contextos-agents 1.6.1 → 2.0.0-beta.2

package/.agents/ctx.js

@@ -36,16 +36,20 @@ function printHelp() {
   console.log('  export aider [--profile <p>]    Compile skills → .aider.conf.yml + CONVENTIONS.md');
   console.log('  export zed [--profile <p>]      Compile skills → .zed/rules.md & .zed/prompts/*.md');
   console.log('  export all [--profile <p>]      Compile skills for all supported agents');
-  console.log('  profile list                    List available project profiles');
-  console.log('  profile show <name>             Show profile configuration');
-  console.log('  profile apply <name>            Apply a profile (e.g. mvp, startup, enterprise, frontend)');
-  console.log('  profile remove                  Remove active profile filter');
+  console.log('  profile list [--json]           List available project profiles');
+  console.log('  profile show <name> [--json]    Show profile configuration');
+  console.log('  profile explain <name> [--json] Detailed explanation of profile skills, policies & defaults');
+  console.log('  profile apply <name>            Apply a profile (supports --scope <pkg> --no-export --json)');
+  console.log('  profile remove [--scope <pkg>]  Remove active profile or scoped package override');
   console.log('  resolve <prompt>                Resolve minimal skills needed for a task');
+  console.log('  explain [id] [--rules]          Inspect rule catalog, enforcement levels, and automated checkers');
   console.log('  index                           Generate progressive skills-index.json');
   console.log('  detect                          Auto-detect project tech stack');
+  console.log('  compile [--check] [--sarif]     Compile skill manifests into deterministic registry v2');
   console.log('  audit                           Alias for validate (check skills)');
   console.log('  validate                        Validate skill sources, frontmatter, deps & sync');
   console.log('  clean-worktrees                 Clean up lingering .swarm-worktrees and swarm/* branches');
+  console.log('  recover [--status|rollback|cont] Inspect, rollback, or resume interrupted transactions');
   console.log('  doctor                          Run project diagnostic health check');
   console.log('  stats                           Display token context savings report');
   console.log('  watch                           Start continuous file watcher and auto-sync daemon');
@@ -90,108 +94,189 @@ const target  = args[1];
 
 // ── export ────────────────────────────────────────────────────────────────────
 if (command === 'export') {
+  const pureCompiler = require('./adapters/pure-compiler.js');
+  const driftDetector = require('./adapters/drift-detector.js');
+
   const profileFlagIdx = args.indexOf('--profile');
+  let overrideProfile = null;
   if (profileFlagIdx !== -1 && args[profileFlagIdx + 1]) {
     const profiles = require('./profiles.js');
-    const profileName = args[profileFlagIdx + 1];
+    overrideProfile = args[profileFlagIdx + 1];
     try {
-      profiles.applyProfile(profileName);
-      console.log(`[PROFILE] Applied profile '${profileName}' for this export.\n`);
+      profiles.applyProfile(overrideProfile);
+      console.log(`[PROFILE] Applied profile '${overrideProfile}' for this export.\n`);
     } catch (err) {
       console.error(`[ERROR] ${err.message}`);
       process.exit(1);
     }
   }
 
-  const runGemini = () => {
-    const adapter = require('./adapters/gemini/export.js');
-    adapter.run();
-  };
-
-  const runClaude = () => {
-    const adapter = require('./adapters/claude/export.js');
-    adapter.run();
-  };
-
-  const runCursor = () => {
-    const adapter = require('./adapters/cursor/export.js');
-    adapter.run();
-  };
-
-  const runCopilot = () => {
-    const adapter = require('./adapters/copilot/export.js');
-    adapter.run();
-  };
-
-  const runAider = () => {
-    const adapter = require('./adapters/aider/export.js');
-    adapter.run();
-  };
-
-  const runZed = () => {
-    const adapter = require('./adapters/zed/export.js');
-    adapter.run();
-  };
-
-  if (target === 'gemini') {
-    runGemini();
-  } else if (target === 'claude') {
-    runClaude();
-  } else if (target === 'cursor') {
-    runCursor();
-  } else if (target === 'copilot') {
-    runCopilot();
-  } else if (target === 'aider') {
-    runAider();
-  } else if (target === 'zed') {
