@jaguilar87/gaia 5.0.0-rc1

package/bin/gaia-update.js

@@ -0,0 +1,816 @@
+#!/usr/bin/env node
+
+/**
+ * @jaguilar87/gaia - Update script
+ *
+ * Runs automatically on npm install/update (postinstall hook).
+ * Also available as: npx gaia-update
+ *
+ * Behavior:
+ * - First-time install (.claude/ doesn't exist):
+ *   1. Check Python 3 is available
+ *   2. Run gaia-scan --npm-postinstall to create .claude/, symlinks, settings, project-context
+ *   3. Create plugin-registry.json
+ *   4. Merge permissions into settings.local.json
+ *   5. Merge hooks into settings.local.json
+ *   6. Fall through to verification
+ * - Update (.claude/ exists):
+ *   1. Show version transition (previous → current)
+ *   2. settings.json: create only if missing (non-invasive, never overwrites)
+ *   3. Merge permissions, env vars, and agent key into settings.local.json (union, preserves user config)
+ *   4. Merge hooks from hooks.json into settings.local.json (npm mode requires this)
+ *   5. Symlinks: recreate if missing, fix broken ones
+ *   5. Verify: hooks, python, project-context, config files
+ *   6. Report: summary with any issues found
+ *
+ * Usage:
+ *   npm update @jaguilar87/gaia   # Automatic via postinstall
+ *   npx gaia-update                   # Manual trigger
+ *   npx gaia-update --verbose         # Show all checks
+ */
+
+import { fileURLToPath } from 'url';
+import { dirname, join, relative } from 'path';
+import fs from 'fs/promises';
+import { existsSync, realpathSync } from 'fs';
+import { exec } from 'child_process';
+import { promisify } from 'util';
+import chalk from 'chalk';
+import ora from 'ora';
+import { findPython } from './python-detect.js';
+
+const execAsync = promisify(exec);
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = dirname(__filename);
+const CWD = process.env.INIT_CWD || process.cwd();
+const VERBOSE = process.argv.includes('--verbose') || process.argv.includes('-v');
+
+// Use junctions on Windows (no admin required), regular symlinks elsewhere
+const LINK_TYPE = process.platform === 'win32' ? 'junction' : 'dir';
+
+// ============================================================================
+// Version Detection
+// ============================================================================
+
+async function detectVersions() {
+  const current = await readPackageVersion(join(__dirname, '..', 'package.json'));
+
+  // Try to find previous version from the installed package.json backup or lock
+  let previous = null;
+  try {
+    const lockPath = join(CWD, 'package-lock.json');
+    if (existsSync(lockPath)) {
+      const lock = JSON.parse(await fs.readFile(lockPath, 'utf-8'));
+      const dep = lock.packages?.['node_modules/@jaguilar87/gaia']
+        || lock.dependencies?.['@jaguilar87/gaia'];
+      if (dep) previous = dep.version;
+    }
+  } catch { /* ignore */ }
+
+  return { previous, current };
+}
+
+async function readPackageVersion(path) {
+  try {
+    const pkg = JSON.parse(await fs.readFile(path, 'utf-8'));
+    return pkg.version;
+  } catch {
+    return null;
+  }
+}
+
+// ============================================================================
+// Update Steps
+// ============================================================================
+
+async function updateSettingsJson() {
+  const spinner = ora('Checking settings.json...').start();
+  try {
+    const settingsPath = join(CWD, '.claude', 'settings.json');
+
+    if (!existsSync(join(CWD, '.claude'))) {
+      spinner.info('Skipped (.claude/ not found)');
+      return false;
+    }
+
+    // Non-invasive: only create if missing. Never overwrite.
+    // Hooks come from hooks.json (auto-discovered via symlink).
+    // Env vars and permissions live in settings.local.json.
