monomind 1.18.11 → 1.18.13

package/.claude/helpers/graphify-freshen.cjs

@@ -66,6 +66,34 @@ if (!entryPoint) {
   process.exit(0);
 }
 
+// Skip if index is already fresh — don't waste CPU on every session start
+const dbPath = path.join(projectDir, '.monomind', 'monograph.db');
+if (fs.existsSync(dbPath)) {
+  try {
+    const mod = (() => {
+      try { return require(path.join(projectDir, 'packages', '@monomind', 'monograph', 'dist', 'src', 'index.js')); } catch {}
+      try { return require('@monoes/monograph'); } catch {}
+      return null;
+    })();
+    if (mod && mod.openDb) {
+      const db = mod.openDb(dbPath);
+      try {
+        const row = db.prepare("SELECT value FROM index_meta WHERE key='last_commit_hash'").get();
+        if (row && row.value) {
+          const { execSync } = require('child_process');
+          const behind = parseInt(execSync('git rev-list --count ' + row.value + '..HEAD 2>/dev/null', {
+            cwd: projectDir, encoding: 'utf-8', timeout: 2000
+          }).trim(), 10) || 0;
+          if (behind === 0) {
+            console.log('[graph] index is fresh — skipping rebuild');
+            process.exit(0);
+          }
+        }
+      } finally { mod.closeDb(db); }
+    }
+  } catch { /* can't check — proceed with build */ }
+}
+
 // Skip if another build is already in progress (avoids SQLite BUSY on concurrent init + session-start)
 const lockPath = path.join(graphDir, 'build.lock');
 const now = Date.now();

package/.claude/helpers/handlers/route-handler.cjs

@@ -381,7 +381,7 @@ module.exports = {
             }
           } catch (e) { /* ignore */ }
         }
-        if (nodeCount > 100) {
+        if (nodeCount > 100 && hCtx._isGraphFresh()) {
           // Pre-resolve top-3 relevant files for the user's prompt — the LLM
           // sees the answer inline instead of being told to call a tool.
           // 3 is enough signal; more files inflate token cost on every prompt.

package/.claude/helpers/hook-handler.cjs

@@ -216,6 +216,7 @@ var hCtx = {
   _recordToolCall: _recordToolCall,
   _openMonographDb: _openMonographDb,
   _requireMonograph: _requireMonograph,
+  _isGraphFresh: _isGraphFresh,
   _triggerExtractYamlValue: _triggerExtractYamlValue,
   _triggerFinalize: _triggerFinalize,
   _triggerExtractFromFrontmatter: _triggerExtractFromFrontmatter,
@@ -312,7 +313,8 @@ const handlers = {
               if (db) {
                 // Stop words: language keywords + generic single-word identifiers
                 // that match Variable nodes in markdown/scripts (not real code symbols)
-                var _grepStop = {import:1,export:1,from:1,require:1,return:1,function:1,const:1,let:1,var:1,class:1,interface:1,type:1,extends:1,implements:1,async:1,await:1,yield:1,throw:1,catch:1,finally:1,typeof:1,instanceof:1,void:1,null:1,undefined:1,true:1,false:1,this:1,super:1,new:1,delete:1,switch:1,case:1,break:1,continue:1,default:1,else:1,while:1,for:1,with:1,include:1,error:1,string:1,number:1,object:1,boolean:1,array:1,value:1,result:1,data:1,name:1,path:1,file:1,node:1,list:1,item:1,index:1,config:1,options:1,params:1,args:1,event:1,state:1,props:1,context:1,module:1,package:1,version:1,model:1,schema:1,table:1,query:1,response:1,request:1,handler:1,logger:1,graph:1,usage:1,storage:1,pipeline:1,service:1,utils:1,types:1,helpers:1,common:1,shared:1,server:1,client:1,source:1,output:1,input:1,stream:1,buffer:1,worker:1,plugin:1,format:1,render:1,update:1,create:1,remove:1,method:1,define:1,invoke:1,process:1,execute:1,resolve:1,reject:1,promise:1,callback:1,cursor:1,record:1,column:1,filter:1,reduce:1,status:1,action:1,commit:1,revert:1,publish:1,symbol:1,target:1,length:1,string:1,global:1,static:1,struct:1,select:1,insert:1,signal:1,socket:1,system:1,memory:1,parser:1,router:1,docker:1,script:1,bundle:1,deploy:1,search:1,prepare:1};
+                // monolean: only JS/TS reserved words — generic identifiers (handler, config, router, etc.) are valid symbol names
+                var _grepStop = {import:1,export:1,from:1,require:1,return:1,function:1,const:1,let:1,var:1,class:1,interface:1,type:1,extends:1,implements:1,async:1,await:1,yield:1,throw:1,catch:1,finally:1,typeof:1,instanceof:1,void:1,null:1,undefined:1,true:1,false:1,this:1,super:1,new:1,delete:1,switch:1,case:1,break:1,continue:1,default:1,else:1,while:1,for:1,with:1,static:1,enum:1,string:1,number:1,object:1,boolean:1};
 
