@chem-x/starter-kit 26.9.23-1269 → 26.9.24-393

package/cli/audit/history.js

@@ -13,8 +13,12 @@ const RED = '\x1b[31m';
 
 export const ensureChemxDir = (cwd = process.cwd()) => {
   const dir = path.resolve(cwd, '.chemx');
-  if (!fs.existsSync(dir)) {
-    fs.mkdirSync(dir, { recursive: true });
+  try {
+    if (!fs.existsSync(dir)) {
+      fs.mkdirSync(dir, { recursive: true });
+    }
+  } catch {
+    return dir;
   }
 
   // Ensure .chemx is gitignored if git repo exists
@@ -165,7 +169,11 @@ export const getAuditBaseline = (cwd = process.cwd()) => {
 export const setAuditBaseline = (snapshot, cwd = process.cwd()) => {
   ensureChemxDir(cwd);
   const baselinePath = path.resolve(cwd, '.chemx', 'baseline.json');
-  fs.writeFileSync(baselinePath, JSON.stringify(snapshot, null, 2), 'utf-8');
+  try {
+    fs.writeFileSync(baselinePath, JSON.stringify(snapshot, null, 2), 'utf-8');
+  } catch {
+    // Read-only filesystem in sandbox
+  }
   return snapshot;
 };
 
@@ -196,7 +204,11 @@ export const saveAuditSnapshot = (report, cwd = process.cwd()) => {
   // Keep last 50 snapshots
   const trimmed = history.slice(-50);
   const historyPath = path.resolve(cwd, '.chemx', 'history.json');
-  fs.writeFileSync(historyPath, JSON.stringify(trimmed, null, 2), 'utf-8');
+  try {
+    fs.writeFileSync(historyPath, JSON.stringify(trimmed, null, 2), 'utf-8');
+  } catch {
+    // Read-only filesystem in sandbox
+  }
 
   // Auto-establish first run or lower score as baseline floor
   const baselinePath = path.resolve(cwd, '.chemx', 'baseline.json');
@@ -206,8 +218,12 @@ export const saveAuditSnapshot = (report, cwd = process.cwd()) => {
   const baselineScore = currentBaseline?.health?.score ?? 101;
 
   if (!currentBaseline || currentScore < baselineScore) {
-    fs.writeFileSync(baselinePath, JSON.stringify(snapshot, null, 2), 'utf-8');
-    isNewBaseline = true;
+    try {
+      fs.writeFileSync(baselinePath, JSON.stringify(snapshot, null, 2), 'utf-8');
+      isNewBaseline = true;
+    } catch {
+      // Read-only filesystem in sandbox
+    }
   }
 
   const baseline = getAuditBaseline(cwd);

package/cli/audit/hook-shape-validator.js

@@ -1,7 +1,7 @@
 import * as t from '@babel/types';
 import { RULE_REGISTRY } from './rules-registry.js';
 
-const VERB_PREFIX_REGEX = /^(add|remove|toggle|set|get|fetch|load|save|delete|clear|reset|refresh|update|create|edit|send|sync|init|dispose|trigger|post|put|patch|apply|dismiss|select|deselect|filter|sort|search|open|close|show|hide|start|stop|cancel|execute|run|retry|submit|validate|mutate|next|prev|step|increment|decrement|insert|upsert|drop|enable|disable|register|unregister|login|logout|checkout|publish|archive|discard|confirm|undo|redo|claim|complete|acquire|release|download|upload|export|import|handle)([A-Z0-9_].*)?$/;
+const VERB_PREFIX_REGEX = /^(add|remove|toggle|set|get|fetch|load|save|delete|clear|reset|refresh|update|create|edit|send|sync|init|setup|dispose|trigger|post|put|patch|apply|dismiss|select|deselect|filter|sort|search|open|close|show|hide|start|stop|cancel|execute|run|retry|submit|validate|mutate|next|prev|step|increment|decrement|insert|upsert|drop|enable|disable|register|unregister|login|logout|checkout|publish|archive|discard|confirm|undo|redo|claim|complete|acquire|release|download|upload|export|import|handle|play|pause|resume|seek|unlock|restore|advance|focus|notify|broadcast|copy|format)([A-Z0-9_].*)?$/;
 
 const STATUS_HEURISTIC_REGEX = /^(is[A-Z]|has[A-Z]|can[A-Z]|should[A-Z])|.*(Error|Status)$/;
 const STATUS_EXACT_NAMES = new Set(['status', 'error', 'loading', 'pending', 'ready']);

package/cli/audit/prompts.js

@@ -36,7 +36,7 @@ const renderTreeLines = (node, depth = 0) => {
   return lines;
 };
 
