hypomnema 1.1.0 → 1.2.0

package/scripts/doctor.mjs

@@ -20,24 +20,44 @@ import { fileURLToPath } from 'url';
 import { resolveHypoRoot, expandHome } from './lib/hypo-root.mjs';
 import { loadHypoIgnore, isIgnored } from './lib/hypo-ignore.mjs';
 import { parseFrontmatter } from './lib/frontmatter.mjs';
+import { readSyncState, projectSuggestionsPath } from '../hooks/hypo-shared.mjs';
+import {
+  discoverExtensions,
+  parseManifest,
+  buildExpectedSettingsEntries,
+  readExtensionPkgStateNoMutate,
+  collectOurOccurrences,
+  pickCanonicalOccurrence,
+  EXT_TYPES,
+  CODEX_TYPES,
+} from './lib/extensions.mjs';
+import { sha256, readFileIfRegular } from './lib/pkg-json.mjs';
 
-const HOME     = homedir();
+const HOME = homedir();
 const SCRIPT_DIR = fileURLToPath(new URL('.', import.meta.url));
-const PKG_ROOT   = join(SCRIPT_DIR, '..');
+const PKG_ROOT = join(SCRIPT_DIR, '..');
 
 // Shown after every fatal package-integrity error. These conditions mean the
 // shipped hooks/hooks.json is missing or malformed — never a user mistake —
 // so the only useful next step is a re-install of the package.
-const PKG_INTEGRITY_HINT = '→ This indicates a corrupt or incomplete install. Re-install with `npm install -g hypomnema` (or re-install the Claude Code plugin).';
+const PKG_INTEGRITY_HINT =
+  '→ This indicates a corrupt or incomplete install. Re-install with `npm install -g hypomnema` (or re-install the Claude Code plugin).';
 
 // ── arg parsing ──────────────────────────────────────────────────────────────
 
 function parseArgs(argv) {
-  const args = { hypoDir: null, json: false };
+  const args = { hypoDir: null, json: false, codex: false, claudeHome: null, projectId: null };
   for (const arg of argv.slice(2)) {
     if (arg.startsWith('--hypo-dir=')) args.hypoDir = expandHome(arg.slice(11));
-    else if (arg === '--json')         args.json = true;
+    else if (arg === '--json') args.json = true;
+    else if (arg === '--codex') args.codex = true;
+    else if (arg.startsWith('--claude-home=')) args.claudeHome = expandHome(arg.slice(14));
+    else if (arg.startsWith('--project-id=')) args.projectId = arg.slice(13);
   }
+  if (!args.claudeHome) args.claudeHome = join(HOME, '.claude');
+  // projectId intentionally left null when not user-supplied — let feedback-sync
+  // derive it and exercise its own "derived dir missing → skip MEMORY" path so
+  // doctor reports "unresolved/skipped" rather than a misleading stale warning.
   if (!args.hypoDir) args.hypoDir = resolveHypoRoot();
   return args;
 }
@@ -46,9 +66,15 @@ function parseArgs(argv) {
 
 const checks = [];
 
-function pass(label, detail = '') { checks.push({ status: 'pass', label, detail }); }
-function warn(label, detail = '') { checks.push({ status: 'warn', label, detail }); }
-function fail(label, detail = '') { checks.push({ status: 'fail', label, detail }); }
+function pass(label, detail = '') {
+  checks.push({ status: 'pass', label, detail });
+}
+function warn(label, detail = '') {
+  checks.push({ status: 'warn', label, detail });
+}
+function fail(label, detail = '') {
+  checks.push({ status: 'fail', label, detail });
+}
 
 // ── hook map (loaded from hooks/hooks.json — single source of truth) ─────────
 
@@ -65,7 +91,11 @@ if (!_hookConfig || typeof _hookConfig !== 'object' || Array.isArray(_hookConfig
   console.error(PKG_INTEGRITY_HINT);
   process.exit(1);
 }
-if (!_hookConfig.hooks || typeof _hookConfig.hooks !== 'object' || Array.isArray(_hookConfig.hooks)) {
+if (
+  !_hookConfig.hooks ||
+  typeof _hookConfig.hooks !== 'object' ||
+  Array.isArray(_hookConfig.hooks)
+) {
   console.error('Error: hooks/hooks.json must contain a "hooks" object');
   console.error(PKG_INTEGRITY_HINT);
   process.exit(1);
@@ -83,50 +113,93 @@ function _isHookFileName(file) {
 }
 
 function _isHookGroup(group) {
-  return group &&
+  return (
+    group &&
     typeof group === 'object' &&
     !Array.isArray(group) &&
     Array.isArray(group.hooks) &&
     group.hooks.length > 0 &&
-    group.hooks.every(hook =>
-      hook &&
-      typeof hook === 'object' &&
-      !Array.isArray(hook) &&
-      hook.type === 'command' &&
-      _extractCommandFileName(hook.command)
-    );
+    group.hooks.every(
+      (hook) =>
+        hook &&
+        typeof hook === 'object' &&
+        !Array.isArray(hook) &&
+        hook.type === 'command' &&
+        _extractCommandFileName(hook.command),
+    )
+  );
 }
 
