aether-colony 3.1.17 → 5.0.0

package/bin/cli.js

@@ -67,12 +67,16 @@ if (!HOME) {
 // Claude Code paths (global)
 const COMMANDS_SRC = path.join(PACKAGE_DIR, 'commands', 'ant');
 const COMMANDS_DEST = path.join(HOME, '.claude', 'commands', 'ant');
+const AGENTS_DEST = path.join(HOME, '.claude', 'agents', 'ant');
 
 // Hub paths
 const HUB_DIR = path.join(HOME, '.aether');
-const HUB_COMMANDS_CLAUDE = path.join(HUB_DIR, 'commands', 'claude');
-const HUB_COMMANDS_OPENCODE = path.join(HUB_DIR, 'commands', 'opencode');
-const HUB_AGENTS = path.join(HUB_DIR, 'agents');
+const HUB_SYSTEM_DIR = path.join(HUB_DIR, 'system');
+const HUB_COMMANDS_CLAUDE = path.join(HUB_SYSTEM_DIR, 'commands', 'claude');
+const HUB_COMMANDS_OPENCODE = path.join(HUB_SYSTEM_DIR, 'commands', 'opencode');
+const HUB_AGENTS = path.join(HUB_SYSTEM_DIR, 'agents');
+const HUB_AGENTS_CLAUDE = path.join(HUB_SYSTEM_DIR, 'agents-claude');
+const HUB_RULES = path.join(HUB_SYSTEM_DIR, 'rules');
 const HUB_REGISTRY = path.join(HUB_DIR, 'registry.json');
 const HUB_VERSION = path.join(HUB_DIR, 'version.json');
 
@@ -374,47 +378,6 @@ function removeDirSync(dir) {
   return count;
 }
 
-// System files allowlist — only these are copied during updates (never colony data)
-const SYSTEM_FILES = [
-  'aether-utils.sh',
-  'coding-standards.md',
-  'debugging.md',
-  'DISCIPLINES.md',
-  'learning.md',
-  'planning.md',
-  'QUEEN_ANT_ARCHITECTURE.md',
-  'tdd.md',
-  'verification-loop.md',
-  'verification.md',
-  'workers.md',
-  'docs/constraints.md',
-  'docs/pathogen-schema-example.json',
-  'docs/pathogen-schema.md',
-  'docs/pheromones.md',
-  'docs/progressive-disclosure.md',
-  'utils/atomic-write.sh',
-  'utils/colorize-log.sh',
-  'utils/file-lock.sh',
-  'utils/watch-spawn-tree.sh',
-];
-
-function copySystemFiles(srcDir, destDir) {
-  let count = 0;
-  for (const file of SYSTEM_FILES) {
-    const srcPath = path.join(srcDir, file);
-    const destPath = path.join(destDir, file);
-    if (fs.existsSync(srcPath)) {
-      fs.mkdirSync(path.dirname(destPath), { recursive: true });
-      fs.copyFileSync(srcPath, destPath);
-      if (file.endsWith('.sh')) {
-        fs.chmodSync(destPath, 0o755);
-      }
-      count++;
-    }
-  }
-  return count;
-}
-
 function readJsonSafe(filePath) {
   try {
     return JSON.parse(fs.readFileSync(filePath, 'utf8'));
@@ -585,65 +548,15 @@ function computeFileHash(filePath) {
   }
 }
 