-export const formatGroupedPromptViolations = (violations = []) => {
+export const formatGroupedPromptViolations = (violations = [], options = {}) => {
   const hasNoViolations = violations.length === 0;
   if (hasNoViolations) return [];
 
@@ -49,11 +49,14 @@ export const formatGroupedPromptViolations = (violations = []) => {
     lines.push(`${idx + 1}. ${sevColor}[${rg.rule}]${RESET} ${BOLD}(${countLabel})${RESET}`);
     lines.push(`   Hazard:    ${rg.hazard}`);
     lines.push(`   Directive: ${CYAN}${rg.directive}${RESET}`);
-    lines.push('   Locations:');
+    lines.push(`   Action:    chemx team task list --rule=${rg.rule}`);
 
-    const tree = buildPathTree(rg.violations);
-    const treeLines = renderTreeLines(tree, 0);
-    lines.push(...treeLines);
+    if (options.detailedLocations) {
+      lines.push('   Locations:');
+      const tree = buildPathTree(rg.violations);
+      const treeLines = renderTreeLines(tree, 0);
+      lines.push(...treeLines);
+    }
     lines.push('');
   });
 
@@ -62,10 +65,10 @@ export const formatGroupedPromptViolations = (violations = []) => {
 
 export const buildAgentCommandsSection = () => [
   '### AI AGENT DISCOVERY & REFACTORING COMMANDS:',
-  '- Query & Inspect: Run `pnpm q "<target>" --inspect` (or `npx chemx search "<target>" --inspect`) to inspect component props, symbols, and hooks before editing.',
-  '- Tier Filter: Run `pnpm q "<query>" --tier=molecule` (or `atom`, `organism`, `hook`) to find related capsules.',
-  '- Zero-Overhead JSON: Run `pnpm q "<query>" --json` for minified AST metadata without burning context tokens on whole files.',
-  '- Re-Verify Score: Run `npx chemx audit` after refactoring to ensure Molecular Health Index (MHI) and letter grades improve.'
+  '- Claim Work: Run `chemx team task list --status=queued` and claim via `chemx team task claim <id> --as=@coder`.',
+  '- Inspect Target: Run `chemx read <target_path> --outline` to inspect AST signatures without token bloat.',
+  '- Verify & Auto-Resolve: Run `chemx verify`. Clean files auto-reconcile tasks to done in SQLite.',
+  '- MCP Invocations: If invoking via MCP, pass command string directly via `chemx({ command: "..." })`.'
 ].join('\n');
 
 export const buildGradeFPrompt = (report, options = {}) => {

package/cli/audit/prompts.spec.js

@@ -10,7 +10,8 @@ import {
   buildAiSlopPrompt,
   buildHotspotsPrompt,
   buildPillarPrompt,
-  buildMasterPrompt
+  buildMasterPrompt,
+  formatGroupedPromptViolations
 } from './prompts.js';
 