-    runZed();
-  } else if (target === 'all') {
-    console.log('Exporting skills for all agents...\n');
-    runGemini();
-    console.log('');
-    runClaude();
-    console.log('');
-    runCursor();
-    console.log('');
-    runCopilot();
-    console.log('');
-    runAider();
-    console.log('');
-    runZed();
-    console.log('\nAll exports complete.');
+  const isCheck = args.includes('--check');
+  const isDiff = args.includes('--diff');
+  const isDryRun = args.includes('--dry-run');
+  const asJson = args.includes('--json');
+
+  const rawTarget = args[1] && !args[1].startsWith('--') ? args[1] : 'all';
+
+  // 1. Drift Check Mode (--check)
+  if (isCheck) {
+    const drift = driftDetector.detectDrift(process.cwd(), rawTarget, { profile: overrideProfile });
+    if (asJson) {
+      console.log(JSON.stringify(drift, null, 2));
+    } else {
+      console.log('\nContextOS — Adapter Output Drift Check\n');
+      if (!drift.hasDrift) {
+        console.log(`✓ No adapter drift detected. All ${drift.projectedCount} output artifacts are synchronized.`);
+      } else {
+        console.log(`! Drift detected (${drift.totalFindings} finding(s)):\n`);
+        for (const [state, items] of Object.entries(drift.findings)) {
+          if (items.length > 0) {
+            console.log(`  [${state}] (${items.length}):`);
+            for (const item of items) {
+              console.log(`    • ${item.path || item.reason || JSON.stringify(item)}`);
+            }
+          }
+        }
+        if (drift.collisions.length > 0) {
+          console.log(`\n  [PATH_COLLISIONS] (${drift.collisions.length}):`);
+          for (const c of drift.collisions) {
+            console.log(`    • ${c.path} (between ${c.firstAdapter} and ${c.secondAdapter})`);
+          }
+        }
+        console.log('\nRun: node .agents/ctx.js export all    to synchronize outputs with source skills.\n');
+      }
+    }
+    process.exit(drift.hasDrift ? 1 : 0);
+  }
+
+  // 2. Diff Preview Mode (--diff)
+  if (isDiff) {
+    const drift = driftDetector.detectDrift(process.cwd(), rawTarget, { profile: overrideProfile });
+    if (asJson) {
+      console.log(JSON.stringify(drift.diffs, null, 2));
+    } else {
+      console.log('\nContextOS — Adapter Output Projected Diffs\n');
+      if (drift.diffs.length === 0) {
+        console.log('✓ Disk is in sync with projected render. No diffs found.');
+      } else {
+        for (const d of drift.diffs) {
+          console.log(`--- ${d.path} (${d.type}) ---`);
+          console.log(d.diff);
+          console.log('');
+        }
+      }
+    }
+    process.exit(0);
+  }
+
+  // 3. Dry-Run Mode (--dry-run)
+  if (isDryRun) {
+    const rendered = pureCompiler.renderAdapters(process.cwd(), rawTarget, { profile: overrideProfile });
+    if (asJson) {
+      console.log(JSON.stringify(rendered, null, 2));
+    } else {
+      console.log('\nContextOS — Adapter Export Dry Run\n');
+      console.log(`Target: ${rawTarget}`);
+      console.log(`Planned artifacts: ${rendered.artifacts.length}\n`);
+      for (const art of rendered.artifacts) {
+        console.log(`  + ${art.path.padEnd(50)} [${art.generator}] (${art.content.length} bytes)`);
+      }
+      if (rendered.collisions.length > 0) {
+        console.log(`\n! Collisions detected: ${rendered.collisions.length}`);
+        for (const c of rendered.collisions) {
+          console.log(`  • ${c.path} (${c.firstAdapter} vs ${c.secondAdapter})`);
+        }
+      }
+      console.log('\nDry run complete. No files were written to disk.');
+    }
+    process.exit(0);
+  }
+
+  // 4. Live Export Execution
+  if (rawTarget === 'all') {
+    console.log('Starting pure compiler export for all adapters...');
+    const rendered = pureCompiler.renderAdapters(process.cwd(), 'all', { profile: overrideProfile });
+
+    if (rendered.collisions.length > 0) {
+      console.error(`[ERROR] Path collisions detected across adapters:`);
+      for (const c of rendered.collisions) {
+        console.error(`  • ${c.path} (${c.firstAdapter} vs ${c.secondAdapter})`);
+      }
+      process.exit(1);
+    }
+
+    const result = pureCompiler.applyArtifacts(process.cwd(), rendered.artifacts, {
+      command: 'export all',
+      context: rendered.context,
+    });
+
+    if (asJson) {
+      console.log(JSON.stringify(result, null, 2));
+    } else {