-function syncSystemFilesWithCleanup(srcDir, destDir, opts) {
-  opts = opts || {};
-  const dryRun = opts.dryRun || false;
-
-  let copied = 0;
-  let skipped = 0;
-  for (const file of SYSTEM_FILES) {
-    const srcPath = path.join(srcDir, file);
-    const destPath = path.join(destDir, file);
-    if (fs.existsSync(srcPath)) {
-      if (!dryRun) {
-        // Compute hashes to determine if copy is needed
-        const srcHash = computeFileHash(srcPath);
-        const destHash = fs.existsSync(destPath) ? computeFileHash(destPath) : null;
-
-        if (srcHash === destHash) {
-          // Files are identical, skip copying
-          skipped++;
-          continue;
-        }
-
-        fs.mkdirSync(path.dirname(destPath), { recursive: true });
-        fs.copyFileSync(srcPath, destPath);
-        if (file.endsWith('.sh')) {
-          fs.chmodSync(destPath, 0o755);
-        }
-      }
-      copied++;
-    }
-  }
-
-  // Remove allowlisted files that no longer exist in src
-  const removed = [];
-  for (const file of SYSTEM_FILES) {
-    const srcPath = path.join(srcDir, file);
-    const destPath = path.join(destDir, file);
-    if (!fs.existsSync(srcPath) && fs.existsSync(destPath)) {
-      removed.push(file);
-      if (!dryRun) {
-        fs.unlinkSync(destPath);
-      }
-    }
-  }
-
-  if (!dryRun && removed.length > 0) {
-    cleanEmptyDirs(destDir);
-  }
-
-  return { copied, removed, skipped };
-}
-
 // Checkpoint allowlist - only these files are captured in checkpoints
 // NEVER include: data/, dreams/, oracle/, TO-DOs.md (user data)
+// Note: runtime/ was removed in v4.0 — .aether/ is published directly
 const CHECKPOINT_ALLOWLIST = [
   '.aether/*.md',                    // All .md files directly in .aether/
   '.claude/commands/ant/**',         // All files in .claude/commands/ant/ recursively
+  '.claude/agents/ant/**',           // All files in .claude/agents/ant/ recursively
   '.opencode/commands/ant/**',       // All files in .opencode/commands/ant/ recursively
   '.opencode/agents/**',             // All files in .opencode/agents/ recursively
-  'runtime/**',                      // All files in runtime/ recursively
   'bin/cli.js',                      // Specific file: bin/cli.js
 ];
 
@@ -835,7 +748,8 @@ function gitStashFiles(repoPath, files) {
 }
 
 // Directories to exclude from hub sync (user data, local state)
-const HUB_EXCLUDE_DIRS = ['data', 'dreams', 'checkpoints', 'locks', 'temp'];
+// 'rules' is excluded here because it is synced via a dedicated step (rulesSrc below)
+const HUB_EXCLUDE_DIRS = ['data', 'dreams', 'checkpoints', 'locks', 'temp', 'rules'];
 
 /**
  * Check if a path should be excluded from hub sync
@@ -955,6 +869,47 @@ function setupHub() {
   try {
     fs.mkdirSync(HUB_DIR, { recursive: true });
 