                 // --- Strategy 1: clean identifier → exact name match (case-sensitive) ---
                 if (/^[a-zA-Z_$][a-zA-Z0-9_$]*$/.test(pattern) && pattern.length >= 4
@@ -479,7 +481,8 @@ const handlers = {
         var db = _openMonographDb();
         if (db) {
           try {
-            var _searchStop = {import:1,export:1,from:1,require:1,return:1,function:1,const:1,let:1,var:1,class:1,interface:1,type:1,extends:1,implements:1,async:1,await:1,yield:1,throw:1,catch:1,finally:1,typeof:1,instanceof:1,void:1,null:1,undefined:1,true:1,false:1,this:1,super:1,new:1,delete:1,switch:1,case:1,break:1,continue:1,default:1,else:1,while:1,for:1,with:1,include:1,error:1,string:1,number:1,object:1,boolean:1,array:1,value:1,result:1,data:1,name:1,path:1,file:1,node:1,list:1,item:1,index:1,config:1,options:1,params:1,args:1,event:1,state:1,props:1,context:1,module:1,package:1,version:1,model:1,schema:1,table:1,query:1,response:1,request:1,handler:1,logger:1,graph:1,usage:1,storage:1,pipeline:1,service:1,utils:1,types:1,helpers:1,common:1,shared:1,server:1,client:1,source:1,output:1,input:1,stream:1,buffer:1,worker:1,plugin:1,format:1,render:1,update:1,create:1,remove:1,method:1,define:1,invoke:1,process:1,execute:1,resolve:1,reject:1,promise:1,callback:1,cursor:1,record:1,column:1,filter:1,reduce:1,status:1,action:1,commit:1,revert:1,publish:1,symbol:1,target:1,length:1,string:1,global:1,static:1,struct:1,select:1,insert:1,signal:1,socket:1,system:1,memory:1,parser:1,router:1,docker:1,script:1,bundle:1,deploy:1,search:1,prepare:1};
+            // monolean: only JS/TS reserved words — generic identifiers are valid symbol names
+            var _searchStop = {import:1,export:1,from:1,require:1,return:1,function:1,const:1,let:1,var:1,class:1,interface:1,type:1,extends:1,implements:1,async:1,await:1,yield:1,throw:1,catch:1,finally:1,typeof:1,instanceof:1,void:1,null:1,undefined:1,true:1,false:1,this:1,super:1,new:1,delete:1,switch:1,case:1,break:1,continue:1,default:1,else:1,while:1,for:1,with:1,static:1,enum:1,string:1,number:1,object:1,boolean:1};
 
             var isCleanSymbol = /^[a-zA-Z_$][a-zA-Z0-9_$]*$/.test(grepPattern);
 

