       reason: '[gates] ' + result.reason,
-    }));
+    }) + '\n');
     process.exitCode = 2;
   }
 }

package/packages/@monomind/cli/.claude/helpers/handlers/loops-status-handler.cjs

@@ -10,7 +10,7 @@ module.exports = {
     var loopsDir = path.join(CWD, '.monomind', 'loops');
     if (!fs.existsSync(loopsDir)) { console.log('No loops directory.'); return; }
     var files = fs.readdirSync(loopsDir).filter(function(f) {
-      return f.endsWith('.json') && !f.includes('-hil') && !f.endsWith('.stop');
+      return f.endsWith('.json') && !f.includes('-hil') && !f.endsWith('.stop') && !f.startsWith('._');
     }).slice(0, 200); // cap to prevent DoS via many files
     var STALE_MS = 6 * 60 * 60 * 1000;
     var now = Date.now();

package/packages/@monomind/cli/.claude/helpers/handlers/route-handler.cjs

@@ -327,15 +327,15 @@ module.exports = {
             }
           }
         }
-        // Performance metrics (daemon optimize worker)
+        // Performance metrics (optimize worker — a one-shot process, not a daemon)
         var perfFile = path.join(metricsDir, 'performance.json');
         if (fs.existsSync(perfFile) && fs.statSync(perfFile).size < 32768) {
           var perfData = JSON.parse(fs.readFileSync(perfFile, 'utf-8'));
-          if (perfData && perfData.memoryUsage) {
-            var rssBytes = perfData.memoryUsage.rss || 0;
+          if (perfData && perfData.workerProcessMemoryUsage) {
+            var rssBytes = perfData.workerProcessMemoryUsage.rss || 0;
             var rssMB = Math.round(rssBytes / (1024 * 1024));
             if (rssMB > 512) {
-              console.log('[PERF] Daemon RSS ' + rssMB + 'MB (>512MB threshold). Consider restarting daemon or reducing worker concurrency');
+              console.log('[PERF] optimize worker RSS ' + rssMB + 'MB (>512MB threshold) at last run — reflects that one-shot process, not a persistent daemon');
             }
           }
         }

package/packages/@monomind/cli/.claude/helpers/handlers/session-handler.cjs

@@ -89,17 +89,48 @@ module.exports = {
           // Only write the success flag when derived from actual evidence (commits, outcomes)
           if (typeof sessionSuccess === 'boolean') feedbackEntry.intelligenceFeedback = sessionSuccess;
           fs.appendFileSync(feedbackPath, JSON.stringify(feedbackEntry) + '\n', 'utf-8');
-          // Rotate: keep last 1000 lines to prevent unbounded growth
+          // Rotate: keep last 1000 lines to prevent unbounded growth.
           try {
             var MAX_FEEDBACK = 512 * 1024; // 512 KiB
-            if (fs.existsSync(feedbackPath) && fs.statSync(feedbackPath).size > MAX_FEEDBACK) {
-              // File too large — emergency trim without full read
-              throw new Error('skip-rotation');
-            }
-            var raw = fs.readFileSync(feedbackPath, 'utf-8');
-            var lines = raw.split('\n').filter(Boolean);
-            if (lines.length > 1000) {
-              fs.writeFileSync(feedbackPath, lines.slice(-1000).join('\n') + '\n', 'utf-8');
+            var feedbackStat = fs.existsSync(feedbackPath) ? fs.statSync(feedbackPath) : null;
+            if (feedbackStat && feedbackStat.size > MAX_FEEDBACK) {
+              // Emergency tail-trim: the file is too large to comfortably read+split
+              // in full, so seek to a byte offset near the end, read only that tail,
+              // drop the first (possibly partial) line, and keep the rest — instead
+              // of the previous behavior which threw here and skipped trimming
+              // entirely, leaving the file to grow forever and permanently disabling
+              // consumers (router.cjs, route-handler.cjs) that bail out on oversized
+              // files.
+              var TAIL_BYTES = 256 * 1024; // ~256 KiB of tail content
+              var fd = fs.openSync(feedbackPath, 'r');
+              try {
+                var readSize = Math.min(TAIL_BYTES, feedbackStat.size);
+                var startOffset = feedbackStat.size - readSize;
+                var buf = Buffer.alloc(readSize);
+                fs.readSync(fd, buf, 0, readSize, startOffset);
+                var tailRaw = buf.toString('utf-8');
+                var tailLines = tailRaw.split('\n');
+                // Drop the first line if we didn't start at byte 0 — it's likely partial.
+                if (startOffset > 0) tailLines.shift();
+                var validTailLines = tailLines.filter(function(l) {
+                  if (!l) return false;
+                  try { JSON.parse(l); return true; } catch (eParse) { return false; }
+                });
+                var trimmedTail = validTailLines.slice(-1000);
+                var tmpFeedbackPath = feedbackPath + '.' + process.pid + '.tmp';
+                fs.writeFileSync(tmpFeedbackPath, trimmedTail.join('\n') + (trimmedTail.length > 0 ? '\n' : ''), 'utf-8');
+                fs.renameSync(tmpFeedbackPath, feedbackPath);
+              } finally {
+                fs.closeSync(fd);
+              }
+            } else {
+              var raw = fs.readFileSync(feedbackPath, 'utf-8');
+              var lines = raw.split('\n').filter(Boolean);
+              if (lines.length > 1000) {
+                var tmpFeedbackPath2 = feedbackPath + '.' + process.pid + '.tmp';
+                fs.writeFileSync(tmpFeedbackPath2, lines.slice(-1000).join('\n') + '\n', 'utf-8');
+                fs.renameSync(tmpFeedbackPath2, feedbackPath);
+              }
             }
           } catch (e2) { /* rotation is best-effort */ }
         }
@@ -141,19 +172,6 @@ module.exports = {
 