 test('deduplicateRolePreambles: handles invalid and empty inputs', () => {
@@ -314,3 +315,53 @@ test('deduplicateRefactoringCommands: collapses multiple occurrences to single b
   assert.ok(result.includes('Section 2 content'));
   assert.ok(result.includes('- Command B'));
 });
+
+test('formatGroupedPromptViolations: outputs token-compact task action by default', () => {
+  const violations = [
+    {
+      rule: 'SECURITY_RAW_HTML_INJECTION',
+      severity: 'CRITICAL',
+      hazard: 'Unsanitized HTML injection',
+      directive: 'Sanitize dynamic HTML via DOMPurify',
+      filePath: 'src/view-a.vue',
+      line: 10
+    },
+    {
+      rule: 'SECURITY_RAW_HTML_INJECTION',
+      severity: 'CRITICAL',
+      hazard: 'Unsanitized HTML injection',
+      directive: 'Sanitize dynamic HTML via DOMPurify',
+      filePath: 'src/view-b.vue',
+      line: 25
+    }
+  ];
+
+  const lines = formatGroupedPromptViolations(violations);
+  const text = lines.join('\n');
+
+  assert.ok(text.includes('[SECURITY_RAW_HTML_INJECTION]'));
+  assert.ok(text.includes('(2 items)'));
+  assert.ok(text.includes('Action:    chemx team task list --rule=SECURITY_RAW_HTML_INJECTION'));
+  // Does not dump file locations tree by default
+  assert.ok(!text.includes('Locations:'));
+  assert.ok(!text.includes('view-a.vue:10'));
+});
+
+test('formatGroupedPromptViolations: renders file tree when detailedLocations is enabled', () => {
+  const violations = [
+    {
+      rule: 'SECURITY_RAW_HTML_INJECTION',
+      severity: 'CRITICAL',
+      hazard: 'Unsanitized HTML injection',
+      directive: 'Sanitize dynamic HTML via DOMPurify',
+      filePath: 'src/view-a.vue',
+      line: 10
+    }
+  ];
+
+  const lines = formatGroupedPromptViolations(violations, { detailedLocations: true });
+  const text = lines.join('\n');
+
+  assert.ok(text.includes('Locations:'));
+  assert.ok(text.includes('view-a.vue:10'));
+});

package/cli/commands/cmd-audit.js

@@ -104,41 +104,45 @@ export const runAudit = async (customDir, isCli, rawArgs, loadProjectConfig) =>
   const auditOptions = { outputFile, model, costPerMillion, fast: isFast, fileList, stage };
   const report = executeAstAudit(targetDir, auditOptions);
   saveAuditSnapshot(report);
-  const syncRes = syncSearchIndex(targetDir, process.cwd());
-
-  if (syncRes?.db) {
-    syncViolationsIndex(syncRes.db, report.violations);
-    recordAuditSnapshot(syncRes.db, report);
-    if (rawArgs.includes('--triage')) {
-      const createdTasks = autoGenerateTasksFromAudit(syncRes.db, { cwd: process.cwd(), targetDir });
-      if (isCli && !isJson) {
-        process.stdout.write(`\x1b[32m✔\x1b[0m Auto-triage generated ${createdTasks.length} team task(s) from audit violations.\n`);
+  try {
+    const syncRes = syncSearchIndex(targetDir, process.cwd());
+
+    if (syncRes?.db) {
+      syncViolationsIndex(syncRes.db, report.violations);
+      const shouldTriage = !rawArgs.includes('--no-triage');
+      if (shouldTriage) {
+        const createdTasks = autoGenerateTasksFromAudit(syncRes.db, { cwd: process.cwd(), targetDir });
+        if (isCli && !isJson && createdTasks.length > 0) {
+          process.stdout.write(`\x1b[32m✔\x1b[0m Auto-triage synchronized ${createdTasks.length} team task(s) in SQLite backlog.\n`);
+        }
       }
-    }
-    if (rawArgs.includes('--clones')) {
-      const { detectSemanticClones } = await import('../audit/clone-detector.js');
-      const { formatCloneReport } = await import('../audit/reporter-clones.js');
-      const cloneThresholdArg = rawArgs.find((a) => a.startsWith('--clone-threshold='));
-      const threshold = cloneThresholdArg ? parseFloat(cloneThresholdArg.split('=')[1]) : 0.85;
-      const clones = detectSemanticClones(syncRes.db, { threshold });
-      if (isJson) {
-        report.clones = clones;
-      } else {
-        process.stdout.write(formatCloneReport(clones));
+      if (rawArgs.includes('--clones')) {
+        const { detectSemanticClones } = await import('../audit/clone-detector.js');
+        const { formatCloneReport } = await import('../audit/reporter-clones.js');
+        const cloneThresholdArg = rawArgs.find((a) => a.startsWith('--clone-threshold='));
+        const threshold = cloneThresholdArg ? parseFloat(cloneThresholdArg.split('=')[1]) : 0.85;
+        const clones = detectSemanticClones(syncRes.db, { threshold });
+        if (isJson) {
+          report.clones = clones;
+        } else {
+          process.stdout.write(formatCloneReport(clones));
+        }
       }
-    }
-    if (rawArgs.includes('--hotspot-graph')) {
-      const { calculateCascadingHotspotGraph } = await import('../search-queries-hotspot-graph.js');
-      const { formatHotspotGraphReport } = await import('../audit/reporter-hotspot-graph.js');
-      const limitArg = rawArgs.find((a) => a.startsWith('--limit='));
-      const limit = limitArg ? parseInt(limitArg.split('=')[1], 10) : 10;
-      const graph = calculateCascadingHotspotGraph(syncRes.db, { limit });
-      if (isJson) {
-        report.hotspotGraph = graph;
-      } else {
-        process.stdout.write(formatHotspotGraphReport(graph));
+      if (rawArgs.includes('--hotspot-graph')) {
+        const { calculateCascadingHotspotGraph } = await import('../search-queries-hotspot-graph.js');
+        const { formatHotspotGraphReport } = await import('../audit/reporter-hotspot-graph.js');
+        const limitArg = rawArgs.find((a) => a.startsWith('--limit='));
+        const limit = limitArg ? parseInt(limitArg.split('=')[1], 10) : 10;
+        const graph = calculateCascadingHotspotGraph(syncRes.db, { limit });
+        if (isJson) {
+          report.hotspotGraph = graph;
+        } else {
+          process.stdout.write(formatHotspotGraphReport(graph));
+        }
       }
     }
+  } catch {
+    // Gracefully bypass indexing when database is readonly in sandboxed environment
   }
 