+      console.log(`✓ All exports complete: ${result.appliedCount} artifacts applied in a single transaction (tx: ${result.txId}).`);
+      console.log(`  Active adapters: Gemini, Claude, Cursor, Copilot, Aider, Zed`);
+    }
   } else {
-    console.error(`Adapter for '${target}' not implemented yet.`);
-    console.error('Supported agents: gemini, claude, cursor, copilot, aider, zed, all');
-    process.exit(1);
+    const adapter = pureCompiler.getAdapter(rawTarget);
+    if (!adapter) {
+      if (asJson) {
+        console.error(JSON.stringify({ success: false, error: `Adapter for '${rawTarget}' not implemented yet.` }));
+      } else {
+        console.error(`Adapter for '${rawTarget}' not implemented yet.`);
+        console.error(`Supported agents: ${pureCompiler.listAdapters().join(', ')}, all`);
+      }
+      process.exit(1);
+    }
+
+    const result = adapter.run({ profile: overrideProfile, projectRoot: process.cwd() });
+    if (asJson) {
+      console.log(JSON.stringify(result, null, 2));
+    }
   }
 
 // ── profile ───────────────────────────────────────────────────────────────────
 } else if (command === 'profile') {
   const subcommand = args[1] || 'list';
-  const profileName = args[2];
+  const profileName = args[2] && !args[2].startsWith('-') ? args[2] : null;
   const profiles = require('./profiles.js');
+  const asJson = args.includes('--json');
+
+  const scopeIdx = args.indexOf('--scope');
+  const scopeArg = scopeIdx !== -1 && args[scopeIdx + 1] && !args[scopeIdx + 1].startsWith('--')
+    ? args[scopeIdx + 1]
+    : (args.find(a => a.startsWith('--scope=')) || '').split('=')[1] || null;
 
   if (subcommand === 'list') {
     const list = profiles.listProfiles();
     const active = profiles.getActiveProfile();
-    console.log('\nAvailable ContextOS Profiles:\n');
-    for (const p of list) {
-      const isActive = active && active.profile === p.id;
-      const marker = isActive ? '● [ACTIVE]' : '○';
-      console.log(`  ${marker} ${p.id.padEnd(12)} - ${p.name}: ${p.description}`);
-      if (p.exclude_skills && p.exclude_skills.length > 0) {
-        console.log(`      Excludes: ${p.exclude_skills.join(', ')}`);
+    if (asJson) {
+      console.log(JSON.stringify({ active, profiles: list }, null, 2));
+    } else {
+      console.log('\nAvailable ContextOS Profiles:\n');
+      for (const p of list) {
+        const isActive = active && active.profile === p.id;
+        const marker = isActive ? '● [ACTIVE]' : '○';
+        console.log(`  ${marker} ${p.id.padEnd(12)} - ${p.name}: ${p.description}`);
+        if (p.exclude_skills && p.exclude_skills.length > 0) {
+          console.log(`      Excludes: ${p.exclude_skills.join(', ')}`);
+        }
       }
+      console.log('\nApply a profile: node .agents/ctx.js profile apply <name> [--scope <pkg>]');
+      if (active) {
+        console.log(`Current active profile: ${active.profile} (${active.name || active.profile})`);
+        if (active.overrides && Object.keys(active.overrides).length > 0) {
+          console.log('Package Overrides:');
+          for (const [s, oProf] of Object.entries(active.overrides)) {
+            console.log(`  • ${s} → ${oProf}`);
+          }
+        }
+      }
+      console.log('');
     }
-    console.log('\nApply a profile: node .agents/ctx.js profile apply <name>');
-    if (active) {
-      console.log(`Current active profile: ${active.profile} (${active.name})`);
-    }
-    console.log('');
   } else if (subcommand === 'show') {
     const name = profileName || (profiles.getActiveProfile() || {}).profile;
     if (!name) {
-      console.error('[ERROR] Usage: node ctx.js profile show <name>');
+      console.error('[ERROR] Usage: node ctx.js profile show <name> [--json]');
       process.exit(1);
     }
     const profile = profiles.getProfile(name);
@@ -199,52 +284,168 @@ if (command === 'export') {
       console.error(`[ERROR] Profile '${name}' not found.`);
       process.exit(1);
     }
-    console.log(`\nProfile: ${profile.name} (${profile.id})`);
-    console.log(`Description: ${profile.description}`);
-    console.log(`Preferred Skills: ${(profile.prefer_skills || []).join(', ') || 'none'}`);
-    console.log(`Excluded Skills: ${(profile.exclude_skills || []).join(', ') || 'none'}\n`);
+    if (asJson) {
+      console.log(JSON.stringify(profile, null, 2));
+    } else {
+      console.log(`\nProfile: ${profile.name} (${profile.id})`);