package/.claude/helpers/utils/monograph.cjs

@@ -183,19 +183,31 @@ function _getDollarRate() {
 
 // Staleness guard — skip graph DB lookups when the index is too far behind HEAD.
 // Returns true if it's safe to use the graph, false if stale.
+// Uses last_commit_hash from the DB (not file mtime, which drifts from backups/WAL/VACUUM).
 var _graphFreshnessCache = undefined;
 function _isGraphFresh() {
   if (_graphFreshnessCache !== undefined) return _graphFreshnessCache;
   try {
-    var dbPath = path.join(CWD, '.monomind', 'monograph.db');
-    var dbStat = fs.statSync(dbPath);
+    var db = _openMonographDb();
+    if (!db) { _graphFreshnessCache = true; return true; }
+    var row = null;
+    try {
+      row = db.prepare("SELECT value FROM index_meta WHERE key='last_commit_hash'").get() ||
+            db.prepare("SELECT value FROM index_meta WHERE key='lastCommit'").get();
+    } catch (_) {}
+    if (!row || !row.value) {
+      // No commit hash → can't check staleness, but DB may still have useful data
+      var nodeCount = 0;
+      try { nodeCount = db.prepare('SELECT COUNT(*) AS c FROM nodes').get().c; } catch (_) {}
+      _graphFreshnessCache = nodeCount > 0;
+      return _graphFreshnessCache;
+    }
     var { execSync } = require('child_process');
-    var buildIso = new Date(dbStat.mtimeMs).toISOString();
-    var out = execSync("git rev-list --count --since='" + buildIso + "' HEAD 2>/dev/null", {
+    var out = execSync('git rev-list --count ' + row.value + '..HEAD 2>/dev/null', {
       encoding: 'utf-8', timeout: 1500, stdio: ['pipe', 'pipe', 'pipe']
     }).trim();
     var behind = parseInt(out, 10) || 0;
-    _graphFreshnessCache = behind <= 50; // monolean: 50 commits is generous enough
+    _graphFreshnessCache = behind <= 50;
   } catch(e) {
     _graphFreshnessCache = true; // can't check → assume fresh
   }
@@ -354,14 +366,24 @@ function injectGodNodesContext(CWD) {
     try {
       var nodeCount = db.prepare('SELECT COUNT(*) AS c FROM nodes').get().c;
       var edgeCount = db.prepare('SELECT COUNT(*) AS c FROM edges').get().c;
+      // Precompute degree via indexed edge lookups to avoid O(N) correlated subquery
       var godNodes = db.prepare(
-        "SELECT n.name, n.label, n.file_path, " +
-        "(SELECT COUNT(*) FROM edges WHERE source_id=n.id OR target_id=n.id) AS deg " +
-        "FROM nodes n " +
+        "WITH deg AS (" +
+        "  SELECT id, cnt FROM (" +
+        "    SELECT source_id AS id, COUNT(*) AS cnt FROM edges GROUP BY source_id " +
+        "    UNION ALL " +
+        "    SELECT target_id AS id, COUNT(*) AS cnt FROM edges GROUP BY target_id" +
+        "  ) GROUP BY id" +
+        "  HAVING SUM(cnt) > 0" +
+        "), ranked AS (" +
+        "  SELECT d.id, SUM(d.cnt) AS deg FROM deg d GROUP BY d.id ORDER BY deg DESC LIMIT 50" +
+        ") " +
+        "SELECT n.name, n.label, n.file_path, r.deg " +
+        "FROM ranked r JOIN nodes n ON n.id = r.id " +
         "WHERE n.label NOT IN ('Concept') " +
         "AND n.file_path IS NOT NULL AND n.file_path != '' " +
         "AND n.file_path NOT LIKE '%/node_modules/%' AND n.file_path NOT LIKE '%node_modules%' " +
-        "ORDER BY deg DESC LIMIT 12"
+        "ORDER BY r.deg DESC LIMIT 12"
       ).all();
 
       // Staleness indicator: compare stored commit hash with current HEAD.
@@ -396,6 +418,7 @@ function injectGodNodesContext(CWD) {
           return n.name + ' (' + n.label + ', ' + n.deg + ' links)';
         }).join(', ');
         console.log('[MONOGRAPH_CONTEXT] ' + nodeCount + ' nodes · ' + edgeCount + ' edges. Key nodes: ' + godStr + staleIndicator);
+        console.log('[MONOGRAPH_ACTIVE] Indexed knowledge graph available — prefer monograph_query / monograph_suggest over grep/find for symbol and definition lookups.');
 
         // Write god nodes into knowledge/chunks.jsonl so semantic search finds them.
         var knowledgeDir = path.join(CWD, '.monomind', 'knowledge');
@@ -416,7 +439,10 @@ function injectGodNodesContext(CWD) {
             try { return JSON.parse(line).id !== 'monograph-god-nodes'; } catch(e) { return true; }
           });
           existing.push(godChunk);
-          fs.writeFileSync(chunksFile, existing.join('\n') + '\n');
+          // Atomic write: tmp file + rename to avoid corruption on kill/timeout
+          var tmpChunks = chunksFile + '.tmp.' + process.pid;
+          fs.writeFileSync(tmpChunks, existing.join('\n') + '\n');
+          fs.renameSync(tmpChunks, chunksFile);
         } catch(e) {}
       }
     } catch(e) { /* non-fatal */ }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "monomind",
-  "version": "1.18.11",
+  "version": "1.18.13",
   "description": "Monomind - Enterprise AI agent orchestration for Claude Code. Deploy 60+ specialized agents in coordinated swarms with self-learning, fault-tolerant consensus, vector memory, and MCP integration",
   "main": "dist/index.js",
   "type": "module",