   // Stage 1: Atomic failure predicates

package/cli/commands/cmd-router.js

@@ -200,7 +200,24 @@ export const dispatchCommand = async (firstArg, rawArgs, runAudit, getPackageVer
       const { startUiServer } = await import('../ui-server.js');
       const portArg = rawArgs.find((a) => a.startsWith('--port='));
       const port = portArg ? parseInt(portArg.split('=')[1], 10) : 4173;
-      await startUiServer({ port, isCli: true, cwd: process.cwd() });
+      const hostArg = rawArgs.find((a) => a.startsWith('--host='));
+      const host = hostArg ? hostArg.split('=')[1] : '0.0.0.0';
+      const { server } = await startUiServer({ port, host, isCli: true, cwd: process.cwd() });
+      await new Promise((resolve) => {
+        const shutdown = () => {
+          server.close(() => resolve());
+        };
+        process.on('SIGINT', shutdown);
+        process.on('SIGTERM', shutdown);
+        server.on('close', resolve);
+      });
+      break;
+    }
+    case 'tesseract':
+    case 'cube':
+    case 'matrix': {
+      const { runTesseract } = await import('../tesseract.js');
+      await runTesseract(rawArgs.slice(1), true);
       break;
     }
     case 'help':

package/cli/commands-schema.js

@@ -208,5 +208,19 @@ export const COMMANDS_SCHEMA = [
       'npx chemx ui',
       'npx chemx dashboard --port=3000'
     ]
+  },
+  {
+    name: 'tesseract',
+    aliases: ['cube', 'matrix'],
+    usage: 'npx chemx tesseract [options]',
+    summary: 'Autonomous AI Cognitive Bridge and Human-AI Symbiosis Interface.',
+    description: 'Deploys the full Chemical X cognitive lattice, AST topology, swarm telemetry, and Jarvis operational directives for instant AI onboarding.',
+    flags: [
+      { flag: '--json', desc: 'Output machine-readable JSON cognitive payload' }
+    ],
+    examples: [
+      'npx chemx tesseract',
+      'npx chemx tesseract --json'
+    ]
   }
 ];

package/cli/index.js

@@ -69,6 +69,7 @@ export const writeFile       = async (...a) => (await import('./patcher.js')).wr
 export const runTeamCli      = async (...a) => (await import('./team/index.js')).runTeamCli(...a);
 export const runTrend        = async (...a) => (await import('./trend.js')).runTrend(...a);
 export const runPillarsWizard = async (...a) => (await import('./pillars-wizard.js')).runPillarsWizard(...a);
+export const runTesseract    = async (...a) => (await import('./tesseract.js')).runTesseract(...a);
 export { handleError, withErrorCatcher, publishIssue };
 