+    if (existsSync(settingsPath)) {
+      spinner.succeed('settings.json already exists (not overwriting)');
+      return false;
+    }
+
+    await fs.writeFile(settingsPath, '{}\n');
+    spinner.succeed('settings.json created (minimal — hooks from hooks.json)');
+    return true;
+  } catch (error) {
+    spinner.fail(`settings.json: ${error.message}`);
+    return false;
+  }
+}
+
+async function updateLocalPermissions() {
+  const spinner = ora('Merging permissions into settings.local.json...').start();
+  try {
+    const claudeDir = join(CWD, '.claude');
+    const localPath = join(claudeDir, 'settings.local.json');
+
+    if (!existsSync(claudeDir)) {
+      spinner.info('Skipped (.claude/ not found)');
+      return false;
+    }
+
+    // Load existing settings.local.json — preserve everything (enabledPlugins, MCP servers, etc.)
+    let existing = {};
+    if (existsSync(localPath)) {
+      try {
+        existing = JSON.parse(await fs.readFile(localPath, 'utf-8'));
+      } catch {
+        existing = {};
+      }
+    }
+
+    // Track what changed
+    let changed = false;
+
+    // Set the orchestrator agent identity (always, even if Python extraction fails)
+    if (existing.agent !== 'gaia-orchestrator') {
+      existing.agent = 'gaia-orchestrator';
+      changed = true;
+    }
+
+    // Add env vars (smart merge: add if not present, don't overwrite)
+    existing.env = existing.env || {};
+    if (!('CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS' in existing.env)) {
+      existing.env.CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS = '1';
+      changed = true;
+    }
+
+    // Load permissions from plugin_setup.py — the single source of truth.
+    // We use ast.literal_eval to extract the constants without importing
+    // the module (which has relative imports that fail standalone).
+    let gaiaPerms;
+    try {
+      const setupPath = join(__dirname, '..', 'hooks', 'modules', 'core', 'plugin_setup.py');
+      const pythonCmd = findPython() || 'python3';
+
+      // Write the extraction script to a temp file instead of using -c with
+      // inline code.  This avoids shell quoting issues on Windows where
+      // backslash paths and nested quotes break the inline Python string.
+      const tempScript = join(claudeDir, '.gaia-extract-perms.py');
+      const scriptContent = `
+import ast, json, re, sys
+
+setup_path = sys.argv[1]
+source = open(setup_path, encoding="utf-8").read()
+
+# Extract _DENY_RULES list
+deny_match = re.search(r'^_DENY_RULES\\s*=\\s*\\[', source, re.MULTILINE)
+if deny_match:
+    bracket_start = deny_match.start() + source[deny_match.start():].index('[')
+    depth, i = 0, bracket_start
+    for i, ch in enumerate(source[bracket_start:], bracket_start):
+        if ch == '[': depth += 1
+        elif ch == ']': depth -= 1
+        if depth == 0: break
+    deny_rules = ast.literal_eval(source[bracket_start:i+1])
+else:
+    deny_rules = []
+
+# Extract OPS_PERMISSIONS allow list
+ops_match = re.search(r'^OPS_PERMISSIONS\\s*=', source, re.MULTILINE)
+if ops_match:
+    bracket_start = source.index('{', ops_match.start())
+    depth, i = 0, bracket_start
+    for i, ch in enumerate(source[bracket_start:], bracket_start):
+        if ch == '{': depth += 1
+        elif ch == '}': depth -= 1
+        if depth == 0: break
+    # Replace _DENY_RULES reference with actual list for eval
+    ops_str = source[bracket_start:i+1].replace('_DENY_RULES', json.dumps(deny_rules))
+    ops_perms = ast.literal_eval(ops_str)
+else:
+    ops_perms = {'permissions': {'allow': [], 'deny': deny_rules, 'ask': []}}
+
+print(json.dumps(ops_perms))
+`;
+      await fs.writeFile(tempScript, scriptContent);
+      try {
+        const { stdout } = await execAsync(
+          `${pythonCmd} "${tempScript}" "${setupPath}"`,