+      console.log(`Description: ${profile.description}`);
+      console.log(`Required Skills: ${(profile.skills?.required || profile.require_skills || []).join(', ') || 'none'}`);
+      console.log(`Preferred Skills: ${(profile.skills?.preferred || profile.prefer_skills || []).join(', ') || 'none'}`);
+      console.log(`Excluded Skills: ${(profile.skills?.excluded || profile.exclude_skills || []).join(', ') || 'none'}\n`);
+    }
+  } else if (subcommand === 'explain') {
+    const name = profileName || (profiles.getActiveProfile() || {}).profile;
+    if (!name) {
+      console.error('[ERROR] Usage: node ctx.js profile explain <name> [--json]');
+      process.exit(1);
+    }
+    try {
+      const explanation = profiles.explainProfile(name);
+      if (asJson) {
+        console.log(JSON.stringify(explanation, null, 2));
+      } else {
+        console.log('\n' + profiles.formatProfileExplanation(explanation) + '\n');
+      }
+    } catch (err) {
+      console.error(`[ERROR] ${err.message}`);
+      process.exit(1);
+    }
   } else if (subcommand === 'apply') {
     if (!profileName) {
-      console.error('[ERROR] Usage: node ctx.js profile apply <name>');
+      console.error('[ERROR] Usage: node ctx.js profile apply <name> [--scope <pkg>] [--no-export] [--json]');
       process.exit(1);
     }
     try {
-      const applied = profiles.applyProfile(profileName);
-      console.log(`\n✓ Profile '${applied.name}' successfully applied!`);
-      console.log(`  Excluded skills: ${(applied.exclude_skills || []).join(', ') || 'none'}`);
-      console.log('  Run: node .agents/ctx.js export all  (to rebuild exports with this profile)\n');
+      const applied = profiles.applyProfile(profileName, process.cwd(), {
+        scope: scopeArg,
+        noExport: args.includes('--no-export'),
+      });
+      if (asJson) {
+        console.log(JSON.stringify(applied, null, 2));
+      } else {
+        if (scopeArg) {
+          console.log(`\n✓ Scoped profile override '${profileName}' applied to scope: ${scopeArg}!`);
+        } else {
+          console.log(`\n✓ Profile '${applied.name || profileName}' successfully applied as root profile!`);
+          console.log(`  Excluded skills: ${(applied.exclude_skills || []).join(', ') || 'none'}`);
+        }
+        if (!args.includes('--no-export')) {
+          console.log('  Run: node .agents/ctx.js export all  (to rebuild exports with this profile)\n');
+        }
+      }
     } catch (err) {
       console.error(`[ERROR] ${err.message}`);
       process.exit(1);
     }
   } else if (subcommand === 'remove' || subcommand === 'reset') {
-    const removed = profiles.removeActiveProfile();
-    if (removed) {
-      console.log('\n✓ Active profile filter removed. All skills will be included.\n');
+    const removed = profiles.removeActiveProfile(process.cwd(), { scope: scopeArg });
+    if (asJson) {
+      console.log(JSON.stringify({ removed, scope: scopeArg }, null, 2));
     } else {
-      console.log('\nNo active profile was set.\n');
+      if (removed) {
+        if (scopeArg) {
+          console.log(`\n✓ Profile override for scope '${scopeArg}' removed.\n`);
+        } else {
+          console.log('\n✓ Active profile filter removed. All skills will be included.\n');
+        }
+      } else {
+        console.log(`\nNo active profile${scopeArg ? ` override for '${scopeArg}'` : ''} was found.\n`);
+      }
     }
   } else {
     console.error(`Unknown profile subcommand: ${subcommand}`);
-    console.error('Valid subcommands: list, show, apply, remove');
+    console.error('Valid subcommands: list, show, explain, apply, remove');
     process.exit(1);
   }
 
 // ── resolve ───────────────────────────────────────────────────────────────────
 } else if (command === 'resolve') {
-  const resolver = require('./resolver.js');
+  const { CanonicalResolver } = require('./resolver/canonical-resolver.js');
   const promptArgs = args.slice(1).filter(a => !a.startsWith('-')).join(' ');
   const filesIdx = args.indexOf('--files');
   const files = filesIdx !== -1 && args[filesIdx + 1] ? args[filesIdx + 1].split(',') : [];
   const phaseIdx = args.indexOf('--phase');
-  const phase = phaseIdx !== -1 && args[phaseIdx + 1] ? args[phaseIdx + 1] : 'Build';
+  const phase = phaseIdx !== -1 && args[phaseIdx + 1] ? args[phaseIdx + 1] : undefined;