 // ---------------------------------------------------------------------------
@@ -100,6 +101,7 @@ export const ALLOWED_COMMANDS = new Set([
   'init',
   'hook', 'hooks', 'install-hooks', 'setup-ci',
   'add:prop', 'add:state', 'add:action', 'fix',
+  'tesseract', 'cube', 'matrix',
   'help', '--help', '-h',
   'version', '--version', '-v'
 ]);

package/cli/mcp/antigravity.js

@@ -11,6 +11,8 @@ export const buildMcpInstructions = () => {
     'Provides all Chemical X operations through a single tool. This avoids requiring',
     'separate approval for each sub-operation in MCP clients that gate tool access per-tool.',
     'Pass the desired operation via the action parameter; see action: \'help\' for the full list.',
+    '0. AUTONOMOUS COGNITIVE BRIDGE (TESSERACT):',
+    '   - chemx({ action: "tesseract" }) or chemx({ command: "tesseract" }) -> Boot Jarvis cognitive lattice and mission protocol',
     '',
     '1. TESTING, BUILDS & VERIFICATION:',
     '   - chemx({ action: "test" }) or chemx({ command: "test" })',

package/cli/mcp/manifests.js

@@ -33,7 +33,8 @@ export const MASTER_MCP_TOOL = {
           'generate',
           'patterns',
           'issue',
-          'project'
+          'project',
+          'tesseract'
         ],
         description: 'The Chemical X subsystem action to execute.'
       },

package/cli/mcp/tools-audit.js

@@ -11,6 +11,7 @@ import {
   buildHotspotsPrompt
 } from '../audit/prompts.js';
 import { syncSearchIndex, syncViolationsIndex, recordAuditSnapshot } from '../search.js';
+import { autoGenerateTasksFromAudit } from '../team/team-triage.js';
 import { resolveTargetCwd } from './tools-search.js';
 
 export const handleAudit = (args = {}, cwd = process.cwd()) => {
@@ -43,6 +44,7 @@ export const handleAudit = (args = {}, cwd = process.cwd()) => {
     if (syncRes?.db) {
       syncViolationsIndex(syncRes.db, report.violations);
       recordAuditSnapshot(syncRes.db, report);
+      autoGenerateTasksFromAudit(syncRes.db, { cwd: baseCwd, targetDir: resolvedTarget });
     }
   } catch (syncError) {
     process.stderr.write(`[chemx] Search index sync bypassed: ${syncError?.message || String(syncError)}\n`);

package/cli/mcp/tools-team-tasks.js

@@ -18,7 +18,8 @@ export const handleChemxTeamTask = async (args = {}, cwd = process.cwd()) => {
 
   if (action === 'list') {
     const parentId = args.parentId !== undefined ? args.parentId : args.parent;
-    const tasks = listTasks(db, { status: args.status, assigned_agent_id: args.agentId, parentId });
+    const rule = args.rule || args.ruleId;
+    const tasks = listTasks(db, { status: args.status, assigned_agent_id: args.agentId, parentId, rule, priority: args.priority });
     const col = toColumnar(tasks, ['id', 'title', 'tier', 'status', 'priority', 'assigned_agent_id', 'target_path', 'parent_id']);
     return { ...col, total: tasks.length, card: formatTaskListCard(tasks) };
   }

package/cli/mcp/tools.js

@@ -9,7 +9,7 @@ import { handleChemxProject } from './tools-project.js';
 