 // Extract .mjs file names from both old format (string[]) and new format (hook-group object[])
 function _extractFileNames(groups) {
-  return groups.flatMap(group => {
+  return groups.flatMap((group) => {
     if (typeof group === 'string') return [group.trim()];
-    return group.hooks.map(hook => _extractCommandFileName(hook.command));
+    return group.hooks.map((hook) => _extractCommandFileName(hook.command));
   });
 }
 
 for (const [event, groups] of Object.entries(_hookConfig.hooks)) {
-  const valid = Array.isArray(groups) &&
+  const valid =
+    Array.isArray(groups) &&
     groups.length > 0 &&
-    groups.every(group => _isHookFileName(group) || _isHookGroup(group)) &&
+    groups.every((group) => _isHookFileName(group) || _isHookGroup(group)) &&
     _extractFileNames(groups).length > 0;
   if (!valid) {
-    console.error(`Error: hooks/hooks.json "hooks.${event}" must be a non-empty array of .mjs file names or Claude hook groups`);
+    console.error(
+      `Error: hooks/hooks.json "hooks.${event}" must be a non-empty array of .mjs file names or Claude hook groups`,
+    );
     console.error(PKG_INTEGRITY_HINT);
     process.exit(1);
   }
 }
-if (_hookConfig.shared !== undefined && (!Array.isArray(_hookConfig.shared) || !_hookConfig.shared.every(f => _isHookFileName(f)))) {
+if (
+  _hookConfig.shared !== undefined &&
+  (!Array.isArray(_hookConfig.shared) || !_hookConfig.shared.every((f) => _isHookFileName(f)))
+) {
   console.error('Error: hooks/hooks.json "shared" must be an array of .mjs file names');
   console.error(PKG_INTEGRITY_HINT);
   process.exit(1);
 }
 
-const HOOK_MAP     = Object.fromEntries(Object.entries(_hookConfig.hooks).map(([e, gs]) => [e, _extractFileNames(gs)]));
+const HOOK_MAP = Object.fromEntries(
+  Object.entries(_hookConfig.hooks).map(([e, gs]) => [e, _extractFileNames(gs)]),
+);
 const SHARED_FILES = _hookConfig.shared ?? [];
 
 // ── checks ───────────────────────────────────────────────────────────────────
 
+function checkExternalDeps() {
+  const nodeMajor = parseInt(process.versions.node.split('.')[0], 10);
+  if (nodeMajor >= 18) {
+    pass('Node.js ≥ 18', `v${process.versions.node}`);
+  } else {
+    fail('Node.js ≥ 18', `v${process.versions.node} — upgrade to Node.js 18+`);
+  }
+
+  const npm = spawnSync('npm', ['--version'], { encoding: 'utf-8' });
+  if (npm.status === 0) {
+    pass('npm', `v${npm.stdout.trim()}`);
+  } else {
+    fail('npm', 'Not found — install npm');
+  }
+
+  const git = spawnSync('git', ['--version'], { encoding: 'utf-8' });
+  if (git.status === 0) {
+    pass('git', git.stdout.trim().replace('git version ', 'v'));
+  } else {
+    fail('git', 'Not found — install git');
+  }
+
+  const shell = process.env.SHELL || '';
+  if (shell.endsWith('zsh') || shell.endsWith('bash')) {
+    pass('Shell (zsh/bash)', shell);
+  } else if (!shell) {
+    warn('Shell (zsh/bash)', '$SHELL not set');
+  } else {
+    warn('Shell (zsh/bash)', `${shell} — zsh or bash recommended`);
+  }
+}
+
 function checkHypoRoot(hypoDir) {
   if (!existsSync(hypoDir)) {
     fail('Wiki root exists', hypoDir);
@@ -143,7 +216,17 @@ function checkHypoRoot(hypoDir) {
 }
 