package/packages/@monomind/cli/.claude/helpers/graphify-freshen.cjs

@@ -66,6 +66,34 @@ if (!entryPoint) {
   process.exit(0);
 }
 
+// Skip if index is already fresh — don't waste CPU on every session start
+const dbPath = path.join(projectDir, '.monomind', 'monograph.db');
+if (fs.existsSync(dbPath)) {
+  try {
+    const mod = (() => {
+      try { return require(path.join(projectDir, 'packages', '@monomind', 'monograph', 'dist', 'src', 'index.js')); } catch {}
+      try { return require('@monoes/monograph'); } catch {}
+      return null;
+    })();
+    if (mod && mod.openDb) {
+      const db = mod.openDb(dbPath);
+      try {
+        const row = db.prepare("SELECT value FROM index_meta WHERE key='last_commit_hash'").get();
+        if (row && row.value) {
+          const { execSync } = require('child_process');
+          const behind = parseInt(execSync('git rev-list --count ' + row.value + '..HEAD 2>/dev/null', {
+            cwd: projectDir, encoding: 'utf-8', timeout: 2000
+          }).trim(), 10) || 0;
+          if (behind === 0) {
+            console.log('[graph] index is fresh — skipping rebuild');
+            process.exit(0);
+          }
+        }
+      } finally { mod.closeDb(db); }
+    }
+  } catch { /* can't check — proceed with build */ }
+}
+
 // Skip if another build is already in progress (avoids SQLite BUSY on concurrent init + session-start)
 const lockPath = path.join(graphDir, 'build.lock');
 const now = Date.now();

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

@@ -381,7 +381,7 @@ module.exports = {
             }
           } catch (e) { /* ignore */ }
         }
-        if (nodeCount > 100) {
+        if (nodeCount > 100 && hCtx._isGraphFresh()) {
           // Pre-resolve top-3 relevant files for the user's prompt — the LLM
           // sees the answer inline instead of being told to call a tool.
           // 3 is enough signal; more files inflate token cost on every prompt.

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

@@ -216,6 +216,7 @@ var hCtx = {
   _recordToolCall: _recordToolCall,
   _openMonographDb: _openMonographDb,
   _requireMonograph: _requireMonograph,
+  _isGraphFresh: _isGraphFresh,
   _triggerExtractYamlValue: _triggerExtractYamlValue,
   _triggerFinalize: _triggerFinalize,
   _triggerExtractFromFrontmatter: _triggerExtractFromFrontmatter,
@@ -312,7 +313,8 @@ const handlers = {
               if (db) {
                 // Stop words: language keywords + generic single-word identifiers
                 // that match Variable nodes in markdown/scripts (not real code symbols)
-                var _grepStop = {import:1,export:1,from:1,require:1,return:1,function:1,const:1,let:1,var:1,class:1,interface:1,type:1,extends:1,implements:1,async:1,await:1,yield:1,throw:1,catch:1,finally:1,typeof:1,instanceof:1,void:1,null:1,undefined:1,true:1,false:1,this:1,super:1,new:1,delete:1,switch:1,case:1,break:1,continue:1,default:1,else:1,while:1,for:1,with:1,include:1,error:1,string:1,number:1,object:1,boolean:1,array:1,value:1,result:1,data:1,name:1,path:1,file:1,node:1,list:1,item:1,index:1,config:1,options:1,params:1,args:1,event:1,state:1,props:1,context:1,module:1,package:1,version:1,model:1,schema:1,table:1,query:1,response:1,request:1,handler:1,logger:1,graph:1,usage:1,storage:1,pipeline:1,service:1,utils:1,types:1,helpers:1,common:1,shared:1,server:1,client:1,source:1,output:1,input:1,stream:1,buffer:1,worker:1,plugin:1,format:1,render:1,update:1,create:1,remove:1,method:1,define:1,invoke:1,process:1,execute:1,resolve:1,reject:1,promise:1,callback:1,cursor:1,record:1,column:1,filter:1,reduce:1,status:1,action:1,commit:1,revert:1,publish:1,symbol:1,target:1,length:1,string:1,global:1,static:1,struct:1,select:1,insert:1,signal:1,socket:1,system:1,memory:1,parser:1,router:1,docker:1,script:1,bundle:1,deploy:1,search:1,prepare:1};
+                // monolean: only JS/TS reserved words — generic identifiers (handler, config, router, etc.) are valid symbol names
+                var _grepStop = {import:1,export:1,from:1,require:1,return:1,function:1,const:1,let:1,var:1,class:1,interface:1,type:1,extends:1,implements:1,async:1,await:1,yield:1,throw:1,catch:1,finally:1,typeof:1,instanceof:1,void:1,null:1,undefined:1,true:1,false:1,this:1,super:1,new:1,delete:1,switch:1,case:1,break:1,continue:1,default:1,else:1,while:1,for:1,with:1,static:1,enum:1,string:1,number:1,object:1,boolean:1};
 