     // Memory Palace tombstone writes removed — redundant with raw session JSONL
 
-    // ── Context Persistence Auto-Archive ─────────────────────────────────
-    // Archive conversation context so it survives compaction and new sessions
-    try {
-      var cpHook = await import('file://' + path.join(__dirname, '..', 'context-persistence-hook.mjs'));
-      if (cpHook && cpHook.archive) {
-        await hCtx.runWithTimeout(function() { return cpHook.archive(); }, 'context-persistence.archive()');
-        console.log('[CONTEXT_PERSIST] Session transcript archived');
-      } else if (cpHook && cpHook.default && cpHook.default.archive) {
-        await hCtx.runWithTimeout(function() { return cpHook.default.archive(); }, 'context-persistence.archive()');
-        console.log('[CONTEXT_PERSIST] Session transcript archived');
-      }
-    } catch (e) { /* non-fatal — context-persistence may not export archive() */ }
-
     // ── Auto-populate: write session episode for every session ─────
     // Even solo sessions (no subagents) produce an episode so the
     // route handler can surface relevant past sessions.

package/packages/@monomind/cli/.claude/helpers/handlers/session-restore-handler.cjs

@@ -206,18 +206,6 @@ module.exports = {
       }
     } catch (e) { /* non-fatal — hooks workers unavailable */ }
 
-    // Context Persistence Auto-Restore
-    try {
-      var cpHook = await import('file://' + path.join(helpersDir, 'context-persistence-hook.mjs'));
-      var restoreFn = (cpHook && cpHook.restore) || (cpHook && cpHook.default && cpHook.default.restore);
-      if (restoreFn) {
-        var restored = await runWithTimeout(function() { return restoreFn(); }, 'context-persistence.restore()');
-        if (restored && restored.turns > 0) {
-          console.log('[CONTEXT_RESTORED] ' + restored.turns + ' turns from previous session');
-        }
-      }
-    } catch (e) { /* non-fatal */ }
-
     // AgentKnowledgeBase — preload shared knowledge context on session restore.
     try {
       var knowledgeDir = path.join(CWD, '.monomind', 'knowledge');

package/packages/@monomind/cli/.claude/helpers/handlers/task-handler.cjs

@@ -5,6 +5,8 @@
 
 const path = require('path');
 const fs = require('fs');
+const { purgeStaleRegistrations } = require('../utils/agent-registrations.cjs');
+const { atomicWriteFileSync, withLock } = require('../utils/fs-helpers.cjs');
 