 function checkDirectories(hypoDir) {
-  const required = ['pages', 'projects', 'sources'];
+  const required = [
+    'pages',
+    'projects',
+    'sources',
+    // Extensions baseline (ADR 0024). Existence only — SHA / settings /
+    // manifest integrity is E5 (#33).
+    'extensions/hooks',
+    'extensions/commands',
+    'extensions/skills',
+    'extensions/agents',
+  ];
   for (const d of required) {
     if (existsSync(join(hypoDir, d))) {
       pass(`Directory: ${d}/`);
@@ -206,8 +289,8 @@ function checkSettingsJson() {
       total++;
       const cmd = `node ${hooksDir.replace(HOME, '$HOME')}/${file}`;
       const found = (Array.isArray(settings.hooks?.[event]) ? settings.hooks[event] : [])
-        .flatMap(g => g.hooks || [])
-        .some(h => h.command === cmd);
+        .flatMap((g) => g.hooks || [])
+        .some((h) => h.command === cmd);
       if (found) registered++;
     }
   }
@@ -215,25 +298,111 @@ function checkSettingsJson() {
   if (registered === total) {
     pass('settings.json hook registrations', `${registered}/${total} registered`);
   } else if (registered > 0) {
-    warn('settings.json hook registrations', `${registered}/${total} registered — run /hypo:init to merge missing entries`);
+    warn(
+      'settings.json hook registrations',
+      `${registered}/${total} registered — run /hypo:init to merge missing entries`,
+    );
   } else {
     fail('settings.json hook registrations', `0/${total} registered — run /hypo:init`);
   }
+
+  // fix #7: stale hypo-* entries (uninstall remnants).
+  // hypo-ext-* commands are user-extension entries (ADR 0024) — not core hooks,
+  // so they are intentionally absent from HOOK_MAP. Excluded here; their
+  // integrity (SHA + manifest + entry match) is checked separately in E5 (#33).
+  const isExtCommand = (cmd) => /(?:^|[/\s])hypo-ext-[^/\s]+\.mjs(?=$|["'\s])/.test(cmd);
+  const expectedCmds = new Set(
+    Object.entries(HOOK_MAP).flatMap(([, files]) =>
+      files.map((f) => `node ${hooksDir.replace(HOME, '$HOME')}/${f}`),
+    ),
+  );
+  const stale = [];
+  for (const [, groups] of Object.entries(settings.hooks || {})) {
+    if (!Array.isArray(groups)) continue;
+    for (const g of groups) {
+      if (!g || typeof g !== 'object') continue;
+      for (const h of g.hooks || []) {
+        if (
+          typeof h.command === 'string' &&
+          /hypo-[^/]+\.mjs/.test(h.command) &&
+          !isExtCommand(h.command) &&
+          !expectedCmds.has(h.command)
+        ) {
+          stale.push(h.command);
+        }
+      }
+    }
+  }
+  if (stale.length > 0) {
+    warn(
+      'settings.json stale hypo-* entries',
+      `${stale.length} unrecognised hypo-* command(s) — run /hypo:uninstall then /hypo:init: ${stale.slice(0, 3).join(', ')}`,
+    );
+  } else {
+    pass('settings.json stale hypo-* entries', 'None');
+  }
+
+  // fix #7: duplicate hypo-* entries per event
+  const dupes = [];
+  for (const [event, groups] of Object.entries(settings.hooks || {})) {
+    if (!Array.isArray(groups)) continue;
+    const seen = new Set();
+    for (const g of groups) {
+      if (!g || typeof g !== 'object') continue;
+      for (const h of g.hooks || []) {
+        if (typeof h.command !== 'string' || !/hypo-[^/]+\.mjs/.test(h.command)) continue;
+        if (isExtCommand(h.command)) continue; // ext duplicates are E5's concern (#33)
+        if (seen.has(h.command)) dupes.push(`${event}:${h.command}`);
+        else seen.add(h.command);
+      }
+    }
+  }
+  if (dupes.length > 0) {
+    warn(
+      'settings.json duplicate hypo-* entries',
+      `${dupes.length} duplicate(s) — run /hypo:init to repair: ${dupes.slice(0, 2).join(', ')}`,
+    );
+  } else {
+    pass('settings.json duplicate hypo-* entries', 'None');
+  }
 }
 
 function checkGit(hypoDir) {
   if (!existsSync(join(hypoDir, '.git'))) {
-    warn('Git repository', 'Not a git repo — run /hypo:init with git-remote option for sync/backup');
+    warn(
+      'Git repository',
+      'Not a git repo — run /hypo:init with git-remote option for sync/backup',
+    );
     return;
   }
   pass('Git repository');
 
-  const remote = spawnSync('git', ['-C', hypoDir, 'remote', 'get-url', 'origin'], { encoding: 'utf-8' });
+  const remote = spawnSync('git', ['-C', hypoDir, 'remote', 'get-url', 'origin'], {
+    encoding: 'utf-8',
+  });
   if (remote.status === 0 && remote.stdout.trim()) {
     pass('Git remote origin', remote.stdout.trim());
   } else {
     warn('Git remote origin', 'No remote configured — wiki will not sync/backup automatically');
   }
+
+  const preCommitPath = join(hypoDir, '.git', 'hooks', 'pre-commit');
+  if (existsSync(preCommitPath)) {
+    const content = readFileSync(preCommitPath, 'utf-8');
+    if (content.includes('# hypo-managed:pre-commit:start')) {
+      pass('.git/hooks/pre-commit', 'Hypomnema .hypoignore guard installed');
+    } else {
+      warn(
+        '.git/hooks/pre-commit',
+        'Exists but not managed by Hypomnema — manual git add can bypass .hypoignore',
+      );
+    }
+  } else {
+    warn(
+      '.git/hooks/pre-commit',
+      'Not installed — run /hypo:init to install .hypoignore guard (fix #24)',
+    );
+  }
 }
 
 function checkBrokenLinks(hypoDir, ignorePatterns = []) {
@@ -244,7 +413,9 @@ function checkBrokenLinks(hypoDir, ignorePatterns = []) {
   for (const file of mdFiles) {
     const raw = readFileSync(file, 'utf-8');
     const content = raw.replace(/<!--[\s\S]*?-->/g, '').replace(/`[^`\n]+`/g, '');
-    const links = [...content.matchAll(/\[\[([^\]|#\n]+?)(?:[|#][^\]]*?)?\]\]/g)].map(m => m[1].trim());
+    const links = [...content.matchAll(/\[\[([^\]|#\n]+?)(?:[|#][^\]]*?)?\]\]/g)].map((m) =>
+      m[1].trim(),
+    );
     for (const link of links) {
       // skip object-path references (e.g. [[hooks.SessionStart]])
       if (link.includes('.') && !link.endsWith('.md')) continue;
@@ -260,8 +431,11 @@ function checkBrokenLinks(hypoDir, ignorePatterns = []) {
   if (broken.length === 0) {
     pass('Broken wiki links', `Scanned ${mdFiles.length} files`);
   } else {
-    const sample = broken.slice(0, 5).map(b => `${b.file} → [[${b.link}]]`).join(', ');
-    const extra  = broken.length > 5 ? ` (+${broken.length - 5} more)` : '';
+    const sample = broken
+      .slice(0, 5)
+      .map((b) => `${b.file} → [[${b.link}]]`)
+      .join(', ');
+    const extra = broken.length > 5 ? ` (+${broken.length - 5} more)` : '';
     warn('Broken wiki links', `${broken.length} broken: ${sample}${extra}`);
   }
 }
@@ -272,7 +446,7 @@ function collectMdFiles(dir, acc = [], hypoDir = '', ignorePatterns = []) {
     if (entry.startsWith('.')) continue;
     const full = join(dir, entry);
     if (hypoDir && isIgnored(full, hypoDir, ignorePatterns)) continue;
-    const st   = statSync(full);
+    const st = statSync(full);
     if (st.isDirectory()) collectMdFiles(full, acc, hypoDir, ignorePatterns);
     else if (extname(entry) === '.md') acc.push(full);
   }
@@ -295,14 +469,14 @@ function buildSlugSet(files, hypoDir) {
 }
 