+    // MIGRATION: Check for old structure and migrate to system/
+    const oldStructureFiles = [
+      path.join(HUB_DIR, 'aether-utils.sh'),
+      path.join(HUB_DIR, 'workers.md'),
+    ];
+    const hasOldStructure = oldStructureFiles.some(f => fs.existsSync(f));
+    const hasNewStructure = fs.existsSync(HUB_SYSTEM_DIR);
+
+    if (hasOldStructure && !hasNewStructure) {
+      log('  Migrating hub to new structure...');
+      fs.mkdirSync(HUB_SYSTEM_DIR, { recursive: true });
+
+      // Move system files to system/
+      const systemFiles = ['aether-utils.sh', 'workers.md', 'CONTEXT.md', 'model-profiles.yaml'];
+      const systemDirs = ['docs', 'utils', 'commands', 'agents', 'schemas', 'exchange', 'templates', 'lib'];
+
+      for (const file of systemFiles) {
+        const oldPath = path.join(HUB_DIR, file);
+        if (fs.existsSync(oldPath)) {
+          fs.renameSync(oldPath, path.join(HUB_SYSTEM_DIR, file));
+        }
+      }
+
+      for (const dir of systemDirs) {
+        const oldPath = path.join(HUB_DIR, dir);
+        if (fs.existsSync(oldPath)) {
+          fs.renameSync(oldPath, path.join(HUB_SYSTEM_DIR, dir));
+        }
+      }
+
+      log('  Migration complete: system files moved to ~/.aether/system/');
+    }
+
+    // Create system/ directory structure
+    fs.mkdirSync(HUB_SYSTEM_DIR, { recursive: true });
+    fs.mkdirSync(path.join(HUB_SYSTEM_DIR, 'commands', 'claude'), { recursive: true });
+    fs.mkdirSync(path.join(HUB_SYSTEM_DIR, 'commands', 'opencode'), { recursive: true });
+    fs.mkdirSync(path.join(HUB_SYSTEM_DIR, 'agents'), { recursive: true });
+    fs.mkdirSync(path.join(HUB_SYSTEM_DIR, 'agents-claude'), { recursive: true });
+    fs.mkdirSync(path.join(HUB_SYSTEM_DIR, 'rules'), { recursive: true });
+
     // Read previous manifest for delta reporting
     const prevManifestRaw = readJsonSafe(path.join(HUB_DIR, 'manifest.json'));
     const prevManifest = prevManifestRaw && validateManifest(prevManifestRaw).valid ? prevManifestRaw : null;
@@ -962,21 +917,32 @@ function setupHub() {
       log(`  Warning: previous manifest is invalid, regenerating`);
     }
 
-    // Sync runtime/ -> ~/.aether/ (clean production files)
-    // runtime/ is the staging area - explicit allowlist via sync-to-runtime.sh
-    const runtimeSrc = path.join(PACKAGE_DIR, 'runtime');
-    if (fs.existsSync(runtimeSrc)) {
-      const result = syncAetherToHub(runtimeSrc, HUB_DIR);
-      log(`  Hub system: ${result.copied} files, ${result.skipped} unchanged -> ${HUB_DIR}`);
+    // Sync .aether/ -> ~/.aether/system/ (direct packaging, no staging)
+    // v4.0: .aether/ is published directly — runtime/ staging removed
+    const aetherSrc = path.join(PACKAGE_DIR, '.aether');
+    if (fs.existsSync(aetherSrc)) {
+      const result = syncAetherToHub(aetherSrc, HUB_SYSTEM_DIR);
+      log(`  Hub system: ${result.copied} files, ${result.skipped} unchanged -> ${HUB_SYSTEM_DIR}`);
       if (result.removed.length > 0) {
         log(`  Hub system: removed ${result.removed.length} stale files`);
         for (const f of result.removed) log(`    - ${f}`);
       }
     }
 
-    // Clean up legacy directories from old hub structure
+    // Migration message for users upgrading from pre-4.0 (runtime/ era)
+    const prevManifestForMigration = readJsonSafe(path.join(HUB_DIR, 'manifest.json'));
+    if (prevManifestForMigration && prevManifestForMigration.version && prevManifestForMigration.version.startsWith('3.')) {
+      log('');
+      log('  Distribution pipeline simplified (v4.0 change):');
+      log('  - runtime/ staging directory has been removed');
+      log('  - .aether/ is now published directly (private dirs excluded)');
+      log('  - Your colony state and data are unaffected');
+      log('  - See CHANGELOG.md for details');
+      log('');
+    }
+
+    // Clean up legacy directories from very old hub structure (pre-system/)
     const legacyDirs = [
-      path.join(HUB_DIR, 'system'),
       path.join(HUB_DIR, '.aether'),
       path.join(HUB_DIR, 'visualizations'),
     ];
@@ -991,7 +957,7 @@ function setupHub() {
       }
     }
 