+          { timeout: 10000 }
+        );
+        gaiaPerms = JSON.parse(stdout.trim());
+      } finally {
+        // Clean up temp script
+        try { await fs.unlink(tempScript); } catch { /* ignore */ }
+      }
+    } catch (pyError) {
+      spinner.warn(`Could not load permissions from Python — ${pyError.message || 'unknown error'}`);
+      // Still write agent and env changes even if permissions extraction fails
+      if (changed) {
+        await fs.writeFile(localPath, JSON.stringify(existing, null, 2) + '\n');
+        spinner.succeed('settings.local.json agent and env merged (permissions skipped)');
+        return true;
+      }
+      return false;
+    }
+
+    const ourAllow = new Set(gaiaPerms.permissions.allow || []);
+    const ourDeny = new Set(gaiaPerms.permissions.deny || []);
+
+    const perms = existing.permissions || {};
+    const currentAllow = new Set(perms.allow || []);
+    const currentDeny = new Set(perms.deny || []);
+
+    // Union merge — add ours without removing user's
+    const mergedAllow = [...new Set([...currentAllow, ...ourAllow])].sort();
+    const mergedDeny = [...new Set([...currentDeny, ...ourDeny])].sort();
+
+    // Check if permissions changed
+    const allowChanged = mergedAllow.length !== currentAllow.size
+      || mergedAllow.some(r => !currentAllow.has(r));
+    const denyChanged = mergedDeny.length !== currentDeny.size
+      || mergedDeny.some(r => !currentDeny.has(r));
+
+    if (allowChanged || denyChanged) {
+      existing.permissions = existing.permissions || {};
+      existing.permissions.allow = mergedAllow;
+      existing.permissions.deny = mergedDeny;
+      existing.permissions.ask = existing.permissions.ask || [];
+      changed = true;
+    }
+
+    if (!changed) {
+      spinner.succeed('settings.local.json permissions already up to date');
+      return false;
+    }
+
+    await fs.writeFile(localPath, JSON.stringify(existing, null, 2) + '\n');
+    spinner.succeed('settings.local.json permissions, env, and agent merged');
+    return true;
+  } catch (error) {
+    spinner.fail(`settings.local.json: ${error.message}`);
+    return false;
+  }
+}
+
+async function updateLocalHooks() {
+  const spinner = ora('Merging hooks into settings.local.json...').start();
+  try {
+    const claudeDir = join(CWD, '.claude');
+    const localPath = join(claudeDir, 'settings.local.json');
+
+    if (!existsSync(claudeDir)) {
+      spinner.info('Skipped (.claude/ not found)');
+      return false;
+    }
+
+    // Read hooks.json from the installed package
+    const hooksJsonPath = join(__dirname, '..', 'hooks', 'hooks.json');
+    if (!existsSync(hooksJsonPath)) {
+      spinner.warn('hooks.json not found in package');
+      return false;
+    }
+
+    let hooksData;
+    try {
+      hooksData = JSON.parse(await fs.readFile(hooksJsonPath, 'utf-8'));
+    } catch {
+      spinner.warn('hooks.json is invalid JSON');
+      return false;
+    }
+
+    // Unwrap outer "hooks" key if present
+    const sourceHooks = hooksData.hooks || hooksData;
+
+    // Resolve absolute path to hooks directory so hooks work regardless of
+    // CWD at execution time (Stop/PostCompact hooks may run from unknown CWD)
+    const hooksSymlink = join(claudeDir, 'hooks');
+    let hooksAbs;
+    try {
+      hooksAbs = realpathSync(hooksSymlink);
+    } catch {
+      hooksAbs = hooksSymlink; // Fallback if symlink not yet created
+    }
+    const convertCommand = (cmd) => {
+      return cmd.replace(/\$\{CLAUDE_PLUGIN_ROOT\}\/hooks\//g, `${hooksAbs}/`);
+    };
+
+    const convertedHooks = {};
+    for (const [event, entries] of Object.entries(sourceHooks)) {
+      convertedHooks[event] = entries.map(entry => {
+        const converted = { ...entry };
+        if (converted.hooks) {
+          converted.hooks = converted.hooks.map(h => ({