 export {
   MCP_TOOLS, ALL_MCP_TOOLS, handleChemxQ, handleChemxRead, handleChemxPatch, handleChemxCheck, handleChemxWrite,
-  handleChemxTeamStatus, handleChemxTeamFeed, handleChemxTeamPost, handleChemxTeamTask, handleChemxTeamLock, handleChemxReportIssue, handleChemxProject
+  handleChemxTeamStatus, handleChemxTeamFeed, handleChemxTeamPost, handleChemxTeamTask, handleChemxTeamLock, handleChemxReportIssue, handleChemxProject, handleChemxTesseract
 };
 
 const parseCommand = (command, params) => {
@@ -40,9 +40,19 @@ const parseCommand = (command, params) => {
   }
   if (subCmd === 'autofix') return { action: 'autofix', params: { path: parts[1] || 'src', ...params } };
   if (subCmd === 'trend' || subCmd === 'trends') return { action: 'trend', params };
+  if (['tesseract', 'cube', 'matrix'].includes(subCmd)) return { action: 'tesseract', params };
   return { action: subCmd, params };
 };
 
+const handleChemxTesseract = async (params = {}, cwd = process.cwd()) => {
+  const { runTesseract } = await import('../tesseract.js');
+  const result = await runTesseract(params.args || [], false, cwd);
+  const textOutput = result.text || JSON.stringify(result.payload, null, 2);
+  return {
+    content: [{ type: 'text', text: textOutput }]
+  };
+};
+
 const DISPATCHER = {
   audit: handleAudit, trend: handleChemxTrend, build: handleAuditBuild, verify: handleChemxVerify,
   typecheck: handleChemxTypecheck, test: handleChemxTest, check: handleChemxCheck,
@@ -51,7 +61,8 @@ const DISPATCHER = {
   team_status: handleChemxTeamStatus, team_feed: handleChemxTeamFeed, team_post: handleChemxTeamPost,
   team_task: handleChemxTeamTask, team_lock: handleChemxTeamLock, q: handleChemxQ, search: handleChemxQ,
   autofix: handleAutofix, generate: handleGenerateCapsule, patterns: handleQueryPatterns,
-  issue: handleChemxReportIssue, project: handleChemxProject, coordinator: handleChemxProject
+  issue: handleChemxReportIssue, project: handleChemxProject, coordinator: handleChemxProject,
+  tesseract: handleChemxTesseract, cube: handleChemxTesseract, matrix: handleChemxTesseract
 };
 
 export const handleChemx = async (args = {}, cwd = process.cwd()) => {

package/cli/search-schema.js

@@ -1,4 +1,5 @@
 import './silence-warnings.js';
+import fs from 'node:fs';
 import path from 'node:path';
 import { ensureChemxDir } from './audit/history.js';
 import { initTeamSchema } from './team/team-schema.js';
@@ -36,14 +37,61 @@ export const openIndexDb = (cwd = process.cwd(), options = {}) => {
     return DB_CACHE.get(dbPath);
   }
 
-  const db = new DatabaseSync(dbPath);
-
+  let isReadOnly = false;
   try {
-    db.exec('PRAGMA busy_timeout = 5000;');
-    db.exec('PRAGMA journal_mode = WAL;');
-    db.exec('PRAGMA foreign_keys = ON;');
+    fs.accessSync(path.dirname(dbPath), fs.constants.W_OK);
+    if (fs.existsSync(dbPath)) {
+      fs.accessSync(dbPath, fs.constants.W_OK);
+    }
   } catch {
-    // Safe retry/fallback if concurrent worker holds active lock
+    isReadOnly = true;
+  }
+
+  let db = null;
+  try {
+    db = new DatabaseSync(dbPath, isReadOnly ? { readOnly: true } : {});
+    if (!isReadOnly) {
+      try {
+        db.exec('PRAGMA busy_timeout = 5000;');
+        db.exec('PRAGMA journal_mode = WAL;');
+        db.exec('PRAGMA foreign_keys = ON;');
+      } catch {
+        // Safe retry/fallback if concurrent worker holds active lock
+      }
+    }
+  } catch (err) {
+    if (!isReadOnly) {
+      try {
+        db = new DatabaseSync(dbPath, { readOnly: true });
+        isReadOnly = true;
+      } catch {
+        return null;
+      }
+    } else {
+      return null;
+    }
+  }
+
+  if (isReadOnly) {
+    if (typeof db.function === 'function') {
+      try {
+        db.function('vec_cosine', (b1, b2) => {
+          if (!b1 || !b2) return 0;
+          const a = new Float32Array(b1.buffer, b1.byteOffset, b1.byteLength / 4);
+          const b = new Float32Array(b2.buffer, b2.byteOffset, b2.byteLength / 4);
+          let dot = 0;
+          const len = Math.min(a.length, b.length);
+          for (let i = 0; i < len; i++) {
+            dot += a[i] * b[i];
+          }
+          return Math.max(0, Math.min(1, dot));
+        });
+      } catch {
+        // Ignored if already registered
+      }
+    }
+    DB_CACHE.set(dbPath, db);
+    return db;
   }
 