-    // Sync .claude/commands/ant/ -> ~/.aether/commands/claude/
+    // Sync .claude/commands/ant/ -> ~/.aether/system/commands/claude/
     const claudeCmdSrc = fs.existsSync(COMMANDS_SRC)
       ? COMMANDS_SRC
       : path.join(PACKAGE_DIR, '.claude', 'commands', 'ant');
@@ -1004,7 +970,7 @@ function setupHub() {
       }
     }
 
-    // Sync .opencode/commands/ant/ -> ~/.aether/commands/opencode/
+    // Sync .opencode/commands/ant/ -> ~/.aether/system/commands/opencode/
     const opencodeCmdSrc = path.join(PACKAGE_DIR, '.opencode', 'commands', 'ant');
     if (fs.existsSync(opencodeCmdSrc)) {
       const result = syncDirWithCleanup(opencodeCmdSrc, HUB_COMMANDS_OPENCODE);
@@ -1015,7 +981,7 @@ function setupHub() {
       }
     }
 
-    // Sync .opencode/agents/ -> ~/.aether/agents/
+    // Sync .opencode/agents/ -> ~/.aether/system/agents/
     const agentsSrc = path.join(PACKAGE_DIR, '.opencode', 'agents');
     if (fs.existsSync(agentsSrc)) {
       const result = syncDirWithCleanup(agentsSrc, HUB_AGENTS);
@@ -1026,7 +992,30 @@ function setupHub() {
       }
     }
 
-    // Create/preserve registry.json
+    // Sync .claude/agents/ant/ -> ~/.aether/system/agents-claude/
+    const claudeAgentsSrc = path.join(PACKAGE_DIR, '.claude', 'agents', 'ant');
+    if (fs.existsSync(claudeAgentsSrc)) {
+      const result = syncDirWithCleanup(claudeAgentsSrc, HUB_AGENTS_CLAUDE);
+      log(`  Hub agents (claude): ${result.copied} files, ${result.skipped} unchanged -> ${HUB_AGENTS_CLAUDE}`);
+      if (result.removed.length > 0) {
+        log(`  Hub agents (claude): removed ${result.removed.length} stale files`);
+        for (const f of result.removed) log(`    - ${f}`);
+      }
+    }
+
+    // Sync rules/ from .aether/ -> ~/.aether/system/rules/
+    // v4.0: source is .aether/rules/ directly (no runtime/ staging)
+    const rulesSrc = path.join(PACKAGE_DIR, '.aether', 'rules');
+    if (fs.existsSync(rulesSrc)) {
+      const result = syncDirWithCleanup(rulesSrc, HUB_RULES);
+      log(`  Hub rules: ${result.copied} files -> ${HUB_RULES}`);
+      if (result.removed.length > 0) {
+        log(`  Hub rules: removed ${result.removed.length} stale files`);
+        for (const f of result.removed) log(`    - ${f}`);
+      }
+    }
+
+    // Create/preserve registry.json (at root, not in system/)
     if (!fs.existsSync(HUB_REGISTRY)) {
       writeJsonSync(HUB_REGISTRY, { schema_version: 1, repos: [] });
       log(`  Registry: initialized ${HUB_REGISTRY}`);
@@ -1034,7 +1023,7 @@ function setupHub() {
       log(`  Registry: preserved existing ${HUB_REGISTRY}`);
     }
 
-    // Generate and write manifest
+    // Generate and write manifest (at root, tracks everything)
     const manifest = generateManifest(HUB_DIR);
     const manifestPath = path.join(HUB_DIR, 'manifest.json');
     writeJsonSync(manifestPath, manifest);
@@ -1053,7 +1042,7 @@ function setupHub() {
       }
     }
 
-    // Write version.json
+    // Write version.json (at root)
     writeJsonSync(HUB_VERSION, { version: VERSION, updated_at: new Date().toISOString() });
     log(`  Hub version: ${VERSION}`);
   } catch (err) {
@@ -1079,7 +1068,7 @@ async function updateRepo(repoPath, sourceVersion, opts) {
   const currentVer = currentVersion ? currentVersion.version : 'unknown';
 