 module.exports = {
   handlePreTask: async function(hCtx) {
@@ -50,36 +52,65 @@ module.exports = {
         intelligence.feedback(taskSuccess);
       } catch (e) { /* non-fatal */ }
     }
-    // Each TeammateIdle/TaskCompleted = one agent done → remove oldest registration (FIFO)
+    // Each TeammateIdle/TaskCompleted = one agent done → remove its registration.
     const regDir = path.join(CWD, '.monomind', 'agents', 'registrations');
     try {
       if (fs.existsSync(regDir)) {
         const files = fs.readdirSync(regDir).filter(f => f.endsWith('.json'));
-        if (files.length > 0) {
-          // Sort by mtime ascending (oldest first) and remove the oldest one
+        // P3-15: post-task (TeammateIdle/TaskCompleted) also fires for the MAIN
+        // session's own tasks — e.g. the team lead completing a self-assigned
+        // TaskList item — which never wrote an agent-start registration in the
+        // first place. Blindly popping the oldest registration on EVERY
+        // post-task event therefore deregistered an unrelated, still-running
+        // agent whenever the lead (not a subagent) finished a task, silently
+        // drifting the count negative-equivalent (undercounting active agents).
+        //
+        // Registrations now carry an `agentType` (agent-start-handler.cjs), and
+        // this hook's payload may carry the same identifying field under one of
+        // several possible names — mirroring the precedence agent-start-handler
+        // already uses to derive it. If this event carries NO such field at
+        // all, there's no evidence it corresponds to a real agent completion
+        // (as opposed to the main session's own task), so we skip touching
+        // registrations entirely rather than guessing via FIFO. When the field
+        // IS present, prefer removing the registration recorded with the SAME
+        // type; fall back to oldest-of-all only if no type match is found
+        // (e.g. a legacy registration written before this fix, with no
+        // agentType stored).
+        const completingType = hookInput.subagent_type || hookInput.agentType || hookInput.agent_type
+          || hookInput.agentSlug || hookInput.agent_slug || '';
+        if (files.length > 0 && completingType) {
           const sorted = files
-            .map(f => ({ f, mtime: (() => { try { return fs.statSync(path.join(regDir, f)).mtimeMs; } catch { return 0; } })() }))
+            .map(f => {
+              let mtime = 0, agentType = null;
+              try { mtime = fs.statSync(path.join(regDir, f)).mtimeMs; } catch { /* ignore */ }
+              try { agentType = JSON.parse(fs.readFileSync(path.join(regDir, f), 'utf-8')).agentType || null; } catch { /* ignore */ }
+              return { f, mtime, agentType };
+            })
             .sort((a, b) => a.mtime - b.mtime);
-          try { fs.unlinkSync(path.join(regDir, sorted[0].f)); } catch { /* ignore */ }
+          const typeMatch = sorted.find(r => r.agentType === completingType);
+          const toRemove = typeMatch || sorted[0];
+          try { fs.unlinkSync(path.join(regDir, toRemove.f)); } catch { /* ignore */ }
         }
-        // Also purge any stragglers older than 30 min
-        const now = Date.now();
-        for (const f of fs.readdirSync(regDir).filter(f => f.endsWith('.json'))) {
-          try { if (now - fs.statSync(path.join(regDir, f)).mtimeMs > 30 * 60 * 1000) fs.unlinkSync(path.join(regDir, f)); } catch { /* ignore */ }
-        }
-        const remaining = fs.readdirSync(regDir).filter(f => f.endsWith('.json')).length;
+        // Also purge any stragglers older than 30 min (shared with agent-start-handler.cjs)
+        const remaining = purgeStaleRegistrations(regDir) || 0;
+        // P2-21: shares a lock with agent-start-handler.cjs's swarm-activity.json
+        // writer (same path + '.lock') so the read-prevLastActive-then-write
+        // cycle can't race with that handler's concurrent write and silently
+        // drop whichever one wrote last — see that file for full rationale.
         const _actPath = path.join(CWD, '.monomind', 'metrics', 'swarm-activity.json');
-        let _prevLastActive = 0;
-        try { var _actSt = fs.statSync(_actPath); if (_actSt.size < 65536) { _prevLastActive = (JSON.parse(fs.readFileSync(_actPath, 'utf-8'))?.swarm?.lastActive) || 0; } } catch { /* ignore */ }
-        fs.writeFileSync(_actPath, JSON.stringify({
-          timestamp: new Date().toISOString(),
-          swarm: {
-            active: remaining > 0,
-            agent_count: remaining,
-            coordination_active: remaining > 0,
-            lastActive: Math.max(remaining, _prevLastActive), // preserve peak across completion
-          },
-        }));
+        withLock(_actPath + '.lock', function() {
+          let _prevLastActive = 0;
+          try { var _actSt = fs.statSync(_actPath); if (_actSt.size < 65536) { _prevLastActive = (JSON.parse(fs.readFileSync(_actPath, 'utf-8'))?.swarm?.lastActive) || 0; } } catch { /* ignore */ }
+          atomicWriteFileSync(_actPath, JSON.stringify({
+            timestamp: new Date().toISOString(),
+            swarm: {
+              active: remaining > 0,
+              agent_count: remaining,
+              coordination_active: remaining > 0,
+              lastActive: Math.max(remaining, _prevLastActive), // preserve peak across completion
+            },
+          }));
+        }, 5000);
       }
     } catch (e) { /* non-fatal */ }
 