 function checkVerifyBy(hypoDir, ignorePatterns = []) {
-  const today    = new Date().toISOString().slice(0, 10);
-  const mdFiles  = collectMdFiles(hypoDir, [], hypoDir, ignorePatterns);
-  const overdue  = [];
-  const missing  = [];
+  const today = new Date().toISOString().slice(0, 10);
+  const mdFiles = collectMdFiles(hypoDir, [], hypoDir, ignorePatterns);
+  const overdue = [];
+  const missing = [];
 
   for (const file of mdFiles) {
     const content = readFileSync(file, 'utf-8');
-    const fm      = parseFrontmatter(content);
+    const fm = parseFrontmatter(content);
     if (!fm) continue;
 
     const type = fm.type || '';
@@ -312,30 +486,533 @@ function checkVerifyBy(hypoDir, ignorePatterns = []) {
     if (!fm.verify_by) {
       missing.push(relative(hypoDir, file));
     }
-    if (fm.verify_by_date && /^\d{4}-\d{2}-\d{2}$/.test(fm.verify_by_date) && fm.verify_by_date < today) {
+    if (
+      fm.verify_by_date &&
+      /^\d{4}-\d{2}-\d{2}$/.test(fm.verify_by_date) &&
+      fm.verify_by_date < today
+    ) {
       overdue.push({ file: relative(hypoDir, file), due: fm.verify_by_date });
     }
   }
 
   if (overdue.length > 0) {
-    const sample = overdue.slice(0, 3).map(o => `${o.file} (due ${o.due})`).join(', ');
-    const extra  = overdue.length > 3 ? ` (+${overdue.length - 3} more)` : '';
+    const sample = overdue
+      .slice(0, 3)
+      .map((o) => `${o.file} (due ${o.due})`)
+      .join(', ');
+    const extra = overdue.length > 3 ? ` (+${overdue.length - 3} more)` : '';
     warn('verify_by_date overdue', `${overdue.length} overdue: ${sample}${extra}`);
   } else {
     pass('verify_by_date overdue', 'No overdue pages');
   }
 
   if (missing.length > 0) {
-    warn('verify_by coverage', `${missing.length} pages (adr/page/learning) missing verify_by question`);
+    warn(
+      'verify_by coverage',
+      `${missing.length} pages (adr/page/learning) missing verify_by question`,
+    );
   } else {
     pass('verify_by coverage', 'All tracked pages have verify_by question');
   }
 }
 