   // Target directories for git safety checks
-  const targetDirs = ['.aether', '.claude/commands/ant', '.opencode/commands/ant', '.opencode/agents'];
+  const targetDirs = ['.aether', '.claude/commands/ant', '.claude/agents/ant', '.claude/rules', '.opencode/commands/ant', '.opencode/agents'];
 
   // Git safety: check for dirty files in target directories (skip in dry-run mode)
   let dirtyFiles = [];
@@ -1101,17 +1090,25 @@ async function updateRepo(repoPath, sourceVersion, opts) {
     const systemCopied = result.sync_result?.system?.copied || 0;
     const commandsCopied = (result.sync_result?.commands?.copied || 0);
     const agentsCopied = result.sync_result?.agents?.copied || 0;
+    const rulesCopied = result.sync_result?.rules?.copied || 0;
+    const agentsClaudeCopied = result.sync_result?.agents_claude?.copied || 0;
 
     const systemRemoved = result.sync_result?.system?.removed?.length || 0;
     const commandsRemoved = result.sync_result?.commands?.removed?.length || 0;
     const agentsRemoved = result.sync_result?.agents?.removed?.length || 0;
+    const rulesRemoved = result.sync_result?.rules?.removed?.length || 0;
+    const agentsClaudeRemoved = result.sync_result?.agents_claude?.removed?.length || 0;
 
     const allRemovedFiles = [
       ...(result.sync_result?.system?.removed || []),
       ...(result.sync_result?.commands?.removed || []).map(f => `.claude/commands/ant/${f}`),
       ...(result.sync_result?.agents?.removed || []).map(f => `.opencode/agents/${f}`),
+      ...(result.sync_result?.rules?.removed || []).map(f => `.claude/rules/${f}`),
+      ...(result.sync_result?.agents_claude?.removed || []).map(f => `.claude/agents/ant/${f}`),
     ];
 
+    const cleanupResult = result.cleanup_result || { cleaned: [], failed: [] };
+
     return {
       status: result.status,
       from: currentVer,
@@ -1119,10 +1116,13 @@ async function updateRepo(repoPath, sourceVersion, opts) {
       system: systemCopied,
       commands: commandsCopied,
       agents: agentsCopied,
-      removed: systemRemoved + commandsRemoved + agentsRemoved,
+      rules: rulesCopied,
+      agentsClaude: agentsClaudeCopied,
+      removed: systemRemoved + commandsRemoved + agentsRemoved + rulesRemoved + agentsClaudeRemoved,
       removedFiles: allRemovedFiles,
       stashCreated: !!transaction.checkpoint?.stashRef,
       checkpoint_id: result.checkpoint_id,
+      cleanup: cleanupResult,
     };
   } catch (error) {
     // Handle UpdateError with recovery commands
@@ -1161,7 +1161,7 @@ program.on('option:quiet', () => {
 // Install command
 program
   .command('install')
-  .description('Install slash-commands to ~/.claude/commands/ant/ and set up distribution hub')
+  .description('Install commands and agents to ~/.claude/ and set up distribution hub')
   .action(wrapCommand(async () => {
     log(c.header(`aether-colony v${VERSION} — installing...`));
 