+  const budgetIdx = args.indexOf('--budget');
+  const budget = budgetIdx !== -1 && args[budgetIdx + 1] ? parseInt(args[budgetIdx + 1], 10) : undefined;
+  const explain = args.includes('--explain');
+  const asJson = args.includes('--json');
+
+  const resolver = new CanonicalResolver({ rootDir: process.cwd() });
+  const result = resolver.resolve({
+    task: promptArgs,
+    files,
+    explicitPhase: phase,
+    contextBudgetTokens: budget,
+  });
+
+  if (asJson) {
+    console.log(JSON.stringify(result, null, 2));
+  } else if (explain) {
+    console.log(resolver.formatExplanation(result));
+  } else {
+    console.log('\n══════════════════════════════════════════');
+    console.log('  ContextOS — Dynamic Skill Resolution');
+    console.log('══════════════════════════════════════════');
+    console.log(resolver.formatDeclaration(result));
+    console.log('──────────────────────────────────────────\n');
+  }
 
-  const result = resolver.resolveSkills({ prompt: promptArgs, files, phase });
-  console.log('\n══════════════════════════════════════════');
-  console.log('  ContextOS — Dynamic Skill Resolution');
-  console.log('══════════════════════════════════════════');
-  console.log(resolver.formatDeclaration(result));
-  console.log('──────────────────────────────────────────\n');
+// ── explain ───────────────────────────────────────────────────────────────────
+} else if (command === 'explain') {
+  const { RuleCatalog } = require('./rules/rule-catalog.js');
+  const catalog = new RuleCatalog({ rootDir: process.cwd() });
+  const fs = require('fs');
+
+  // Load compiled registry rules if available
+  const registryPath = path.join(process.cwd(), '.agents', 'compiled', 'registry.v2.json');
+  if (fs.existsSync(registryPath)) {
+    try {
+      const reg = JSON.parse(fs.readFileSync(registryPath, 'utf8'));
+      catalog.loadFromRegistry(reg);
+    } catch {
+      // ignore
+    }
+  }
+
+  const asJson = args.includes('--json');
+  const showRules = args.includes('--rules');
+  const showCheckers = args.includes('--checkers');
+  const targetId = args.slice(1).find(a => !a.startsWith('-'));
+
+  if (asJson) {
+    if (showCheckers) {
+      console.log(JSON.stringify(catalog.getAllCheckers(), null, 2));
+    } else if (targetId) {
+      const rule = catalog.getRule(targetId);
+      if (rule) {
+        console.log(JSON.stringify(rule, null, 2));
+      } else {
+        const skillRules = catalog.getAllRules().filter(r => r.sourceSkill === targetId);
+        console.log(JSON.stringify({ skill: targetId, rules: skillRules }, null, 2));
+      }
+    } else {
+      console.log(JSON.stringify({
+        rules: catalog.getAllRules(),
+        checkers: catalog.getAllCheckers(),
+      }, null, 2));
+    }
+  } else if (showCheckers) {
+    console.log(catalog.formatCheckersSummary());
+  } else if (showRules) {
+    console.log(catalog.formatRulesSummary());
+  } else if (targetId) {
+    const rule = catalog.getRule(targetId);
+    if (rule) {
+      console.log(catalog.explainRule(targetId));
+    } else {
+      console.log(catalog.explainSkill(targetId));
+    }
+  } else {
+    // Default: print both rules summary and checkers
+    console.log(catalog.formatRulesSummary());
+    console.log(catalog.formatCheckersSummary());
+  }
 
 // ── index ─────────────────────────────────────────────────────────────────────
 } else if (command === 'index') {
@@ -257,17 +458,139 @@ if (command === 'export') {
 
 // ── detect ────────────────────────────────────────────────────────────────────
 } else if (command === 'detect') {
+  const { WorkspaceGraphBuilder } = require('./workspace/workspace-graph.js');
   const profiles = require('./profiles.js');
-  const detection = profiles.detectStack(process.cwd());
-  console.log('\nContextOS — Tech Stack Detection\n');
-  if (detection.detected.length === 0) {
-    console.log('  Detected stack: Generic / Vanilla JavaScript');
+  const asJson = args.includes('--json');
+  const explain = args.includes('--explain');
+  const scopeIdx = args.indexOf('--scope');
+  const scopeArg = scopeIdx !== -1 && args[scopeIdx + 1] && !args[scopeIdx + 1].startsWith('--')
+    ? args[scopeIdx + 1]
+    : (args.find(a => a.startsWith('--scope=')) || '').split('=')[1];
+
+  const builder = new WorkspaceGraphBuilder();
+  const graph = builder.build(process.cwd());
+
+  if (scopeArg) {
+    const nearestPkg = builder.findNearestPackage(scopeArg, graph);