+            ...h,
+            command: h.command ? convertCommand(h.command) : h.command,
+          }));
+        }
+        return converted;
+      });
+    }
+
+    // Load existing settings.local.json
+    let existing = {};
+    if (existsSync(localPath)) {
+      try {
+        existing = JSON.parse(await fs.readFile(localPath, 'utf-8'));
+      } catch {
+        existing = {};
+      }
+    }
+
+    // Migrate existing relative .claude/hooks/ paths to absolute
+    const existingHooks = existing.hooks || {};
+    let changed = false;
+
+    for (const [event, entries] of Object.entries(existingHooks)) {
+      for (const entry of entries) {
+        for (const h of (entry.hooks || [])) {
+          if (h.command && h.command.startsWith('.claude/hooks/')) {
+            h.command = h.command.replace('.claude/hooks/', `${hooksAbs}/`);
+            changed = true;
+          }
+        }
+      }
+    }
+
+    // Smart merge: for each hook event, deduplicate by command string
+    for (const [event, newEntries] of Object.entries(convertedHooks)) {
+      if (!existingHooks[event]) {
+        existingHooks[event] = newEntries;
+        changed = true;
+        continue;
+      }
+
+      // Collect existing command strings for deduplication
+      const existingCommands = new Set();
+      for (const entry of existingHooks[event]) {
+        for (const h of (entry.hooks || [])) {
+          if (h.command) existingCommands.add(h.command);
+        }
+      }
+
+      // Add new entries whose commands are not already present
+      for (const newEntry of newEntries) {
+        const newCommands = (newEntry.hooks || []).map(h => h.command).filter(Boolean);
+        const allPresent = newCommands.length > 0 && newCommands.every(c => existingCommands.has(c));
+        if (!allPresent) {
+          existingHooks[event].push(newEntry);
+          changed = true;
+        }
+      }
+    }
+
+    if (!changed) {
+      spinner.succeed('settings.local.json hooks already up to date');
+      return false;
+    }
+
+    existing.hooks = existingHooks;
+    await fs.writeFile(localPath, JSON.stringify(existing, null, 2) + '\n');
+    spinner.succeed('settings.local.json hooks merged');
+    return true;
+  } catch (error) {
+    spinner.fail(`hooks merge: ${error.message}`);
+    return false;
+  }
+}
+
+async function updateSymlinks() {
+  const spinner = ora('Checking symlinks...').start();
+  try {
+    const claudeDir = join(CWD, '.claude');
+    if (!existsSync(claudeDir)) {
+      spinner.info('Skipped (.claude/ not found)');
+      return { updated: false, fixed: 0, total: 0 };
+    }
+
+    const packagePath = join(CWD, 'node_modules', '@jaguilar87', 'gaia-ops');
+    if (!existsSync(packagePath)) {
+      spinner.fail('Package not found in node_modules');
+      return { updated: false, fixed: 0, total: 0 };
+    }
+
+    const relativePath = relative(claudeDir, packagePath);
+    const symlinks = ['agents', 'tools', 'hooks', 'commands', 'templates', 'config', 'skills'];
+    let fixed = 0;
+
+    for (const name of symlinks) {
+      const link = join(claudeDir, name);
+      // Junctions on Windows require absolute targets; symlinks on Unix use relative
+      const target = process.platform === 'win32'
+        ? join(packagePath, name)
+        : join(relativePath, name);
+
+      if (!existsSync(link)) {
+        try {
+          await fs.symlink(target, link, LINK_TYPE);
+          fixed++;
+        } catch { /* skip */ }
+      } else {
+        // Check if symlink is broken (target doesn't resolve)
+        try {
+          await fs.realpath(link);
+        } catch {
+          // Broken symlink — remove and recreate
+          try {
+            await fs.unlink(link);
+            await fs.symlink(target, link, LINK_TYPE);