@@ -1188,6 +1188,17 @@ program
       }
     }
 
+    // Sync agents to ~/.claude/agents/ant/ (with orphan cleanup)
+    const repoAgents = path.join(PACKAGE_DIR, '.claude', 'agents', 'ant');
+    if (fs.existsSync(repoAgents)) {
+      const result = syncDirWithCleanup(repoAgents, AGENTS_DEST);
+      log(`  Agents (claude): ${result.copied} files -> ${AGENTS_DEST}`);
+      if (result.removed.length > 0) {
+        log(`  Agents (claude): removed ${result.removed.length} stale files`);
+        for (const f of result.removed) log(`    - ${f}`);
+      }
+    }
+
     // Set up distribution hub at ~/.aether/
     log('');
     log(c.colony('Setting up distribution hub...'));
@@ -1288,19 +1299,31 @@ program
             console.error(`  Skipping. Use --force to stash and update.`);
             dirty++;
           } else if (result.status === 'dry-run') {
-            log(`  Would update: ${repo.path} (${result.from} -> ${result.to}) [${result.system} system, ${result.commands} commands, ${result.agents} agents]`);
+            log(`  Would update: ${repo.path} (${result.from} -> ${result.to}) [${result.system} system, ${result.commands} commands, ${result.agents} agents, ${result.agentsClaude} claude agents]`);
             if (result.removed > 0) {
               log(`  Would remove ${result.removed} stale files:`);
               for (const f of result.removedFiles) log(`    - ${f}`);
             }
             updated++;
           } else if (result.status === 'updated') {
-            log(`  ${c.success('Updated:')} ${repo.path} (${result.from} -> ${result.to}) [${result.system} system, ${result.commands} commands, ${result.agents} agents]`);
+            log(`  ${c.success('Updated:')} ${repo.path} (${result.from} -> ${result.to}) [${result.system} system, ${result.commands} commands, ${result.agents} agents, ${result.agentsClaude} claude agents]`);
             if (result.removed > 0) {
               log(`  Removed ${result.removed} stale files:`);
               for (const f of result.removedFiles) log(`    - ${f}`);
               totalRemoved += result.removed;
             }
+            // Distribution chain cleanup reporting
+            if (result.cleanup && result.cleanup.cleaned.length > 0) {
+              for (const label of result.cleanup.cleaned) {
+                log(`    ${c.success('\u2713')} Removed ${label}`);
+              }
+            }
+            for (const failure of (result.cleanup?.failed || [])) {
+              log(`    ${c.error('\u2717')} Failed to remove ${failure.label}: ${failure.error}`);
+            }
+            if (result.cleanup && result.cleanup.cleaned.length === 0 && result.cleanup.failed.length === 0) {
+              log(`    Distribution chain: ${c.success('\u2713')} clean`);
+            }
             if (result.stashCreated) {
               log(`  Stash created. Recover with: cd ${repo.path} && git stash pop`);
             }
@@ -1324,7 +1347,7 @@ program
       }
 
       const label = dryRun ? 'would update' : 'updated';
-      let summary = `\nSummary: ${updated} ${label}, ${upToDate} up-to-date, ${pruned} pruned`;
+      let summary = `\nSummary: ${updated} ${label}, ${upToDate} up to date, ${pruned} pruned`;
       if (dirty > 0) summary += `, ${dirty} dirty (skipped)`;
       if (totalRemoved > 0) summary += `, ${totalRemoved} stale files removed`;
       console.log(summary);
@@ -1343,11 +1366,19 @@ program
         process.exit(getExitCode(error.code));
       }
 
+      const pendingPath = path.join(repoAether, '.update-pending');
+      const hasPending = fs.existsSync(pendingPath);
+
+      if (hasPending) {
+        console.log('Detected incomplete update, re-syncing...');
+        try { fs.unlinkSync(pendingPath); } catch { /* ignore */ }
+      }
+
       const currentVersion = readJsonSafe(path.join(repoAether, 'version.json'));
       const currentVer = currentVersion ? currentVersion.version : 'unknown';
 
-      if (!forceFlag && !dryRun && currentVer === sourceVersion) {
-        console.log(c.info(`Already up-to-date (v${sourceVersion}).`));
+      if (!hasPending && !forceFlag && !dryRun && currentVer === sourceVersion) {
+        console.log(c.info(`Already up to date (v${sourceVersion}).`));
         return;
       }
 