+    const evidence = builder.extractPackageEvidence(scopeArg, graph);
+
+    if (asJson) {
+      console.log(JSON.stringify({
+        scope: scopeArg,
+        nearestPackage: nearestPkg,
+        evidence,
+      }, null, 2));
+    } else {
+      console.log('\n══════════════════════════════════════════');
+      console.log('  ContextOS — Workspace Scoped Detection');
+      console.log('══════════════════════════════════════════\n');
+      console.log(`  Scope Path       : ${scopeArg}`);
+      if (nearestPkg) {
+        console.log(`  Nearest Package  : ${nearestPkg.id} (${nearestPkg.ecosystem})`);
+        console.log(`  Package Root     : ${nearestPkg.root}`);
+        console.log(`  Languages        : ${nearestPkg.languages.join(', ') || 'unspecified'}`);
+        console.log(`  Dependencies     : ${nearestPkg.dependencies.length} (${nearestPkg.dependencies.slice(0, 8).join(', ')}${nearestPkg.dependencies.length > 8 ? '...' : ''})`);
+        console.log(`  Configs          : ${nearestPkg.configs.join(', ') || 'none'}`);
+        if (nearestPkg.internalDependencies.length > 0) {
+          console.log(`  Internal Links   : ${nearestPkg.internalDependencies.join(', ')}`);
+        }
+        if (evidence.length > 0) {
+          console.log('\n  Scoped Evidence:');
+          for (const ev of evidence.slice(0, 10)) {
+            console.log(`    • [${ev.source}] ${ev.target} (+${ev.weight}) — ${ev.description}`);
+          }
+          if (evidence.length > 10) {
+            console.log(`      ... and ${evidence.length - 10} more signals`);
+          }
+        }
+      } else {
+        console.log('  Nearest Package  : (none found)');
+      }
+      console.log('\n──────────────────────────────────────────\n');
+    }
+  } else if (asJson) {
+    const stack = profiles.detectStack(process.cwd());
+    console.log(JSON.stringify({
+      workspaceGraph: graph,
+      stack,
+    }, null, 2));
+  } else if (explain) {
+    console.log('\n══════════════════════════════════════════');
+    console.log('  ContextOS — Workspace Evidence Graph');
+    console.log('══════════════════════════════════════════\n');
+    console.log(`  Repository Root  : ${graph.repositoryRoot}`);
+    console.log(`  Fingerprint      : ${graph.fingerprint}`);
+    console.log(`  Packages Found   : ${graph.packages.length} ${graph.partial ? '(partial: true)' : ''}\n`);
+    for (const pkg of graph.packages) {
+      console.log(`  • ${pkg.id} [${pkg.ecosystem}]`);
+      console.log(`    Root           : ${pkg.root}`);
+      console.log(`    Manifests      : ${pkg.manifests.join(', ')}`);
+      console.log(`    Languages      : ${pkg.languages.join(', ') || 'unspecified'}`);
+      console.log(`    Dependencies   : ${pkg.dependencies.length}`);
+      if (pkg.configs.length > 0) {
+        console.log(`    Configs        : ${pkg.configs.join(', ')}`);
+      }
+      if (pkg.internalDependencies.length > 0) {
+        console.log(`    Internal Links : ${pkg.internalDependencies.join(', ')}`);
+      }
+      console.log('');
+    }
+    console.log('──────────────────────────────────────────\n');
   } else {
-    console.log(`  Detected stack: ${detection.detected.join(', ')}`);
+    const detection = profiles.detectStack(process.cwd());
+    console.log('\nContextOS — Workspace & Tech Stack Detection\n');
+    console.log(`  Repository Root   : ${graph.repositoryRoot}`);
+    console.log(`  Packages Detected : ${graph.packages.map(p => `${p.id} (${p.root})`).join(', ')}`);
+    if (detection.detected.length === 0) {
+      console.log('  Detected Stack    : Generic / Vanilla JavaScript');
+    } else {
+      console.log(`  Detected Stack    : ${detection.detected.join(', ')}`);
+    }
+    console.log(`  Recommended Profile: ${detection.recommendedProfile}`);
+    console.log(`  Recommended Skills : ${detection.recommendedSkills.join(', ')}`);
+    console.log(`\nCommands:`);
+    console.log(`  node .agents/ctx.js detect --scope <path>    Scope detection to a specific file/subproject`);
+    console.log(`  node .agents/ctx.js detect --explain         Display full workspace evidence graph`);
+    console.log(`  node .agents/ctx.js profile apply ${detection.recommendedProfile}\n`);
+  }
+
+// ── compile ───────────────────────────────────────────────────────────────────
+} else if (command === 'compile') {