+function checkSyncState(hypoDir) {
+  // "open" = file exists with ≥1 entries; session-start clears once
+  // sync is healthy again. Schema + parsing live in hooks/hypo-shared.mjs.
+  const { entries, parseError } = readSyncState(hypoDir);
+
+  if (parseError) {
+    warn('Sync state', 'Cannot parse .cache/sync-state.json — inspect manually');
+    return;
+  }
+
+  if (entries.length === 0) {
+    pass('Sync state', 'No unresolved sync failures');
+  } else {
+    const last = entries[entries.length - 1];
+    warn(
+      'Sync state',
+      `${entries.length} unresolved failure(s) — last: ${last.op || '?'} at ${last.timestamp || '?'}. Inspect .cache/sync-state.json or push/pull manually to clear.`,
+    );
+  }
+}
+
+function checkProjectSuggestions(hypoDir) {
+  // fix #23 / ADR 0023: the auto-project skip-persistence store. Absent file is
+  // healthy (no offers declined yet). Validate the RAW JSON shape here rather
+  // than via readProjectSuggestions(): that helper deliberately normalizes a
+  // non-array `skips` to [] for fail-open hook reads, which would mask a
+  // malformed file and silently break permanent "N" suppression (codex review
+  // 2026-05-22). Doctor must catch the malformation the helper hides.
+  const path = projectSuggestionsPath(hypoDir);
+  if (!existsSync(path)) {
+    pass('Auto-project suggestions', 'No skip-persistence file (clean)');
+    return;
+  }
+  let data;
+  try {
+    data = JSON.parse(readFileSync(path, 'utf-8'));
+  } catch {
+    warn(
+      'Auto-project suggestions',
+      'Cannot parse .cache/project-suggestions.json — inspect manually',
+    );
+    return;
+  }
+  if (data === null || typeof data !== 'object' || Array.isArray(data)) {
+    warn('Auto-project suggestions', 'project-suggestions.json must be a JSON object');
+    return;
+  }
+  if (!Array.isArray(data.skips)) {
+    warn(
+      'Auto-project suggestions',
+      '`skips` must be an array — declined-cwd suppression will not work',
+    );
+    return;
+  }
+  if (
+    data.cooldowns !== undefined &&
+    (typeof data.cooldowns !== 'object' || data.cooldowns === null || Array.isArray(data.cooldowns))
+  ) {
+    warn('Auto-project suggestions', '`cooldowns` must be a plain object');
+    return;
+  }
+  const bad = data.skips.filter((s) => !s || typeof s.cwd !== 'string' || !s.cwd);
+  if (bad.length > 0) {
+    warn(
+      'Auto-project suggestions',
+      `${bad.length} malformed skip entr(ies) missing a string \`cwd\` in .cache/project-suggestions.json`,
+    );
+  } else {
+    pass('Auto-project suggestions', `${data.skips.length} declined cwd(s) recorded`);
+  }
+}
+
+function checkCodexPaths() {
+  const codexHooks = join(HOME, '.codex', 'hooks');
+  const allFiles = [...Object.values(HOOK_MAP).flat(), ...SHARED_FILES];
+
+  let missing = 0;
+  for (const file of allFiles) {
+    if (!existsSync(join(codexHooks, file))) missing++;
+  }
+
+  if (missing === 0) {
+    pass('Codex hook files installed', codexHooks);
+  } else if (missing < allFiles.length) {
+    warn(
+      'Codex hook files installed',
+      `${missing}/${allFiles.length} missing in ${codexHooks} — run /hypo:init --codex`,
+    );
+  } else {
+    fail(
+      'Codex hook files installed',
+      `No hook files found in ${codexHooks} — run /hypo:init --codex`,
+    );
+  }
+
+  const settingsPath = join(HOME, '.codex', 'settings.json');
+  if (!existsSync(settingsPath)) {
+    warn(
+      'Codex settings.json hook registrations',
+      'settings.json not found — run /hypo:init --codex',
+    );
+    return;
+  }
+
+  let settings;
+  try {
+    settings = JSON.parse(readFileSync(settingsPath, 'utf-8'));
+  } catch {
+    fail('Codex settings.json hook registrations', 'settings.json is not valid JSON');
+    return;
+  }
+
+  const hooksDir = codexHooks;
+  let registered = 0;
+  let total = 0;
+
+  for (const [event, files] of Object.entries(HOOK_MAP)) {
+    for (const file of files) {
+      total++;
+      const cmd = `node ${hooksDir.replace(HOME, '$HOME')}/${file}`;
+      const found = (Array.isArray(settings.hooks?.[event]) ? settings.hooks[event] : [])
+        .flatMap((g) => g.hooks || [])
+        .some((h) => h.command === cmd);
+      if (found) registered++;
+    }
+  }
+
+  if (registered === total) {
+    pass('Codex settings.json hook registrations', `${registered}/${total} registered`);
+  } else if (registered > 0) {
+    warn(
+      'Codex settings.json hook registrations',
+      `${registered}/${total} registered — run /hypo:init --codex`,
+    );
+  } else {
+    fail(
+      'Codex settings.json hook registrations',
+      `0/${total} registered — run /hypo:init --codex`,
+    );
+  }
+}
+
+// ── extensions integrity (ADR 0024, E5) ───────────────────────────
+
+// Detect drift between the user's `~/hypomnema/extensions/` source, the recorded
+// per-target SHA map (`hypo-pkg.json`), and the installed copies + settings.json
+// entries under `~/.claude` (or `~/.codex` with --codex). Reuses E2's read-only
+// helpers (plan §5 D4) — never re-derives discovery/manifest/SHA logic.
+//
+// Severity taxonomy (plan §5 #4 pins manifest; the rest mirror the slash-command
+// / settings-stale precedent that recoverable drift is a warn, not a ship blocker):
+//   manifest malformed (parse fail / unknown event) → FAIL (won't self-heal; §5 #4)
+//   manifest missing                                → warn (hook just won't register; §5 #4)
+//   installed copy SHA ≠ recorded (user-modified)   → warn (--force-extensions recovers)
+//   recorded entry but copy absent / non-regular    → warn (upgrade --apply recovers)
+//   expected settings entry missing                 → warn (upgrade --apply recovers)
+//   orphan settings entry (source removed)          → warn (uninstall recovers; boost #2)
+// A malformed manifest failing here is what makes the §5.1.3 `fails=0` ship gate
+// actually cover §8.12-7(c) — asserted by the doctor-extensions-integrity test.
+//
+// E5 is doctor SURFACE for extensions integrity. The mixed-group surgical
+// *write* (preserve sibling-plugin hooks, swap only ours) used to be deferred
+// here; fix #47 (ADR 0024 amendment 2026-05-23) lifted that deferral —
+// registerSettings (extensions.mjs:478 docstring) now does occurrence-first +
+// 8-rank canonical write, and the (b) loop below mirrors that read-path via
+// collectOurOccurrences so a valid mixed-group occurrence is no longer warned
+// as `not registered`.
+function checkExtensions(hypoDir, claudeHome, target = 'claude') {
+  const extDir = join(hypoDir, 'extensions');
+  // E1 baseline absent (e.g. --from-remote clone, plan §5 #8) → nothing to check.
+  if (!existsSync(extDir)) return;
+
+  const root = target === 'codex' ? join(HOME, '.codex') : claudeHome;
+  const label = target === 'codex' ? 'Codex extensions integrity' : 'Extensions integrity';
+  // The per-target SHA map lives in ~/.claude/hypo-pkg.json under
+  // `extensions.{claude,codex}` (sync writes both targets into the one file —
+  // upgrade.mjs:681), so the pkg path is always claude regardless of target.