+            fixed++;
+          } catch { /* skip */ }
+        }
+      }
+    }
+
+    // CHANGELOG.md
+    const changelogLink = join(claudeDir, 'CHANGELOG.md');
+    if (!existsSync(changelogLink)) {
+      try {
+        if (process.platform === 'win32') {
+          // Junctions only work for directories; copy the file on Windows
+          await fs.copyFile(join(packagePath, 'CHANGELOG.md'), changelogLink);
+        } else {
+          await fs.symlink(join(relativePath, 'CHANGELOG.md'), changelogLink);
+        }
+        fixed++;
+      } catch { /* skip */ }
+    }
+
+    const total = symlinks.length + 1;
+    if (fixed > 0) {
+      spinner.succeed(`Symlinks: fixed ${fixed}/${total}`);
+    } else {
+      spinner.succeed(`Symlinks: ${total}/${total} valid`);
+    }
+
+    return { updated: fixed > 0, fixed, total };
+  } catch (error) {
+    spinner.fail(`Symlinks: ${error.message}`);
+    return { updated: false, fixed: 0, total: 0 };
+  }
+}
+
+// ============================================================================
+// FTS5 Backfill Safety-Net
+// ============================================================================
+//
+// On upgrade paths, a project may already have episodes in
+// `.claude/project-context/episodic-memory/index.json` but an empty FTS5
+// `search.db`. This happens when episodes were produced before FTS5 was wired
+// in, or when `search.db` was deleted for any reason. Fresh installs have
+// zero episodes and will no-op through this check.
+//
+// Opt-out: pass `--no-fts5-backfill` (or set GAIA_SKIP_FTS5_BACKFILL=1).
+
+async function maybeBackfillFts5() {
+  if (process.argv.includes('--no-fts5-backfill')
+      || process.env.GAIA_SKIP_FTS5_BACKFILL === '1') {
+    return;
+  }
+
+  const claudeDir = join(CWD, '.claude');
+  if (!existsSync(claudeDir)) return;
+
+  const memoryDir = join(claudeDir, 'project-context', 'episodic-memory');
+  const indexPath = join(memoryDir, 'index.json');
+  const dbPath = join(memoryDir, 'search.db');
+
+  if (!existsSync(indexPath)) return; // Fresh install — nothing to backfill
+
+  let total = 0;
+  try {
+    const idx = JSON.parse(await fs.readFile(indexPath, 'utf-8'));
+    total = Array.isArray(idx.episodes) ? idx.episodes.length : 0;
+  } catch {
+    return; // Unreadable index — let doctor handle it
+  }
+  if (total === 0) return; // No episodes to index
+
+  if (!existsSync(dbPath)) return; // doctor --fix will create it on first use
+
+  // Query FTS5 count via python3 subprocess (sqlite3 binary may not be on PATH
+  // on Windows; python3 is already a hard requirement for gaia-ops hooks).
+  const pyCmd = findPython();
+  if (!pyCmd) return; // Python missing — the health check will report it
+
+  const spinner = ora('Checking FTS5 backfill status...').start();
+  let indexed;
+  try {
+    const probeScript = join(memoryDir, '.gaia-fts5-probe.py');
+    const probeContent = `
+import sqlite3, sys
+try:
+    con = sqlite3.connect(sys.argv[1])
+    cur = con.execute("SELECT COUNT(*) FROM episodes_fts")
+    print(cur.fetchone()[0])
+except Exception:
+    print(-1)
+`;
+    await fs.writeFile(probeScript, probeContent);
+    try {
+      const { stdout } = await execAsync(
+        `${pyCmd} "${probeScript}" "${dbPath}"`,
+        { timeout: 10000 }
+      );
+      indexed = parseInt(stdout.trim(), 10);
+    } finally {
+      try { await fs.unlink(probeScript); } catch { /* ignore */ }
+    }
+  } catch {
+    spinner.info('FTS5 probe skipped (sqlite3/python issue)');
+    return;
+  }
+
+  if (!Number.isFinite(indexed) || indexed < 0) {
+    spinner.info('FTS5 probe inconclusive (table may not exist yet)');
+    return;
+  }
+
+  // If indexed is already >=90% of total, no backfill needed — matches doctor
+  // threshold exactly so we don't loop users through unnecessary work.