+  const { ManifestCompiler } = require('./compiler/manifest-compiler.js');
+  const checkOnly = args.includes('--check');
+  const asSarif = args.includes('--sarif');
+  const asJson = args.includes('--json');
+
+  const compiler = new ManifestCompiler();
+  const res = checkOnly ? compiler.compile() : compiler.compileAndWrite();
+
+  if (asSarif) {
+    console.log(JSON.stringify(compiler.formatSarif(), null, 2));
+    process.exit(res.success ? 0 : 1);
+  }
+
+  if (asJson) {
+    console.log(JSON.stringify(res, null, 2));
+    process.exit(res.success ? 0 : 1);
+  }
+
+  if (!res.success) {
+    console.error('\n✗ Manifest compilation failed:\n');
+    for (const d of res.diagnostics) {
+      console.error(`  [${d.code}] ${d.file}${d.path ? ' ' + d.path : ''}: ${d.message}`);
+      if (d.remediation) console.error(`    ↳ Remediation: ${d.remediation}`);
+    }
+    console.error('');
+    process.exit(1);
+  }
+
+  const skillCount = Object.keys(res.registry.skills).length;
+  console.log(`\n✓ Successfully compiled ${skillCount} skills into Registry v2!`);
+  console.log(`  Source Graph Hash: ${res.registry.sourceGraphHash}`);
+  if (!checkOnly) {
+    console.log(`  Registry: .agents/compiled/registry.v2.json`);
+    console.log(`  Checksum: .agents/compiled/registry.v2.sha256\n`);
   }
-  console.log(`  Recommended Profile: ${detection.recommendedProfile}`);
-  console.log(`  Recommended Skills: ${detection.recommendedSkills.join(', ')}`);
-  console.log(`\nApply recommended profile:\n  node .agents/ctx.js profile apply ${detection.recommendedProfile}\n`);
 
 // ── validate / audit ──────────────────────────────────────────────────────────
 } else if (command === 'validate' || command === 'audit') {
@@ -370,7 +693,24 @@ if (command === 'export') {
 // ── doctor ────────────────────────────────────────────────────────────────────
 } else if (command === 'doctor') {
   const doctorModule = require('./doctor.js');
-  doctorModule.runDoctor(process.cwd());
+  const res = doctorModule.runDoctor(process.cwd(), { 
+    json: args.includes('--json'),
+    fix: args.includes('--fix'),
+    strict: args.includes('--strict')
+  });
+  if (res && res.ok === false) {
+    process.exit(1);
+  }
+
+// ── status ────────────────────────────────────────────────────────────────────
+} else if (command === 'status') {
+  const commands = require(path.join(__dirname, '..', 'bin', 'commands.js'));
+  const status = commands.getStatus(process.cwd());
+  if (args.includes('--json')) {
+    console.log(JSON.stringify(status, null, 2));
+  } else {
+    console.log(commands.formatStatusText(status));
+  }
 
 // ── stats ─────────────────────────────────────────────────────────────────────
 } else if (command === 'stats') {
@@ -394,6 +734,142 @@ if (command === 'export') {
   console.log('  node .agents/ctx.js doctor');
   console.log('  node .agents/ctx.js stats\n');
 
+// ── recover ───────────────────────────────────────────────────────────────────
+} else if (command === 'recover') {
+  const { JournaledTransaction, TX_STATES } = require('./filesystem/index.js');
+  const isStatus = args.includes('--status') || (!args.includes('--rollback') && !args.includes('--continue'));
+  const isRollback = args.includes('--rollback');
+  const isContinue = args.includes('--continue');
+
+  const pending = JournaledTransaction.listPending(process.cwd());
+
+  if (isStatus) {
+    console.log('\nContextOS — Transaction Recovery Status\n');
+    if (pending.length === 0) {
+      console.log('✓ No pending or interrupted transactions found. Project state is clean.');
+    } else {
+      console.log(`! Found ${pending.length} pending/interrupted transaction(s):\n`);
+      for (const tx of pending) {
+        console.log(`  • ID: ${tx.txId}`);
+        console.log(`    State: ${tx.state}`);
+        console.log(`    Created: ${tx.createdAt || 'unknown'}`);
+        console.log(`    Operations: ${tx.operations ? tx.operations.length : 'unknown'}`);
+        console.log('');
+      }
+      console.log('Run: node .agents/ctx.js recover --rollback [txId]');
+      console.log('     node .agents/ctx.js recover --continue [txId]\n');
+    }
+  } else if (isRollback || isContinue) {
+    const txIdArg = args.find(a => !a.startsWith('--') && a !== 'recover');
+    const targetTx = txIdArg ? pending.find(p => p.txId === txIdArg) : pending[0];
+
+    if (!targetTx) {