package/packages/@monomind/cli/.claude/helpers/hook-handler.cjs

@@ -136,9 +136,49 @@ async function _ensureHooksModule() {
       _hooksModule = null; // not built — bridge stays a fail-soft no-op
     }
   }
+  if (!_hooksModule) _warnHooksBridgeUnavailable();
   return _hooksModule;
 }
 
+// ── Visible one-time warning when the @monomind/hooks bridge fully fails ───
+// Both load paths above (bare specifier + dev-repo file:// fallback) failed:
+// the 15 background workers (metrics, security scan, DDD tracking, etc.) are
+// unavailable for the rest of this session. This is almost always because
+// @monomind/hooks was never resolvable from npm (it ships with
+// optionalDependencies:"*", which npm silently skips) — NOT a problem with
+// the user's own project setup. Historically this failed completely
+// silently (see docs/AUDIT-BACKLOG.md P1-1), burning debugging time on the
+// wrong target. Warned once per session (file-marker keyed by session id,
+// same pattern as the once-per-day update check below) since every hook
+// event is its own fresh `node` process and would otherwise spam this on
+// every single tool call.
+function _warnHooksBridgeUnavailable() {
+  try {
+    var sessId = String((hookInput && (hookInput.sessionId || hookInput.session_id)) || '');
+    var flagFile = path.join(CWD, '.monomind', 'hooks-bridge-warned.json');
+    var alreadyWarned = false;
+    if (sessId && fs.existsSync(flagFile)) {
+      try {
+        var flagData = JSON.parse(fs.readFileSync(flagFile, 'utf-8'));
+        if (flagData && flagData.sessionId === sessId) alreadyWarned = true;
+      } catch (e) { /* corrupt/unreadable flag file — warn again to be safe */ }
+    }
+    if (alreadyWarned) return;
+    process.stderr.write(
+      '[WARN] @monomind/hooks could not be loaded (bare specifier and dev-repo fallback both failed) — ' +
+      'background workers (metrics, security scan, DDD tracking, etc.) are unavailable this session. ' +
+      'This is not a problem with your project configuration — the package is not resolvable via npm ' +
+      'from this install. See docs/AUDIT-BACKLOG.md P1-1 or https://github.com/monoes/monomind/issues.\n'
+    );
+    if (sessId) {
+      try {
+        fs.mkdirSync(path.join(CWD, '.monomind'), { recursive: true });
+        fs.writeFileSync(flagFile, JSON.stringify({ sessionId: sessId, warnedAt: new Date().toISOString() }), 'utf-8');
+      } catch (e) { /* non-fatal — worst case we warn again next event */ }
+    }
+  } catch (e) { /* never let the warning itself break a hook event */ }
+}
+
 // ── Intelligence timeout protection (fixes #1530, #1531) ───────────────────
 var INTELLIGENCE_TIMEOUT_MS = 1500;
 function runWithTimeout(fn, label) {
@@ -351,7 +391,20 @@ const handlers = {
     h.handle(hCtx);
   },
 