+  if (indexed / total >= 0.9) {
+    spinner.succeed(`FTS5 backfill: ${indexed}/${total} episodes indexed (ok)`);
+    return;
+  }
+
+  spinner.text = `FTS5 backfill: rebuilding ${total} episodes (had ${indexed})...`;
+
+  // Invoke backfill via the gaia CLI doctor --fix. We call `python3 bin/gaia
+  // doctor --fix` from the installed package directory, with CWD set to the
+  // consumer project so doctor locates the right .claude/ tree.
+  const packageDir = join(__dirname, '..');
+  const gaiaEntry = join(packageDir, 'bin', 'gaia');
+
+  if (!existsSync(gaiaEntry)) {
+    spinner.warn('FTS5 backfill skipped (bin/gaia not found)');
+    return;
+  }
+
+  try {
+    const { stdout, stderr } = await execAsync(
+      `${pyCmd} "${gaiaEntry}" doctor --fix`,
+      { timeout: 120000, cwd: CWD }
+    );
+    if (VERBOSE) {
+      if (stdout) console.log(chalk.gray(stdout));
+      if (stderr) console.log(chalk.yellow(stderr));
+    }
+
+    // Re-probe to report outcome.
+    const probeScript = join(memoryDir, '.gaia-fts5-probe.py');
+    const probeContent = `
+import sqlite3, sys
+try:
+    con = sqlite3.connect(sys.argv[1])
+    cur = con.execute("SELECT COUNT(*) FROM episodes_fts")
+    print(cur.fetchone()[0])
+except Exception:
+    print(-1)
+`;
+    await fs.writeFile(probeScript, probeContent);
+    let newIndexed = -1;
+    try {
+      const { stdout: newOut } = await execAsync(
+        `${pyCmd} "${probeScript}" "${dbPath}"`,
+        { timeout: 10000 }
+      );
+      newIndexed = parseInt(newOut.trim(), 10);
+    } finally {
+      try { await fs.unlink(probeScript); } catch { /* ignore */ }
+    }
+
+    if (Number.isFinite(newIndexed) && newIndexed > indexed) {
+      spinner.succeed(`FTS5 backfill: rebuilt ${newIndexed}/${total} episodes`);
+    } else {
+      spinner.warn(`FTS5 backfill completed but index still at ${newIndexed}/${total}`);
+    }
+  } catch (err) {
+    spinner.warn(`FTS5 backfill skipped: ${err.message || 'unknown error'}`);
+  }
+}
+
+// ============================================================================
+// Post-Update Verification
+// ============================================================================
+
+async function runVerification() {
+  const spinner = ora('Verifying installation health...').start();
+  const checks = [];
+  const issues = [];
+
+  // 1. Hooks exist and are reachable
+  const hookFiles = ['pre_tool_use.py', 'post_tool_use.py', 'subagent_stop.py'];
+  for (const hook of hookFiles) {
+    const path = join(CWD, '.claude', 'hooks', hook);
+    if (existsSync(path)) {
+      checks.push({ name: hook, ok: true });
+    } else {
+      checks.push({ name: hook, ok: false });
+      issues.push(`Hook missing: .claude/hooks/${hook}`);
+    }
+  }
+
+  // 2. Python available (try python3 first, fall back to python on Windows)
+  {
+    const pyCmd = findPython();
+    if (pyCmd) {
+      const { stdout } = await execAsync(`${pyCmd} --version`, { timeout: 5000 });
+      checks.push({ name: 'python3', ok: true, detail: stdout.trim() });
+    } else {
+      checks.push({ name: 'python3', ok: false });
+      issues.push('Python 3 not found (required for hooks)');
+    }
+  }
+
+  // 3. project-context.json exists and is valid
+  const ctxPath = join(CWD, '.claude', 'project-context', 'project-context.json');
+  if (existsSync(ctxPath)) {
+    try {
+      const ctx = JSON.parse(await fs.readFile(ctxPath, 'utf-8'));
+      const sections = Object.keys(ctx.sections || {}).length;