                 // --- Strategy 1: clean identifier → exact name match (case-sensitive) ---
                 if (/^[a-zA-Z_$][a-zA-Z0-9_$]*$/.test(pattern) && pattern.length >= 4
@@ -479,7 +481,8 @@ const handlers = {
         var db = _openMonographDb();
         if (db) {
           try {
-            var _searchStop = {import:1,export:1,from:1,require:1,return:1,function:1,const:1,let:1,var:1,class:1,interface:1,type:1,extends:1,implements:1,async:1,await:1,yield:1,throw:1,catch:1,finally:1,typeof:1,instanceof:1,void:1,null:1,undefined:1,true:1,false:1,this:1,super:1,new:1,delete:1,switch:1,case:1,break:1,continue:1,default:1,else:1,while:1,for:1,with:1,include:1,error:1,string:1,number:1,object:1,boolean:1,array:1,value:1,result:1,data:1,name:1,path:1,file:1,node:1,list:1,item:1,index:1,config:1,options:1,params:1,args:1,event:1,state:1,props:1,context:1,module:1,package:1,version:1,model:1,schema:1,table:1,query:1,response:1,request:1,handler:1,logger:1,graph:1,usage:1,storage:1,pipeline:1,service:1,utils:1,types:1,helpers:1,common:1,shared:1,server:1,client:1,source:1,output:1,input:1,stream:1,buffer:1,worker:1,plugin:1,format:1,render:1,update:1,create:1,remove:1,method:1,define:1,invoke:1,process:1,execute:1,resolve:1,reject:1,promise:1,callback:1,cursor:1,record:1,column:1,filter:1,reduce:1,status:1,action:1,commit:1,revert:1,publish:1,symbol:1,target:1,length:1,string:1,global:1,static:1,struct:1,select:1,insert:1,signal:1,socket:1,system:1,memory:1,parser:1,router:1,docker:1,script:1,bundle:1,deploy:1,search:1,prepare:1};
+            // monolean: only JS/TS reserved words — generic identifiers are valid symbol names
+            var _searchStop = {import:1,export:1,from:1,require:1,return:1,function:1,const:1,let:1,var:1,class:1,interface:1,type:1,extends:1,implements:1,async:1,await:1,yield:1,throw:1,catch:1,finally:1,typeof:1,instanceof:1,void:1,null:1,undefined:1,true:1,false:1,this:1,super:1,new:1,delete:1,switch:1,case:1,break:1,continue:1,default:1,else:1,while:1,for:1,with:1,static:1,enum:1,string:1,number:1,object:1,boolean:1};
 
             var isCleanSymbol = /^[a-zA-Z_$][a-zA-Z0-9_$]*$/.test(grepPattern);
 

package/packages/@monomind/cli/.claude/helpers/utils/monograph.cjs

@@ -183,19 +183,31 @@ function _getDollarRate() {
 
 // Staleness guard — skip graph DB lookups when the index is too far behind HEAD.
 // Returns true if it's safe to use the graph, false if stale.
+// Uses last_commit_hash from the DB (not file mtime, which drifts from backups/WAL/VACUUM).
 var _graphFreshnessCache = undefined;
 function _isGraphFresh() {
   if (_graphFreshnessCache !== undefined) return _graphFreshnessCache;
   try {
-    var dbPath = path.join(CWD, '.monomind', 'monograph.db');
-    var dbStat = fs.statSync(dbPath);
+    var db = _openMonographDb();
+    if (!db) { _graphFreshnessCache = true; return true; }
+    var row = null;
+    try {
+      row = db.prepare("SELECT value FROM index_meta WHERE key='last_commit_hash'").get() ||
+            db.prepare("SELECT value FROM index_meta WHERE key='lastCommit'").get();
+    } catch (_) {}
+    if (!row || !row.value) {
+      // No commit hash → can't check staleness, but DB may still have useful data
+      var nodeCount = 0;
+      try { nodeCount = db.prepare('SELECT COUNT(*) AS c FROM nodes').get().c; } catch (_) {}
+      _graphFreshnessCache = nodeCount > 0;
+      return _graphFreshnessCache;
+    }
     var { execSync } = require('child_process');
-    var buildIso = new Date(dbStat.mtimeMs).toISOString();
-    var out = execSync("git rev-list --count --since='" + buildIso + "' HEAD 2>/dev/null", {
+    var out = execSync('git rev-list --count ' + row.value + '..HEAD 2>/dev/null', {
       encoding: 'utf-8', timeout: 1500, stdio: ['pipe', 'pipe', 'pipe']
     }).trim();
     var behind = parseInt(out, 10) || 0;
-    _graphFreshnessCache = behind <= 50; // monolean: 50 commits is generous enough
+    _graphFreshnessCache = behind <= 50;
   } catch(e) {
     _graphFreshnessCache = true; // can't check → assume fresh
   }
@@ -354,14 +366,24 @@ function injectGodNodesContext(CWD) {
     try {
       var nodeCount = db.prepare('SELECT COUNT(*) AS c FROM nodes').get().c;
       var edgeCount = db.prepare('SELECT COUNT(*) AS c FROM edges').get().c;
+      // Precompute degree via indexed edge lookups to avoid O(N) correlated subquery
       var godNodes = db.prepare(
-        "SELECT n.name, n.label, n.file_path, " +
-        "(SELECT COUNT(*) FROM edges WHERE source_id=n.id OR target_id=n.id) AS deg " +
-        "FROM nodes n " +
+        "WITH deg AS (" +
+        "  SELECT id, cnt FROM (" +
+        "    SELECT source_id AS id, COUNT(*) AS cnt FROM edges GROUP BY source_id " +
+        "    UNION ALL " +
+        "    SELECT target_id AS id, COUNT(*) AS cnt FROM edges GROUP BY target_id" +
+        "  ) GROUP BY id" +
+        "  HAVING SUM(cnt) > 0" +
+        "), ranked AS (" +
+        "  SELECT d.id, SUM(d.cnt) AS deg FROM deg d GROUP BY d.id ORDER BY deg DESC LIMIT 50" +
+        ") " +
+        "SELECT n.name, n.label, n.file_path, r.deg " +
+        "FROM ranked r JOIN nodes n ON n.id = r.id " +
         "WHERE n.label NOT IN ('Concept') " +
         "AND n.file_path IS NOT NULL AND n.file_path != '' " +
         "AND n.file_path NOT LIKE '%/node_modules/%' AND n.file_path NOT LIKE '%node_modules%' " +
-        "ORDER BY deg DESC LIMIT 12"
+        "ORDER BY r.deg DESC LIMIT 12"
       ).all();
 