+      console.error(txIdArg ? `Transaction '${txIdArg}' not found in pending list.` : 'No pending transactions found to recover.');
+      process.exit(1);
+    }
+
+    const tx = new JournaledTransaction(process.cwd(), targetTx.txId);
+    if (fs.existsSync(tx.journalPath)) {
+      const jData = JSON.parse(fs.readFileSync(tx.journalPath, 'utf8'));
+      tx.state = jData.state;
+      tx.operations = jData.operations || [];
+      tx.appliedOperations = tx.operations.filter(o => o.backupFilePath);
+    }
+
+    if (isRollback) {
+      console.log(`Rolling back transaction '${targetTx.txId}'...`);
+      try {
+        tx.rollback();
+        console.log(`✓ Transaction '${targetTx.txId}' rolled back cleanly.`);
+      } catch (err) {
+        console.error(`Rollback failed: ${err.message}`);
+        process.exit(1);
+      }
+    } else if (isContinue) {
+      console.log(`Continuing transaction '${targetTx.txId}'...`);
+      try {
+        tx.state = TX_STATES.PREPARED;
+        tx.commit();
+        console.log(`✓ Transaction '${targetTx.txId}' committed cleanly.`);
+      } catch (err) {
+        console.error(`Continue failed: ${err.message}`);
+        process.exit(1);
+      }
+    }
+  }
+
+// ── thread ──────────────────────────────────────────────────────────────────
+} else if (command === 'thread') {
+  const { ThreadStore } = require('./runtime/thread-store.js');
+  const { evaluateMergeReadiness } = require('./runtime/state-machine.js');
+  const store = new ThreadStore({ baseDir: process.cwd() });
+  const subcmd = args[1] || 'list';
+  const isJson = args.includes('--json');
+
+  if (subcmd === 'list') {
+    const list = store.list();
+    if (isJson) {
+      console.log(JSON.stringify(list, null, 2));
+    } else {
+      console.log('\n══════════════════════════════════════════');
+      console.log('  ContextOS — Runtime Execution Threads');
+      console.log('══════════════════════════════════════════\n');
+      if (list.length === 0) {
+        console.log('  No runtime threads recorded yet.');
+      } else {
+        for (const th of list) {
+          const ready = th.merge?.status === 'READY' ? ' [READY TO MERGE]' : '';
+          console.log(`  • ID: ${th.id} (rev: ${th.revision})`);
+          console.log(`    Status      : Exec: ${th.execution.status} | Verify: ${th.verification.status} | Review: ${th.review.status} | Merge: ${th.merge.status}${ready}`);
+          console.log(`    Task        : ${(th.config?.task || '').slice(0, 70)}`);
+          console.log(`    Created     : ${new Date(th.createdAt).toISOString()}`);
+          console.log('');
+        }
+      }
+      console.log('──────────────────────────────────────────\n');
+    }
+  } else if (subcmd === 'get') {
+    const threadId = args[2];
+    if (!threadId) {
+      console.error('Usage: node ctx.js thread get <threadId> [--json]');
+      process.exit(1);
+    }
+    const th = store.get(threadId);
+    if (!th) {
+      console.error(`Thread "${threadId}" not found.`);
+      process.exit(1);
+    }
+    console.log(JSON.stringify(th, null, 2));
+  } else if (subcmd === 'readiness') {
+    const threadId = args[2];
+    if (!threadId) {
+      console.error('Usage: node ctx.js thread readiness <threadId> [--json]');
+      process.exit(1);
+    }
+    const th = store.get(threadId);
+    if (!th) {
+      console.error(`Thread "${threadId}" not found.`);
+      process.exit(1);
+    }
+    const readiness = evaluateMergeReadiness(th);
+    if (isJson) {
+      console.log(JSON.stringify(readiness, null, 2));
+    } else {
+      console.log('\n══════════════════════════════════════════');
+      console.log(`  ContextOS — Merge Readiness (${th.id})`);
+      console.log('══════════════════════════════════════════\n');
+      console.log(`  Overall Verdict: ${readiness.isReady ? 'READY TO MERGE ✓' : 'NOT READY ✗'}\n`);
+      for (const c of readiness.checks) {
+        const mark = c.passed ? '✓' : '✗';
+        console.log(`  ${mark} [${c.name.padEnd(24)}] ${c.message}`);
+      }
+      console.log('\n──────────────────────────────────────────\n');
+    }
+  } else {
+    console.error(`Unknown thread subcommand: ${subcmd}. Available: list, get, readiness`);
+    process.exit(1);
+  }
+
 // ── unknown ───────────────────────────────────────────────────────────────────
 } else {
   console.error(`Unknown command: ${command}`);