+      checks.push({ name: 'project-context.json', ok: sections >= 3, detail: `${sections} sections` });
+      if (sections < 3) issues.push('project-context.json has fewer than 3 sections');
+    } catch {
+      checks.push({ name: 'project-context.json', ok: false });
+      issues.push('project-context.json is invalid JSON');
+    }
+  } else {
+    checks.push({ name: 'project-context.json', ok: false });
+    issues.push('project-context.json not found (run gaia-scan)');
+  }
+
+  // 4. Config files accessible
+  const configFiles = ['git_standards.json', 'universal-rules.json', 'surface-routing.json'];
+  for (const cfg of configFiles) {
+    const path = join(CWD, '.claude', 'config', cfg);
+    if (existsSync(path)) {
+      checks.push({ name: cfg, ok: true });
+    } else {
+      checks.push({ name: cfg, ok: false });
+      if (VERBOSE) issues.push(`Config missing: .claude/config/${cfg}`);
+    }
+  }
+
+  // 5. Agent definitions accessible
+  const agentFiles = ['gaia-orchestrator.md', 'gaia-operator.md', 'terraform-architect.md', 'gitops-operator.md', 'cloud-troubleshooter.md', 'developer.md', 'gaia-system.md', 'gaia-planner.md'];
+  let agentsOk = 0;
+  for (const agent of agentFiles) {
+    if (existsSync(join(CWD, '.claude', 'agents', agent))) agentsOk++;
+  }
+  checks.push({ name: 'agent definitions', ok: agentsOk === agentFiles.length, detail: `${agentsOk}/${agentFiles.length}` });
+  if (agentsOk < agentFiles.length) issues.push(`${agentFiles.length - agentsOk} agent definition(s) missing`);
+
+  // 6. hooks.json exists (hooks are auto-discovered from hooks directory)
+  const hooksJsonPath = join(CWD, '.claude', 'hooks', 'hooks.json');
+  if (existsSync(hooksJsonPath)) {
+    try {
+      const hooksData = JSON.parse(await fs.readFile(hooksJsonPath, 'utf-8'));
+      const hasHooks = hooksData.hooks && Object.keys(hooksData.hooks).length > 0;
+      checks.push({ name: 'hooks.json', ok: hasHooks });
+      if (!hasHooks) issues.push('hooks.json has no hooks configured');
+    } catch {
+      checks.push({ name: 'hooks.json', ok: false });
+      issues.push('hooks.json is invalid');
+    }
+  } else {
+    checks.push({ name: 'hooks.json', ok: false });
+    issues.push('hooks.json not found (hooks symlink may be broken)');
+  }
+
+  const passed = checks.filter(c => c.ok).length;
+  const total = checks.length;
+
+  if (issues.length === 0) {
+    spinner.succeed(`Health check: ${passed}/${total} passed`);
+  } else {
+    spinner.warn(`Health check: ${passed}/${total} passed, ${issues.length} issue(s)`);
+  }
+
+  return { checks, issues, passed, total };
+}
+
+// ============================================================================
+// Main
+// ============================================================================
+
+async function runFreshInstall() {
+  const packageDir = join(__dirname, '..');
+  const scanScript = join(packageDir, 'bin', 'gaia-scan.py');
+  const { current } = await detectVersions();
+
+  console.log(chalk.cyan(`\n  gaia-ops ${chalk.green(current)} — fresh install\n`));
+
+  // 1. Check Python 3 is available (try python3, then python)
+  const spinner = ora('Checking Python 3...').start();
+  const pyCmd = findPython();
+  if (pyCmd) {
+    spinner.succeed(`Python 3 found (${pyCmd})`);
+  } else {
+    spinner.warn('Python 3 not found — skipping project setup');
+    console.log(chalk.gray('  Install Python 3.9+ and run: npx gaia-scan\n'));
+    return;
+  }
+
+  // 2. Run gaia-scan --npm-postinstall
+  const scanSpinner = ora('Running gaia-scan...').start();
+  try {