       // Staleness indicator: compare stored commit hash with current HEAD.
@@ -396,6 +418,7 @@ function injectGodNodesContext(CWD) {
           return n.name + ' (' + n.label + ', ' + n.deg + ' links)';
         }).join(', ');
         console.log('[MONOGRAPH_CONTEXT] ' + nodeCount + ' nodes · ' + edgeCount + ' edges. Key nodes: ' + godStr + staleIndicator);
+        console.log('[MONOGRAPH_ACTIVE] Indexed knowledge graph available — prefer monograph_query / monograph_suggest over grep/find for symbol and definition lookups.');
 
         // Write god nodes into knowledge/chunks.jsonl so semantic search finds them.
         var knowledgeDir = path.join(CWD, '.monomind', 'knowledge');
@@ -416,7 +439,10 @@ function injectGodNodesContext(CWD) {
             try { return JSON.parse(line).id !== 'monograph-god-nodes'; } catch(e) { return true; }
           });
           existing.push(godChunk);
-          fs.writeFileSync(chunksFile, existing.join('\n') + '\n');
+          // Atomic write: tmp file + rename to avoid corruption on kill/timeout
+          var tmpChunks = chunksFile + '.tmp.' + process.pid;
+          fs.writeFileSync(tmpChunks, existing.join('\n') + '\n');
+          fs.renameSync(tmpChunks, chunksFile);
         } catch(e) {}
       }
     } catch(e) { /* non-fatal */ }