   db.exec(`

package/cli/search.js

@@ -105,6 +105,10 @@ export const syncSearchIndex = (targetDir = 'src', cwd = process.cwd(), options
   const db = openIndexDb(cwd);
   if (!db) return null;
 
+  const isWritable = () => { try { fs.accessSync(path.join(cwd, '.chemx'), fs.constants.W_OK); return true; } catch { return false; } };
+  const shouldSkipSync = !isWritable() && !options.reindex;
+  if (shouldSkipSync) return { db, updatedCount: 0 };
+
   const targetDirs = Array.isArray(targetDir) ? targetDir : [targetDir];
   if (targetDir === 'src' && fs.existsSync(path.resolve(cwd, 'cli'))) {
     targetDirs.push('cli');

package/cli/team/team-commands.js

@@ -25,7 +25,7 @@ import { getSwarmTokenBreakdown, formatTokenBreakdownCard } from './team-tokens.
 import { runAblationComparison, formatAblationCard } from './team-memory.js';
 import { parseFlags } from './team-flags.js';
 
-const ARG_VAL_FLAGS = ['--target', '--as', '--to', '--agent', '--since', '--limit', '--thread', '--task', '--parent'];
+const ARG_VAL_FLAGS = ['--target', '--as', '--to', '--agent', '--since', '--limit', '--thread', '--task', '--parent', '--rule', '--priority', '--prio'];
 
 export const runTeamCli = (rawArgs = [], isCli = false, cwd = process.cwd()) => {
   const db = openIndexDb(cwd);
@@ -119,7 +119,9 @@ export const runTeamCli = (rawArgs = [], isCli = false, cwd = process.cwd()) =>
       const tasks = listTasks(db, {
         status: flags.status,
         assigned_agent_id: flags.agent,
-        parentId: flags.parent
+        parentId: flags.parent,
+        rule: flags.rule,
+        priority: flags.priority
       });
       if (flags.isJson) {
         const col = toColumnar(tasks, ['id', 'title', 'tier', 'status', 'priority', 'assigned_agent_id', 'target_path', 'parent_id']);

package/cli/team/team-db-lock-promotion.js

@@ -76,16 +76,20 @@ export const cleanExpiredLeases = (db) => {
   if (!hasDb) return [];
 
   const now = Date.now();
-  const expired = db.prepare('SELECT * FROM file_leases WHERE expires_at <= ?').all(now);
-  for (const lease of expired) {
-    db.prepare('DELETE FROM file_leases WHERE file_path = ?').run(lease.file_path);
-    postFeedEvent(db, {
-      author_id: '@system',
-      event_type: 'lock_expired',
-      file_path: lease.file_path,
-      message: `Lease expired for ${lease.file_path} held by ${lease.locked_by}`
-    });
-    promoteNextWaiter(db, lease.file_path);
+  try {
+    const expired = db.prepare('SELECT * FROM file_leases WHERE expires_at <= ?').all(now);
+    for (const lease of expired) {
+      db.prepare('DELETE FROM file_leases WHERE file_path = ?').run(lease.file_path);
+      postFeedEvent(db, {
+        author_id: '@system',
+        event_type: 'lock_expired',
+        file_path: lease.file_path,
+        message: `Lease expired for ${lease.file_path} held by ${lease.locked_by}`
+      });
+      promoteNextWaiter(db, lease.file_path);
+    }
+    return expired;
+  } catch {
+    return [];
   }
-  return expired;
 };