-  'pre-bash': () => {
+  'pre-bash': async () => {
+    // SECURITY GATE FIRST — destructive-ops enforcement must never be
+    // starved by the slower enrichment work below (monograph hint lookups).
+    // Previously this ran LAST, after up to 10 monograph SQLite strategies,
+    // AND was fired without awaiting its promise — meaning the block
+    // decision (process.exitCode) could still be unset when the process
+    // exited under the global 5s safety timer (see main()'s
+    // `process.exit(0)`), i.e. the gate could fail OPEN under time
+    // pressure. Awaiting it first guarantees the block/allow decision is
+    // computed and set before any enrichment work even starts.
+    var gates = require('./handlers/gates-handler.cjs');
+    await gates.handlePreBash(hCtx);
+    if (process.exitCode === 2) return; // blocked — skip enrichment entirely
+
     var cmd = (hCtx.toolInput && (hCtx.toolInput.command || hCtx.toolInput.cmd)) || '';
     var isGrep = /\b(?:grep|rg|ag)\b/.test(cmd);
     var isFind = /\b(?:find|fd)\b/.test(cmd) && !isGrep;
@@ -596,9 +649,6 @@ const handlers = {
       else if (isGrep) _recordGraphTelemetry('bash_grep_call');
       else _recordGraphTelemetry('bash_find_call');
     }
-    // Enforcement gate: destructive operations
-    var gates = require('./handlers/gates-handler.cjs');
-    gates.handlePreBash(hCtx);
   },
 
   'pre-write': () => {

package/packages/@monomind/cli/.claude/helpers/intelligence.cjs

@@ -13,6 +13,7 @@
 
 const path = require('path');
 const fs = require('fs');
+const { claimLock, releaseLock } = require('./utils/fs-helpers.cjs');
 
 // Resolve base dir at require-time so tests can inject CLAUDE_PROJECT_DIR
 // per fresh require() call.
@@ -35,6 +36,76 @@ function ensureDataDir() {
   try { fs.mkdirSync(DATA_DIR, { recursive: true }); } catch (_) {}
 }
 