@@ -1371,7 +1402,7 @@ program
 
         if (result.status === 'dry-run') {
           console.log(`Would update: ${result.from} -> ${result.to}`);
-          console.log(`  ${result.system} system files, ${result.commands} command files, ${result.agents} agent files`);
+          console.log(`  ${result.system} system files, ${result.commands} command files, ${result.agents} agent files, ${result.agentsClaude} claude agent files`);
           if (result.removed > 0) {
             console.log(`  Would remove ${result.removed} stale files:`);
             for (const f of result.removedFiles) console.log(`    - ${f}`);
@@ -1381,11 +1412,23 @@ program
         }
 
         console.log(c.success(`Updated: ${result.from} -> ${result.to}`));
-        console.log(`  ${result.system} system files, ${result.commands} command files, ${result.agents} agent files, ${result.visualizations} visualization files`);
+        console.log(`  ${result.system} system files, ${result.commands} command files, ${result.agents} agent files, ${result.agentsClaude} claude agent files`);
         if (result.removed > 0) {
           console.log(`  Removed ${result.removed} stale files:`);
           for (const f of result.removedFiles) console.log(`    - ${f}`);
         }
+        // Distribution chain cleanup reporting
+        if (result.cleanup && result.cleanup.cleaned.length > 0) {
+          for (const label of result.cleanup.cleaned) {
+            console.log(`  ${c.success('\u2713')} Removed ${label}`);
+          }
+        }
+        for (const failure of (result.cleanup?.failed || [])) {
+          console.log(`  ${c.error('\u2717')} Failed to remove ${failure.label}: ${failure.error}`);
+        }
+        if (result.cleanup && result.cleanup.cleaned.length === 0 && result.cleanup.failed.length === 0) {
+          console.log(`  Distribution chain: ${c.success('\u2713')} clean`);
+        }
         if (result.stashCreated) {
           console.log('  Git stash created. Recover with: git stash pop');
         }
@@ -1969,6 +2012,85 @@ program
     console.log(tree);
   }));
 
+// Status command - Show colony status
+program
+  .command('status')
+  .description('Show colony status')
+  .option('-j, --json', 'Output as JSON')
+  .action(wrapCommand(async (options) => {
+    const repoPath = process.cwd();
+    const colonyStatePath = path.join(repoPath, '.aether', 'data', 'COLONY_STATE.json');
+
+    // Check if colony exists
+    if (!fs.existsSync(colonyStatePath)) {
+      console.log(c.warning('No colony found in current directory.'));
+      console.log(c.dim('Run /ant:init to create a new colony, or cd to a project with an existing colony.'));
+      return;
+    }
+
+    // Load colony state
+    let state;
+    try {
+      state = JSON.parse(fs.readFileSync(colonyStatePath, 'utf8'));
+    } catch (err) {
+      console.log(c.error('Could not read colony state.'));
+      console.log(c.dim(`Error: ${err.message}`));
+      console.log(c.dim('The colony state file may be corrupted. Consider running /ant:init to reinitialize.'));
+      return;
+    }
+
+    // JSON output
+    if (options.json) {
+      console.log(JSON.stringify(state, null, 2));
+      return;
+    }
+
+    // Dashboard output
+    console.log(c.header('Colony Status\n'));
+
+    // Goal
+    if (state.goal) {
+      console.log(`${c.queen('Goal:')} ${state.goal}`);
+    }
+
+    // State
+    if (state.state) {
+      const stateDisplay = state.state === 'BUILDING' ? c.success(state.state) :
+                          state.state === 'PLANNING' ? c.warning(state.state) :
+                          state.state === 'COMPLETED' ? c.success(state.state) :
+                          state.state;
+      console.log(`${c.colony('State:')} ${stateDisplay}`);
+    }
+
+    // Phase
+    if (state.current_phase !== undefined) {
+      console.log(`${c.info('Phase:')} ${state.current_phase}`);
+    }
+
+    // Version
+    if (state.version) {
+      console.log(`${c.dim('Version:')} ${state.version}`);
+    }
+
+    // Last updated
+    if (state.last_updated) {
+      const lastUpdated = new Date(state.last_updated);
+      const now = new Date();
+      const hoursAgo = Math.round((now - lastUpdated) / (1000 * 60 * 60));
+      const timeDisplay = hoursAgo < 1 ? 'just now' :
+                         hoursAgo < 24 ? `${hoursAgo} hours ago` :
+                         `${Math.round(hoursAgo / 24)} days ago`;
+      console.log(`${c.dim('Last updated:')} ${timeDisplay}`);
+    }
+
+    // Event count
+    if (state.events && state.events.length > 0) {
+      console.log(`${c.dim('Events:')} ${state.events.length}`);
+    }
+
+    console.log('');
+  }));
+
 // Nestmates command - List sibling colonies
 program
   .command('nestmates')
@@ -2242,7 +2364,6 @@ module.exports = {
   saveCheckpointMetadata,
   isUserData,
   syncDirWithCleanup,
-  syncSystemFilesWithCleanup,
   listFilesRecursive,
   cleanEmptyDirs
 };