package/cli/team/team-db-task-helpers.js

@@ -90,7 +90,57 @@ export const buildTaskListQuery = (filter = {}) => {
     conditions.push('parent_id = ?');
     params.push(Number(parentId));
   }
+  const ruleFilter = filter.rule || filter.rule_id;
+  if (ruleFilter) {
+    conditions.push('(rule_id = ? OR rule_id LIKE ?)');
+    params.push(ruleFilter, `%${ruleFilter}%`);
+  }
+  const hasPriority = filter.priority !== undefined && filter.priority !== null && filter.priority !== '';
+  if (hasPriority) {
+    conditions.push('priority = ?');
+    params.push(Number(filter.priority));
+  }
   if (conditions.length > 0) query += ` WHERE ${conditions.join(' AND ')}`;
   query += ' ORDER BY priority ASC, id ASC';
   return { query, params };
 };
+
+export const queryUnassignedHazards = (db) => {
+  if (!db) return [];
+  const query = `
+    SELECT 
+      COALESCE(v.file_path, f.path) as path,
+      COALESCE(f.tier, 'molecule') as tier,
+      COALESCE(f.lines, 0) as lines,
+      COALESCE(f.health_score, CASE WHEN COUNT(v.id) > 0 THEN MAX(20, 100 - COUNT(v.id) * 15) ELSE 100 END) as health_score,
+      COALESCE(MAX(f.hazard_count, COUNT(v.id)), COUNT(v.id)) as hazard_count,
+      COUNT(v.id) as violation_count,
+      GROUP_CONCAT(DISTINCT v.rule) as rules_summary
+    FROM violations v
+    LEFT JOIN files f ON f.path = v.file_path
+    LEFT JOIN agent_tasks t ON t.target_path = v.file_path AND t.status IN ('queued', 'in_progress', 'review')
+    WHERE t.id IS NULL
+    GROUP BY v.file_path
+    UNION
+    SELECT
+      f.path,
+      f.tier,
+      f.lines,
+      f.health_score,
+      f.hazard_count,
+      f.hazard_count as violation_count,
+      'ARCHITECTURAL_HAZARD' as rules_summary
+    FROM files f
+    LEFT JOIN agent_tasks t ON t.target_path = f.path AND t.status IN ('queued', 'in_progress', 'review')
+    WHERE (f.health_score < 90 OR f.hazard_count > 0)
+      AND t.id IS NULL
+      AND f.path NOT IN (SELECT file_path FROM violations)
+    GROUP BY f.path
+    ORDER BY health_score ASC, hazard_count DESC
+  `;
+  try {
+    return db.prepare(query).all();
+  } catch {
+    return [];
+  }
+};

package/cli/team/team-flags.js

@@ -48,7 +48,10 @@ export const parseFlags = (args = []) => {
     if (arg.startsWith('--target=')) flags.target = arg.split('=')[1];
     if (arg === '--target' && hasNext) flags.target = nextArg;
     if (arg.startsWith('--tier=')) flags.tier = arg.split('=')[1];
-    if (arg.startsWith('--prio=')) flags.priority = parseInt(arg.split('=')[1], 10);
+    if (arg.startsWith('--rule=')) flags.rule = arg.split('=')[1];
+    if (arg === '--rule' && hasNext) flags.rule = nextArg;
+    if (arg.startsWith('--prio=') || arg.startsWith('--priority=')) flags.priority = parseInt(arg.split('=')[1], 10);
+    if ((arg === '--prio' || arg === '--priority') && hasNext) flags.priority = parseInt(nextArg, 10);
     if (arg.startsWith('--purpose=')) flags.purpose = arg.split('=')[1];
     if (arg.startsWith('--tokens=')) flags.tokens = parseInt(arg.split('=')[1], 10);
     if (arg.startsWith('--prompt-tokens=')) flags.promptTokens = parseInt(arg.split('=')[1], 10);