+// ── multi-process-safe store flush (P1-14) ──────────────────────────────────
+// STORE_FILE (auto-memory-store.json) is read once into `_entries` at init()
+// and can be written by more than one code path — consolidate() and
+// bootstrapFromDb() — each of which may be running in a *different* process
+// (e.g. the long-lived MCP server process and a short-lived CJS hook
+// subprocess launched concurrently). Without a lock + re-read-before-write,
+// whichever process flushes last silently erases whatever the other process
+// added since its own load. mergeAndWriteStore() re-reads the current
+// on-disk file immediately before writing, merges the caller's updates in by
+// `id` (keeping whichever record has the newer `ts`), and writes atomically
+// via tmp+rename, guarded by a short advisory lock.
+
+const STORE_LOCK_FILE = STORE_FILE + '.lock';
+const STORE_LOCK_STALE_MS = 10 * 1000; // single JSON write — 10s is generous
+
+// Uses fs-helpers.cjs's claimLock/releaseLock: unlike an unlink-then-recreate
+// stale-break, it reclaims via an atomic rename, so two processes that both
+// decide the lock is stale can't both end up believing they hold it (a real
+// TOCTOU race a previous unlink-then-create version of this had — best-effort
+// either way, since a missed lock still merges via mergeAndWriteStore's
+// re-read, this just narrows the window further).
+function claimStoreLock() {
+  return claimLock(STORE_LOCK_FILE, STORE_LOCK_STALE_MS);
+}
+
+function releaseStoreLock() {
+  releaseLock(STORE_LOCK_FILE);
+}
+
+/**
+ * Merge `updates` (new or changed entries) into the on-disk store and write
+ * the result atomically. Re-reads STORE_FILE immediately before writing so a
+ * concurrent flush from another process is merged, not clobbered. When both
+ * sides have an entry with the same `id`, the one with the newer `ts` wins.
+ */
+function mergeAndWriteStore(updates, capTo) {
+  var acquired = claimStoreLock();
+  if (!acquired) acquired = claimStoreLock(); // one retry — lock is short-lived
+
+  try {
+    var diskRaw = safeReadJson(STORE_FILE);
+    var diskEntries = Array.isArray(diskRaw) ? diskRaw : [];
+    var merged = new Map();
+    for (var i = 0; i < diskEntries.length; i++) {
+      var d = diskEntries[i];
+      if (d && d.id) merged.set(String(d.id), d);
+    }
+    for (var j = 0; j < (updates || []).length; j++) {
+      var u = updates[j];
+      if (!u || !u.id) continue;
+      var key = String(u.id);
+      var existing = merged.get(key);
+      if (!existing || (u.ts || 0) >= (existing.ts || 0)) {
+        merged.set(key, u);
+      }
+    }
+    var result = Array.from(merged.values());
+    if (capTo && result.length > capTo) {
+      result.sort(function(a, b) { return (b.ts || 0) - (a.ts || 0); });
+      result = result.slice(0, capTo);
+    }
+    var tmpPath = STORE_FILE + '.' + process.pid + '.tmp';
+    fs.writeFileSync(tmpPath, JSON.stringify(result, null, 2), 'utf-8');
+    fs.renameSync(tmpPath, STORE_FILE);
+    return result;
+  } finally {
+    if (acquired) releaseStoreLock();
+  }
+}
+
 function safeReadJson(filePath) {
   try {
     if (!fs.existsSync(filePath)) return null;
@@ -274,7 +345,11 @@ function consolidate() {
   }
 
   if (newStoreEntries.length > 0) {
-    // Merge with existing store entries
+    // Decide which of newStoreEntries are worth adding, based on a read of
+    // the store as of "now". The actual write below re-reads immediately
+    // before flushing (mergeAndWriteStore), so a concurrent process's writes
+    // in between are merged rather than clobbered — this initial read is
+    // only used for the near-duplicate decision, not as the write's base.
     var existing = safeReadJson(STORE_FILE);
     var store = Array.isArray(existing) ? existing : [];
     var existingIds = new Set(store.map(function(e) { return e && e.id; }));
@@ -283,25 +358,23 @@ function consolidate() {
     var fileSetKey = function(e) { return (e.files || []).slice().sort().join('|'); };
     var seenSummaries = new Set(store.map(function(e) { return e && e.summary; }));
     var seenFileSets = new Set(store.filter(function(e) { return e && Array.isArray(e.files) && e.files.length > 0; }).map(fileSetKey));
+    var toAdd = [];
     var addedCount = 0;
     for (var j = 0; j < newStoreEntries.length; j++) {
       var ne = newStoreEntries[j];
       if (existingIds.has(ne.id)) continue;
       if (seenSummaries.has(ne.summary)) continue;
       if (ne.files && ne.files.length > 0 && seenFileSets.has(fileSetKey(ne))) continue;
-      store.push(ne);
+      toAdd.push(ne);
       seenSummaries.add(ne.summary);
       if (ne.files && ne.files.length > 0) seenFileSets.add(fileSetKey(ne));
       addedCount++;
     }
-    // Cap store at 200 entries to prevent unbounded growth
-    if (store.length > 200) {
-      store.sort(function(a, b) { return (b.ts || 0) - (a.ts || 0); });
-      store = store.slice(0, 200);
+    if (toAdd.length > 0) {
+      try {
+        mergeAndWriteStore(toAdd, 200);
+      } catch (_) {}
     }
-    try {
-      fs.writeFileSync(STORE_FILE, JSON.stringify(store, null, 2), 'utf-8');
-    } catch (_) {}
     count += addedCount;
   }
 