package/bin/generate-commands.sh

@@ -212,9 +212,9 @@ check_content() {
 
     if [[ "$drift_count" -gt 0 ]]; then
         echo ""
-        log_error "Content drift detected in $drift_count file(s):"
+        log_warn "Content drift detected in $drift_count file(s) (non-blocking):"
         echo -e "$drift_files"
-        return 1
+        # Content drift is advisory — structural sync is what matters
     fi
 
     if [[ "$error_count" -gt 0 ]]; then

package/bin/lib/init.js

@@ -15,9 +15,10 @@ const path = require('path');
 const HOME = process.env.HOME || process.env.USERPROFILE;
 const HUB_DIR = HOME ? path.join(HOME, '.aether') : null;
 const HUB_SYSTEM = HUB_DIR ? path.join(HUB_DIR, 'system') : null;
-const HUB_COMMANDS_CLAUDE = HUB_DIR ? path.join(HUB_DIR, 'commands', 'claude') : null;
-const HUB_COMMANDS_OPENCODE = HUB_DIR ? path.join(HUB_DIR, 'commands', 'opencode') : null;
-const HUB_AGENTS = HUB_DIR ? path.join(HUB_DIR, 'agents') : null;
+const HUB_COMMANDS_CLAUDE = HUB_SYSTEM ? path.join(HUB_SYSTEM, 'commands', 'claude') : null;
+const HUB_COMMANDS_OPENCODE = HUB_SYSTEM ? path.join(HUB_SYSTEM, 'commands', 'opencode') : null;
+const HUB_AGENTS = HUB_SYSTEM ? path.join(HUB_SYSTEM, 'agents') : null;
+const HUB_AGENTS_CLAUDE = HUB_SYSTEM ? path.join(HUB_SYSTEM, 'agents-claude') : null;
 const HUB_REGISTRY = HUB_DIR ? path.join(HUB_DIR, 'registry.json') : null;
 const HUB_VERSION = HUB_DIR ? path.join(HUB_DIR, 'version.json') : null;
 
@@ -381,6 +382,15 @@ async function initializeRepo(repoPath, options = {}) {
     }
   }
 
+  // Sync claude agents
+  if (HUB_AGENTS_CLAUDE && fs.existsSync(HUB_AGENTS_CLAUDE)) {
+    const destClaudeAgents = path.join(repoPath, '.claude', 'agents', 'ant');
+    const claudeAgentsResult = syncFiles(HUB_AGENTS_CLAUDE, destClaudeAgents);
+    if (!quiet && claudeAgentsResult.copied > 0) {
+      console.log(`  Agents (claude): ${claudeAgentsResult.copied} copied, ${claudeAgentsResult.skipped} skipped`);
+    }
+  }
+
   // Create directory structure (in case some weren't created by sync)
   const dirs = [
     path.join(repoPath, '.aether', 'data'),