+  const pkgPath = join(claudeHome, 'hypo-pkg.json');
+  const settingsPath = join(root, 'settings.json');
+  const hooksDir = join(root, 'hooks');
+  const types = target === 'codex' ? CODEX_TYPES : EXT_TYPES;
+
+  const patterns = loadHypoIgnore(hypoDir);
+  const discovered = discoverExtensions(extDir, patterns, hypoDir);
+
+  const problems = [];
+
+  // (c) manifest health — hooks only (plan §0 D3: non-hook manifests don't register).
+  for (const ext of discovered.hooks) {
+    if (!ext.manifestPath) {
+      problems.push({
+        severity: 'warn',
+        msg: `${ext.name}.manifest.json missing — hook will not auto-register`,
+      });
+      continue;
+    }
+    const parsed = parseManifest(ext.manifestPath);
+    if (!parsed.ok) {
+      problems.push({ severity: 'fail', msg: `${ext.manifestName} malformed (${parsed.error})` });
+    }
+  }
+
+  // (a) hard-copy SHA: recorded SHA vs the installed copy on disk.
+  const recorded = readExtensionPkgStateNoMutate(pkgPath, target);
+  for (const [key, recSHA] of Object.entries(recorded)) {
+    // Skip keys outside this target's covered types (defensive: a Claude run records
+    // skills/agents that a codex target never installs — don't false-flag them).
+    if (!types.includes(key.split('/')[0])) continue;
+    const destPath = join(root, key);
+    if (!existsSync(destPath)) {
+      problems.push({
+        severity: 'warn',
+        msg: `${key} recorded but not installed — run upgrade --apply`,
+      });
+      continue;
+    }
+    const onDisk = readFileIfRegular(destPath);
+    if (onDisk === null) {
+      problems.push({ severity: 'warn', msg: `${key} is not a regular file — left untouched` });
+      continue;
+    }
+    if (sha256(onDisk) !== recSHA) {
+      problems.push({
+        severity: 'warn',
+        msg: `${key} modified since install (drift) — use --force-extensions`,
+      });
+    }
+  }
+
+  // (b) settings.json entries. Distinguish three states:
+  //   - malformed JSON      → skip (checkSettingsJson / checkCodexPaths already FAILs it;
+  //                            piling on a misleading "not registered" warn helps no one)
+  //   - missing file / no `hooks` object → treat as an EMPTY hooks map, so a synced
+  //     extension whose registration is absent still surfaces as expected-but-missing
+  //     (§8.12-7(b)). A missing file alone with no extensions yields no problem (gate-safe).
+  let settingsParseFailed = false;
+  let hooksObj = {};
+  if (existsSync(settingsPath)) {
+    try {
+      const parsed = JSON.parse(readFileSync(settingsPath, 'utf-8'));
+      if (
+        parsed &&
+        parsed.hooks &&
+        typeof parsed.hooks === 'object' &&
+        !Array.isArray(parsed.hooks)
+      ) {
+        hooksObj = parsed.hooks;
+      }
+    } catch {
+      settingsParseFailed = true;
+    }
+  }
+  if (!settingsParseFailed) {
+    const expected = buildExpectedSettingsEntries(discovered.hooks, hooksDir);
+
+    // (b) for each registrable hook: locate every occurrence of our command
+    // (single-hook OR mixed group, fix #47) and pick the canonical via the
+    // SAME 8-rank logic registerSettings uses.
+    // Without this mirror, doctor picked the first traversal-order occurrence
+    // under the target event and warned "differs" even when a later
+    // occurrence was the rank-1 canonical that upgrade --apply silently
+    // accepts — a confusing gap between report and action.
+    //
+    // Outcomes:
+    //   - no occurrence in any event       → warn `not registered`
+    //   - canonical on a non-target event  → warn `not registered under <event>`
+    //   - canonical rank 1/2 (exact)       → no drift; pass through
+    //     (ext-command duplicates are surfaced separately below — core
+    //     duplicate-warn at line ~344 excludes hypo-ext-* on purpose)
+    //   - canonical rank 3/4/5 on target   → warn `settings entry differs`
+    //
+    // Mixed-group: a foreign sibling sharing our matcher group does NOT itself
+    // count as drift — only our own hook fields ({type, command, timeout?}) and
+    // the group's matcher are compared. Doctor never inspects foreign hook
+    // shape (no peering into `if`/`args`/`async`/`statusMessage` etc.).
+    for (const entry of expected) {
+      const desiredHook = { type: 'command', command: entry.command };
+      if (entry.timeout) desiredHook.timeout = entry.timeout;
+
+      const occurrences = collectOurOccurrences(hooksObj, entry.command);
+      const picked = pickCanonicalOccurrence(occurrences, entry, desiredHook);
+      if (!picked) {
+        problems.push({
+          severity: 'warn',
+          msg: `${entry.name} not registered under ${entry.event} — run upgrade --apply`,
+        });
+        continue;
+      }
+      if (picked.occ.event !== entry.event) {
+        problems.push({
+          severity: 'warn',
+          msg: `${entry.name} not registered under ${entry.event} — run upgrade --apply`,
+        });
+      } else if (picked.rank >= 3) {
+        // ranks 3/4/5 — on target event, but hook or matcher drifted.
+        // The manifest boundary normalize
+        // (extensions.mjs:178) collapses `matcher: ""` → absent only on the
+        // manifest path. A hand-edited settings.json with `matcher: ""` still
+        // mismatches an absent manifest matcher (rankOccurrence treats "" vs
+        // undefined as non-equal). Surface the empty-string-vs-absent
+        // equivalence ONLY when the hook itself is otherwise exact —
+        // otherwise the specific message would hide a co-occurring hook /
+        // timeout drift. The hookExact
+        // comparison mirrors rankOccurrence's own canonical check
+        // (extensions.mjs ~580) so doctor's report tracks --apply intent.
+        const hookExact = JSON.stringify(picked.occ.hook) === JSON.stringify(desiredHook);
+        if (picked.occ.group.matcher === '' && entry.matcher === undefined && hookExact) {
+          problems.push({
+            severity: 'warn',
+            msg: `${entry.name} settings has matcher: "" (equivalent to absent) — run upgrade --apply to normalize`,
+          });
+        } else {
+          problems.push({
+            severity: 'warn',
+            msg: `${entry.name} settings entry differs from manifest (matcher/hook/timeout) — run upgrade --apply`,
+          });
+        }
+      }
+      // ext-aware duplicate surface: core duplicate-warn at checkSettingsJson
+      // intentionally skips hypo-ext-* (line ~353 isExtCommand guard). With
+      // the canonical-pick above, exact rank-1 duplicates would otherwise be
+      // invisible to doctor until upgrade --apply runs cleanup. Surface them
+      // here so the report still names the work that --apply will do.
+      if (occurrences.length > 1) {
+        problems.push({
+          severity: 'warn',
+          msg: `${entry.name} has ${occurrences.length} occurrences in settings — run upgrade --apply to clean up`,
+        });
+      }
+    }
+
+    // orphan (boost #2): a hypo-ext-* command in settings with no source extension.