+    const { stdout, stderr } = await execAsync(
+      `${pyCmd} "${scanScript}" --npm-postinstall --root "${CWD}"`,
+      { timeout: 60000 }
+    );
+    scanSpinner.succeed('Project scanned and configured');
+    if (VERBOSE && stdout) console.log(chalk.gray(stdout));
+    if (VERBOSE && stderr) console.log(chalk.yellow(stderr));
+  } catch (error) {
+    scanSpinner.warn('gaia-scan encountered issues (non-fatal)');
+    if (VERBOSE && error.stderr) console.log(chalk.gray(error.stderr));
+  }
+
+  // 3. Create plugin-registry.json (in .claude/, same path Python hooks expect)
+  try {
+    const claudeDirPath = join(CWD, '.claude');
+    if (!existsSync(claudeDirPath)) {
+      await fs.mkdir(claudeDirPath, { recursive: true });
+    }
+    const registryPath = join(claudeDirPath, 'plugin-registry.json');
+    const registry = {
+      installed: [{ name: 'gaia-ops', version: current || 'unknown' }],
+      source: 'npm-postinstall',
+    };
+    await fs.writeFile(registryPath, JSON.stringify(registry, null, 2) + '\n');
+  } catch {
+    // Non-fatal — plugin-registry is a convenience, not critical
+  }
+
+  // 4. Merge permissions into settings.local.json (same approach as plugin mode)
+  await updateLocalPermissions();
+
+  // 5. Merge hooks into settings.local.json (npm mode — Claude Code reads hooks from settings, not hooks.json)
+  await updateLocalHooks();
+}
+
+async function main() {
+  process.stderr.write('[DEPRECATED] gaia-update.js is deprecated. Use: python3 bin/gaia update\n[DEPRECATED] Migration guide: see CHANGELOG.md\n');
+
+  const claudeDir = join(CWD, '.claude');
+  const isUpdate = existsSync(claudeDir);
+
+  if (!isUpdate) {
+    // First-time install — run gaia-scan to bootstrap everything
+    await runFreshInstall();
+  } else {
+    // Version info
+    const { previous, current } = await detectVersions();
+    const versionLine = previous && previous !== current
+      ? `${chalk.gray(previous)} → ${chalk.green(current)}`
+      : chalk.green(current);
+
+    console.log(chalk.cyan(`\n  gaia-ops update ${versionLine}\n`));
+
+    // Step 1-4: Update files
+    await updateSettingsJson();
+    await updateLocalPermissions();
+    await updateLocalHooks();
+    await updateSymlinks();
+  }
+
+  // Ensure plugin-registry.json exists in .claude/ (both fresh and update)
+  try {
+    const registryPath = join(CWD, '.claude', 'plugin-registry.json');
+    if (!existsSync(registryPath)) {
+      const { current } = await detectVersions();
+      const registry = {
+        installed: [{ name: 'gaia-ops', version: current || 'unknown' }],
+        source: 'npm-postinstall',
+      };
+      await fs.writeFile(registryPath, JSON.stringify(registry, null, 2) + '\n');
+    }
+  } catch { /* non-fatal */ }
+
+  // FTS5 backfill safety-net (no-op on fresh install; only fires when
+  // episodes exist in index.json but search.db is under-indexed)
+  await maybeBackfillFts5();
+
+  // Verify (runs for both fresh install and update)
+  const { issues, passed, total } = await runVerification();
+
+  console.log('');
+  if (issues.length > 0) {
+    console.log(chalk.yellow(`  ${issues.length} issue(s) found:`));
+    for (const issue of issues) {
+      console.log(chalk.yellow(`    - ${issue}`));
+    }
+  } else {
+    console.log(chalk.green('  Everything up to date'));
+  }
+
+  console.log(chalk.gray(`\n  Health: ${passed}/${total} checks passed\n`));
+}
+
+main().catch(error => {
+  console.error(chalk.red(`\n  Update failed: ${error.message}\n`));
+  process.exit(0); // Never fail npm install
+});