package/packages/@monomind/cli/dist/src/mcp-tools/monograph-tools.js

@@ -131,8 +131,18 @@ const monographHealthTool = {
             // Fall back to legacy 'lastCommit' for indexes built with older versions.
             const meta = db.prepare("SELECT value FROM index_meta WHERE key = 'last_commit_hash'").get() ?? db.prepare("SELECT value FROM index_meta WHERE key = 'lastCommit'").get();
             const lastCommit = meta?.value ?? null;
-            if (!lastCommit)
+            if (!lastCommit) {
+                // last_commit_hash can be missing even when the index is populated
+                // (e.g. git rev-parse failed during build). Check actual data before
+                // claiming "never built".
+                const nodeCount = db.prepare('SELECT COUNT(*) AS c FROM nodes').get().c;
+                if (nodeCount > 0) {
+                    const indexedAt = db.prepare("SELECT value FROM index_meta WHERE key = 'indexed_at'").get()?.value;
+                    return text(`Index is built (${nodeCount} nodes${indexedAt ? `, indexed at ${indexedAt}` : ''}) but no commit hash was recorded — staleness tracking unavailable.\n` +
+                        'Run monograph_build to fix commit tracking.');
+                }
                 return text('Index has never been built. Run monograph_build first.');
+            }
             if (!/^[0-9a-f]{7,40}$/i.test(lastCommit)) {
                 return text('Index metadata is corrupt: invalid commit SHA. Run monograph_build to re-index.');
             }
@@ -1809,6 +1819,207 @@ const monographSuggestAutoTool = {
     },
 };
 // ── Export all tools ──────────────────────────────────────────────────────────
+// ── monograph_dead_code ──────────────────────────────────────────────────────
+const monographDeadCodeTool = {
+    name: 'monograph_dead_code',
+    description: 'Detect dead code: exported functions with zero inbound references, files with no importers, and stale dist build artifacts. Returns structured JSON with candidates grouped by category. Always verify candidates with grep before deleting.',
+    inputSchema: {
+        type: 'object',
+        properties: {
+            path: { type: 'string', description: 'Absolute path to the repo (defaults to project cwd)' },
+            categories: {
+                type: 'array',
+                items: { type: 'string', enum: ['dead-functions', 'orphan-files', 'stale-dist'] },
+                description: 'Which categories to check (default: all three)',
+            },
+        },
+    },
+    handler: async (input) => {
+        const { openDb } = await import('@monoes/monograph');
+        const repoPath = input.path ?? getProjectCwd();
+        const cats = input.categories ?? ['dead-functions', 'orphan-files', 'stale-dist'];
+        const result = {};
+        const dbPath = join(repoPath, '.monomind', 'monograph.db');
+        let db = null;
+        try {
+            db = openDb(dbPath);
+        }
+        catch {
+            return text(JSON.stringify({ error: 'No monograph index found. Run monograph_build first.' }));
+        }
+        try {
+            if (cats.includes('dead-functions')) {
+                const { detectDeadCodeNodes } = await import('@monoes/monograph');
+                const { readFileSync } = await import('fs');
+                const nodes = detectDeadCodeNodes(db);
+                // Filter out stale graph nodes: verify the function name actually appears in the source file
+                const verified = nodes.filter(n => {
+                    if (!n.filePath)
+                        return false;
+                    try {
+                        const content = readFileSync(join(repoPath, n.filePath), 'utf-8');
+                        return content.includes(n.name);
+                    }
+                    catch {
+                        return false;
+                    }
+                });
+                const staleCount = nodes.length - verified.length;
+                result['dead-functions'] = {
+                    count: verified.length,
+                    candidates: verified.map(n => ({
+                        name: n.name,
+                        location: n.filePath ? (n.startLine ? `${n.filePath}:${n.startLine}` : n.filePath) : null,
+                    })),
+                    ...(staleCount > 0 ? { staleIndexEntries: staleCount, note: 'Some graph entries reference deleted functions. Rebuild the index with monograph_build to clean up.' } : {}),
+                };
+            }
+            if (cats.includes('orphan-files')) {
+                const rows = db.prepare(`
+          SELECT n.name, n.file_path,
+            (SELECT COUNT(*) FROM edges e WHERE e.source_id = n.id AND e.relation = 'IMPORTS') as imports_out,
+            (SELECT COUNT(*) FROM edges e WHERE e.target_id = n.id AND e.relation = 'IMPORTS') as imported_by
+          FROM nodes n
+          WHERE n.label = 'File'
+            AND (SELECT COUNT(*) FROM edges e WHERE e.target_id = n.id AND e.relation = 'IMPORTS') = 0
+            AND n.file_path NOT LIKE '%test%'
+            AND n.file_path NOT LIKE '%__tests__%'
+            AND n.file_path NOT LIKE '%spec%'
+            AND n.file_path NOT LIKE '%/index.%'
+            AND n.file_path NOT LIKE 'bin/%'
+            AND n.file_path NOT LIKE 'scripts/%'
+            AND n.file_path NOT LIKE '%/cli.ts'
+            AND n.file_path NOT LIKE '%/cli.js'
+            AND n.file_path NOT LIKE '%/main.ts'
+            AND n.file_path NOT LIKE '%/main.js'
+            AND n.file_path NOT LIKE '%/dist/%'
+            AND n.file_path NOT LIKE '%node_modules%'
+          ORDER BY n.file_path
+        `).all();
+                const withOutbound = rows.filter((r) => r.imports_out > 0);
+                const isolated = rows.filter((r) => r.imports_out === 0);