+    // E4 excluded hypo-ext-* from the core stale checker (doctor.mjs:302), so this
+    // is the ONLY place orphaned extension entries are caught.
+    //
+    // Two distinct orphan classes:
+    //   - source-removed: settings entry whose source file is gone → uninstall
+    //   - unregistrable : source file present but manifest malformed/non-hook,
+    //                     so (b) above skipped it and (c) only FAIL/warned the
+    //                     manifest itself, never naming the stale settings entry.
+    //                     Surfaced separately so the user knows the lingering
+    //                     entry needs cleanup independent of the manifest fix.
+    const cmdFor = (ext) => `node ${hooksDir.replace(HOME, '$HOME')}/${ext.file}`;
+    const sourceCmds = new Set(discovered.hooks.map(cmdFor));
+    const unregistrableCmds = new Set();
+    for (const ext of discovered.hooks) {
+      if (!ext.manifestPath) continue; // (c-warn) already names this case
+      const parsed = parseManifest(ext.manifestPath);
+      if (!parsed.ok || !parsed.registrable) unregistrableCmds.add(cmdFor(ext));
+    }
+    // A single hypo-ext-* command can appear
+    // in multiple groups/events when settings.json was hand-edited or migrated
+    // across events. The registrable-entry duplicate surface above
+    // (`occurrences.length > 1`) only iterates `expected`, so orphan-class
+    // duplicates were silently de-duped to a single warn. Count occurrences per
+    // orphan command and append `(N occurrences)` when count > 1.
+    //
+    // Order: check `unregistrableCmds` BEFORE `sourceCmds` — a malformed or
+    // non-hook manifest still has the source file present, so the
+    // `sourceCmds.has` check would otherwise misclassify them as non-orphan.
+    const orphanInfo = new Map(); // command → { kind, count }
+    for (const groups of Object.values(hooksObj)) {
+      if (!Array.isArray(groups)) continue;
+      for (const g of groups) {
+        if (!g || typeof g !== 'object') continue;
+        if (!Array.isArray(g.hooks)) continue;
+        for (const h of g.hooks) {
+          if (typeof h.command !== 'string') continue;
+          if (!/(?:^|[/\s])hypo-ext-[^/\s]+\.mjs(?=$|["'\s])/.test(h.command)) continue;
+          let kind = null;
+          if (unregistrableCmds.has(h.command)) kind = 'unregistrable';
+          else if (!sourceCmds.has(h.command)) kind = 'source-removed';
+          else continue;
+          const info = orphanInfo.get(h.command);
+          if (info) info.count += 1;
+          else orphanInfo.set(h.command, { kind, count: 1 });
+        }
+      }
+    }
+    for (const [cmd, { kind, count }] of orphanInfo) {
+      const suffix = count > 1 ? ` (${count} occurrences)` : '';
+      const msg =
+        kind === 'unregistrable'
+          ? `orphan settings entry (${cmd}) — manifest unregistrable${suffix}; run uninstall`
+          : `orphan settings entry (${cmd}) — source extension removed${suffix}; run uninstall`;
+      problems.push({ severity: 'warn', msg });
+    }
+  }
+
+  if (problems.length === 0) {
+    pass(label, 'All extensions consistent');
+    return;
+  }
+  const hasFail = problems.some((p) => p.severity === 'fail');
+  const sample = problems
+    .slice(0, 4)
+    .map((p) => p.msg)
+    .join('; ');
+  const extra = problems.length > 4 ? ` (+${problems.length - 4} more)` : '';
+  if (hasFail) fail(label, `${sample}${extra}`);
+  else warn(label, `${sample}${extra}`);
+}
+
+// ── feedback projection (ADR 0031) ──────────────────────────────
+
+// Spawn feedback-sync.mjs --check --json and map its drift report onto doctor's
+// pass/warn/fail. Integrity violations (exit-3 class: conflict / unpaired marker
+// / intruder line / block out of container) are FAIL. Plain drift, build errors,
+// over-cap, and an unresolved project-id are WARN — a fresh system that has not
+// run `feedback-sync --write` yet is normal and must not block doctor.
+function checkFeedbackProjection(hypoDir, claudeHome, projectId) {
+  const cliPath = join(PKG_ROOT, 'scripts', 'feedback-sync.mjs');
+  const cliArgs = [
+    cliPath,
+    '--check',
+    '--json',
+    '--no-input', // never let the child block on a TTY prompt under doctor
+    `--hypo-dir=${hypoDir}`,
+    `--claude-home=${claudeHome}`,
+  ];
+  // forward --project-id ONLY when the user supplied one; otherwise let
+  // feedback-sync derive it and run its derived-missing → skip-MEMORY path
+  if (projectId) cliArgs.push(`--project-id=${projectId}`);
+  const r = spawnSync(process.execPath, cliArgs, { encoding: 'utf-8' });
+
+  // feedback-sync exits non-zero on drift/over-cap/conflict — that is expected
+  // and still prints a JSON report on stdout. Only treat a missing process or
+  // unparseable stdout as a doctor-level problem (warn, never crash).
+  if (r.error || r.status === null) {
+    warn(
+      'Feedback projection',
+      `feedback-sync could not run: ${r.error?.message || 'no exit code'}`,
+    );
+    return;
+  }
+  let report;
+  try {
+    report = JSON.parse(r.stdout);
+  } catch {
+    warn('Feedback projection', 'feedback-sync produced no JSON report — inspect manually');
+    return;
+  }
+  if (report.error) {
+    warn('Feedback projection', report.error);
+    return;
+  }
+
+  const targets = Object.entries(report.targets || {});
+
+  // 1) integrity violations → FAIL
+  const broken = targets.find(
+    ([, t]) => (t.conflicts && t.conflicts.length) || t.unpaired || t.intruder || t.outOfContainer,
+  );
+  if (broken) {
+    const [name, t] = broken;
+    const reason =
+      t.conflicts && t.conflicts.length
+        ? `conflict (${t.conflicts.join(', ')})`
+        : t.unpaired
+          ? 'unpaired managed marker'
+          : t.intruder
+            ? 'hand-edited line inside managed region'
+            : 'managed block outside its container';
+    fail(
+      'Feedback projection integrity',
+      `${name}: ${reason} — run \`hypomnema feedback-sync --import-target-change\` to reconcile`,
+    );
+  } else {
+    // 2) build error → WARN
+    const buildErr = targets.find(([, t]) => t.buildError);
+    if (buildErr) {
+      warn('Feedback projection', buildErr[1].buildError);
+    } else if (targets.find(([, t]) => t.overCap)) {
+      warn('Feedback projection', 'projection over cap — demote/archive feedback pages');
+    } else if (targets.find(([, t]) => t.dirty)) {
+      warn('Feedback projection', 'projections stale — run `hypomnema feedback-sync --write`');
+    } else {
+      const candidates = targets.reduce((n, [, t]) => n + (t.candidates || 0), 0);
+      if (candidates > 0) pass('Feedback projection', 'in sync');
+      else pass('Feedback projection', 'no projection candidates');
+    }
+  }
+
+  // 3) unresolved project-id is a separate, non-fatal concern (MEMORY skipped)
+  if (report.projectIdResolved === false) {
+    warn(
+      'Feedback projection',
+      `project-id ${report.projectId} unresolved — MEMORY projection skipped; pass --project-id`,
+    );
+  }
+}
+
 // ── main ─────────────────────────────────────────────────────────────────────
 