@@ -395,19 +468,20 @@ function bootstrapFromDb(db) {
   if (!db || _entries.length >= 5) return 0;
   try {
     var hubs = db.prepare(
-      "SELECT n.name, n.label, n.file, COUNT(e.id) AS deg " +
-      "FROM nodes n JOIN edges e ON (e.source = n.id OR e.target = n.id) " +
-      "WHERE n.label IN ('File','Function','Class') AND n.file NOT LIKE '%node_modules%' AND n.file NOT LIKE '%dist/%' " +
+      "SELECT n.name, n.label, n.file_path AS file, COUNT(e.id) AS deg " +
+      "FROM nodes n JOIN edges e ON (e.source_id = n.id OR e.target_id = n.id) " +
+      "WHERE n.label IN ('File','Function','Class') AND n.file_path NOT LIKE '%node_modules%' AND n.file_path NOT LIKE '%dist/%' " +
       "GROUP BY n.id ORDER BY deg DESC LIMIT 10"
     ).all();
     if (hubs.length === 0) return 0;
     var existingIds = new Set(_entries.map(function(e) { return e.id; }));
+    var newHubEntries = [];
     var added = 0;
     for (var hi = 0; hi < hubs.length; hi++) {
       var h = hubs[hi];
       var bId = 'bootstrap-hub-' + hi;
       if (existingIds.has(bId)) continue;
-      _entries.push({
+      var hubEntry = {
         id: bId,
         type: 'hub',
         content: h.name + ' (' + h.label + ') — ' + (h.file || '').replace(CWD + '/', '') + ' (' + h.deg + ' connections)',
@@ -415,12 +489,17 @@ function bootstrapFromDb(db) {
         confidence: 0.4,
         files: h.file ? [h.file] : [],
         ts: Date.now(),
-      });
+      };
+      _entries.push(hubEntry);
+      newHubEntries.push(hubEntry);
       added++;
     }
     if (added > 0) {
       ensureDataDir();
-      try { fs.writeFileSync(STORE_FILE, JSON.stringify(_entries, null, 2), 'utf-8'); } catch (_) {}
+      // mergeAndWriteStore re-reads STORE_FILE immediately before writing, so
+      // this only ever adds these hub entries into whatever is currently on
+      // disk — it never overwrites entries a concurrent process added.
+      try { mergeAndWriteStore(newHubEntries, 200); } catch (_) {}
     }
     return added;
   } catch (_) { return 0; }

package/packages/@monomind/cli/.claude/helpers/session.cjs

@@ -9,6 +9,7 @@
 
 const path = require('path');
 const fs = require('fs');
+const { atomicWriteFileSync } = require('./utils/fs-helpers.cjs');
 
 const CWD = process.env.CLAUDE_PROJECT_DIR || process.cwd();
 
@@ -54,7 +55,11 @@ function readCurrent() {
 function writeCurrent(data) {
   ensureDir();
   try {
-    fs.writeFileSync(CURRENT_FILE, JSON.stringify(data, null, 2), 'utf-8');
+    // P2-21: tmp+rename — current.json is read+written by metric()/update()
+    // from multiple concurrent hook processes (pre-task, post-edit, etc. can
+    // all fire in one batched tool-call message); a plain writeFileSync lets
+    // a concurrent reader observe a partially-written file.
+    atomicWriteFileSync(CURRENT_FILE, JSON.stringify(data, null, 2), 'utf-8');
   } catch (_) {}
 }
 

package/packages/@monomind/cli/.claude/helpers/statusline.cjs

@@ -18,6 +18,7 @@ const fs = require('fs');
 const path = require('path');
 const { execSync, spawnSync } = require('child_process');
 const os = require('os');
+const { cleanEntries } = require('./utils/fs-helpers.cjs');
 
 // Configuration
 const CONFIG = {
@@ -197,8 +198,7 @@ function getModelFromSessionJSONL() {
     if (!fs.existsSync(projectsDir)) return null;
 