+                result['orphan-files'] = {
+                    count: withOutbound.length,
+                    note: 'Files that import other modules but nothing imports them. May be lazy-loaded or dynamically imported — verify with grep.',
+                    candidates: withOutbound.map((r) => ({ file: r.file_path, outboundImports: r.imports_out })),
+                    ...(isolated.length > 0 ? {
+                        isolated: {
+                            count: isolated.length,
+                            note: 'Files with zero edges in either direction — likely standalone scripts or entry points.',
+                            files: isolated.map((r) => r.file_path),
+                        },
+                    } : {}),
+                };
+            }
+            if (cats.includes('stale-dist')) {
+                result['stale-dist'] = findStaleDist(repoPath);
+            }
+            return text(JSON.stringify(result, null, 2));
+        }
+        finally {
+            db.close();
+        }
+    },
+};
+function findStaleDist(repoPath) {
+    const { readdirSync, existsSync } = require('fs');
+    const distSrc = join(repoPath, 'dist', 'src');
+    const src = join(repoPath, 'src');
+    // Scan a single package for stale dist artifacts
+    const scanPkg = (pkgPath, pkgName) => {
+        const pkgDistSrc = join(pkgPath, 'dist', 'src');
+        const pkgSrc = join(pkgPath, 'src');
+        if (!existsSync(pkgDistSrc) || !existsSync(pkgSrc))
+            return null;
+        const staleDirs = [];
+        const staleFiles = [];
+        let resourceForks = 0;
+        try {
+            const distDirs = readdirSync(pkgDistSrc, { withFileTypes: true })
+                .filter(d => d.isDirectory() && !d.name.startsWith('.') && !d.name.startsWith('._'));
+            const srcDirs = new Set(readdirSync(pkgSrc, { withFileTypes: true })
+                .filter(d => d.isDirectory() && !d.name.startsWith('.'))
+                .map(d => d.name));
+            for (const d of distDirs) {
+                if (!srcDirs.has(d.name))
+                    staleDirs.push(d.name);
+            }
+        }
+        catch { /* skip */ }
+        try {
+            const distFiles = readdirSync(pkgDistSrc)
+                .filter(f => f.endsWith('.js') && !f.startsWith('.') && !f.startsWith('._'));
+            for (const f of distFiles) {
+                const tsName = f.replace(/\.js$/, '.ts');
+                if (!existsSync(join(pkgSrc, tsName)))
+                    staleFiles.push(f);
+            }
+        }
+        catch { /* skip */ }
+        // Count macOS resource fork files
+        const countRF = (dir) => {
+            try {
+                for (const entry of readdirSync(dir, { withFileTypes: true })) {
+                    if (entry.name.startsWith('._'))
+                        resourceForks++;
+                    else if (entry.isDirectory())
+                        countRF(join(dir, entry.name));
+                }
+            }
+            catch { /* skip */ }
+        };
+        countRF(pkgDistSrc);
+        if (staleDirs.length === 0 && staleFiles.length === 0 && resourceForks === 0)
+            return null;
+        return {
+            package: pkgName,
+            staleDirs,
+            staleFiles,
+            ...(resourceForks > 0 ? { macosResourceForks: resourceForks } : {}),
+        };
+    };
+    // Single-package repo
+    if (existsSync(distSrc) && existsSync(src)) {
+        const finding = scanPkg(repoPath, '.');
+        return {
+            count: finding ? finding.staleDirs.length + finding.staleFiles.length : 0,
+            note: 'Directories/files in dist/src/ with no corresponding source. Fix: rm -rf dist && npm run build.',
+            ...(finding ? { findings: [finding] } : {}),
+        };
+    }
+    // Monorepo: scan all packages
+    const packagesDir = join(repoPath, 'packages');
+    if (!existsSync(packagesDir))
+        return { count: 0, note: 'No dist/src or packages/ found' };
+    const findings = [];
+    try {
+        for (const scope of readdirSync(packagesDir, { withFileTypes: true })) {
+            if (!scope.isDirectory())
+                continue;
+            const scopeDir = join(packagesDir, scope.name);
+            if (scope.name.startsWith('@')) {
+                for (const pkg of readdirSync(scopeDir, { withFileTypes: true })) {
+                    if (!pkg.isDirectory())
+                        continue;
+                    const f = scanPkg(join(scopeDir, pkg.name), `${scope.name}/${pkg.name}`);
+                    if (f)
+                        findings.push(f);
+                }
+            }
+            else {
+                const f = scanPkg(scopeDir, scope.name);
+                if (f)
+                    findings.push(f);
+            }
+        }
+    }
+    catch { /* skip */ }
+    return {
+        count: findings.reduce((s, f) => s + (f.staleDirs?.length ?? 0) + (f.staleFiles?.length ?? 0), 0),
+        note: 'Directories/files in dist/src/ with no corresponding source. Fix: rm -rf dist && npm run build.',
+        findings,
+    };
+}
 export const monographTools = [
     monographBuildTool,
     monographQueryTool,
@@ -1854,5 +2065,6 @@ export const monographTools = [
     monographListReposTool,
     monographGroupContractsTool,
     monographGroupStatusTool,
+    monographDeadCodeTool,
 ];
 //# sourceMappingURL=monograph-tools.js.map

package/packages/@monomind/cli/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@monoes/monomindcli",
-  "version": "1.18.11",
+  "version": "1.18.13",
   "type": "module",
   "description": "Monomind CLI - Enterprise AI agent orchestration with 60+ specialized agents, swarm coordination, MCP server, self-learning hooks, and vector memory for Claude Code",
   "main": "dist/src/index.js",