 const args = parseArgs(process.argv);
 
+checkExternalDeps();
 const ignorePatterns = loadHypoIgnore(args.hypoDir);
 const rootOk = checkHypoRoot(args.hypoDir);
 if (rootOk) {
@@ -346,6 +1023,12 @@ if (rootOk) {
 }
 checkHooks();
 checkSettingsJson();
+if (args.codex) checkCodexPaths();
+if (rootOk) checkExtensions(args.hypoDir, args.claudeHome, 'claude');
+if (rootOk && args.codex) checkExtensions(args.hypoDir, args.claudeHome, 'codex');
+if (rootOk) checkSyncState(args.hypoDir);
+if (rootOk) checkProjectSuggestions(args.hypoDir);
+if (rootOk) checkFeedbackProjection(args.hypoDir, args.claudeHome, args.projectId);
 checkGit(args.hypoDir);
 
 // ── report ───────────────────────────────────────────────────────────────────
@@ -359,13 +1042,13 @@ if (args.json) {
     console.log(`${icons[c.status]} ${c.label}${detail}`);
   }
 
-  const fails = checks.filter(c => c.status === 'fail').length;
-  const warns = checks.filter(c => c.status === 'warn').length;
-  const passes = checks.filter(c => c.status === 'pass').length;
+  const fails = checks.filter((c) => c.status === 'fail').length;
+  const warns = checks.filter((c) => c.status === 'warn').length;
+  const passes = checks.filter((c) => c.status === 'pass').length;
 
   console.log('');
   console.log(`Result: ${passes} passed, ${warns} warnings, ${fails} failed`);
   if (fails > 0) console.log('Run /hypo:init to repair installation issues.');
 }
 
-if (checks.some(c => c.status === 'fail')) process.exit(1);
+if (checks.some((c) => c.status === 'fail')) process.exit(1);