     // Most recently modified JSONL = current (or latest) session
-    const files = fs.readdirSync(projectsDir)
-      .filter(f => f.endsWith('.jsonl'))
+    const files = cleanEntries(projectsDir, f => f.endsWith('.jsonl'))
       .map(f => ({ f, mt: (() => { try { return fs.statSync(path.join(projectsDir, f)).mtimeMs; } catch { return 0; } })() }))
       .sort((a, b) => b.mt - a.mt);
     if (files.length === 0) return null;
@@ -303,7 +303,7 @@ function getLearningStats() {
   try {
     const sessDir = path.join(CWD, '.claude', 'sessions');
     if (fs.existsSync(sessDir)) {
-      sessions = fs.readdirSync(sessDir).filter(f => f.endsWith('.json')).length;
+      sessions = cleanEntries(sessDir, f => f.endsWith('.json')).length;
     }
   } catch { /* ignore */ }
 
@@ -357,7 +357,7 @@ function getSecurityStatus() {
   try {
     const scanDir = path.join(CWD, '.claude', 'security-scans');
     if (fs.existsSync(scanDir)) {
-      scanCount = fs.readdirSync(scanDir).filter(f => f.endsWith('.json')).length;
+      scanCount = cleanEntries(scanDir, f => f.endsWith('.json')).length;
     }
   } catch { /* ignore */ }
 
@@ -379,7 +379,7 @@ function getSwarmStatus() {
   const regDir = path.join(CWD, '.monomind', 'agents', 'registrations');
   if (fs.existsSync(regDir)) {
     try {
-      const files = fs.readdirSync(regDir).filter(f => f.endsWith('.json'));
+      const files = cleanEntries(regDir, f => f.endsWith('.json'));
       const liveCount = files.filter(f => {
         try {
           return (now - fs.statSync(path.join(regDir, f)).mtimeMs) < agentRegTtlMs;
@@ -488,7 +488,7 @@ function getADRStatus() {
   for (const adrPath of adrPaths) {
     try {
       if (fs.existsSync(adrPath)) {
-        const files = fs.readdirSync(adrPath).filter(f =>
+        const files = cleanEntries(adrPath, f =>
           f.endsWith('.md') && (f.startsWith('ADR-') || f.startsWith('adr-') || /^\d{4}-/.test(f))
         );
         // Report actual count — don't guess compliance without reading files
@@ -523,7 +523,7 @@ function getHooksStatus() {
   try {
     const hooksDir = path.join(CWD, '.claude', 'hooks');
     if (fs.existsSync(hooksDir)) {
-      const hookFiles = fs.readdirSync(hooksDir).filter(f => f.endsWith('.js') || f.endsWith('.sh')).length;
+      const hookFiles = cleanEntries(hooksDir, f => f.endsWith('.js') || f.endsWith('.sh')).length;
       total = Math.max(total, hookFiles);
       enabled = Math.max(enabled, hookFiles);
     }
@@ -870,7 +870,7 @@ function getLoopStatus() {
   const now = Date.now();
   const loops = [];
   try {
-    const files = fs.readdirSync(loopsDir).filter(f =>
+    const files = cleanEntries(loopsDir, f =>
       f.endsWith('.json') && !f.includes('-hil') && !f.endsWith('.stop'));
     for (const f of files) {
       const d = readJSON(path.join(loopsDir, f));
@@ -895,7 +895,7 @@ function getHILPending() {
   if (!fs.existsSync(loopsDir)) return { pending: 0 };
   let pending = 0;
   try {
-    const files = fs.readdirSync(loopsDir).filter(f => f.endsWith('-hil.md'));
+    const files = cleanEntries(loopsDir, f => f.endsWith('-hil.md'));
     for (const f of files) {
       try {
         const txt = fs.readFileSync(path.join(loopsDir, f), 'utf-8');
@@ -932,7 +932,7 @@ function getActiveOrgs() {
       const runsDir = path.join(orgsDir, orgName, 'runs');
       if (!fs.existsSync(runsDir)) continue;
       try {
-        const files = fs.readdirSync(runsDir).filter(f => f.endsWith('.jsonl'));
+        const files = cleanEntries(runsDir, f => f.endsWith('.jsonl'));
         if (!files.length) continue;
         files.sort();
         const latest = files[files.length - 1];