fix(mcp): skip fs.watch on WSL2 /mnt drives that hang MCP startup (#199) (#210)

Recursive fs.watch on a WSL2 /mnt NTFS/9p mount walks the directory tree
with every readdir/stat crossing the Windows boundary, stalling the event
loop long enough to blow past opencode's 30s MCP handshake timeout so the
tools never appear. This is the file-watcher half of the #172 fix, which
moved the DB/WASM open off the handshake but left the watcher on the
critical path.

- Add watchDisabledReason() policy: CODEGRAPH_NO_WATCH (off) >
  CODEGRAPH_FORCE_WATCH (force on) > WSL2 + /mnt auto-detect (off).
  FileWatcher.start() and the MCP server both honor it; the server now
  logs why watching is off and how to refresh.
- Add `codegraph serve --mcp --no-watch`.
- When watching is off, init/install offer git sync hooks (post-commit,
  post-merge, post-checkout) that run `codegraph sync` in the background,
  or fall back to manual sync; either way the user is told the index
  stays frozen until re-synced. uninit removes the hooks.
- Tests: watch-policy + git-hooks (idempotency, user-content preservation,
  core.hooksPath).

Root-cause analysis and workaround by @mengfanbo123.

Closes #199

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

src/sync/git-hooks.ts

@@ -0,0 +1,208 @@
+/**
+ * Git Sync Hooks
+ *
+ * When the live file watcher is disabled (e.g. on WSL2 `/mnt/*` drives,
+ * see watch-policy.ts), the CodeGraph index would otherwise go stale until
+ * the user runs `codegraph sync` by hand. As an opt-in alternative, we can
+ * install git hooks that refresh the index after the operations that change
+ * files on disk: commit, merge (covers `git pull`), and checkout.
+ *
+ * The hooks run `codegraph sync` in the background so they never block git,
+ * and are guarded by `command -v codegraph` so they no-op cleanly when the
+ * CLI isn't on PATH. Our snippet is delimited by marker comments so install
+ * is idempotent and removal preserves any user-authored hook content.
+ */
+
+import * as fs from 'fs';
+import * as path from 'path';
+import { execFileSync } from 'child_process';
+
+const MARKER_BEGIN = '# >>> codegraph sync hook >>>';
+const MARKER_END = '# <<< codegraph sync hook <<<';
+
+export type GitHookName = 'post-commit' | 'post-merge' | 'post-checkout';
+
+/** Hooks installed by default: commit, merge (git pull), and checkout. */
+export const DEFAULT_SYNC_HOOKS: GitHookName[] = ['post-commit', 'post-merge', 'post-checkout'];
+
+export interface GitHookResult {
+  /** Hook names that were created or updated. */
+  installed: GitHookName[];
+  /** Resolved hooks directory, or null when not a git repo. */
+  hooksDir: string | null;
+  /** Reason nothing happened (e.g. not a git repository). */
+  skipped?: string;
+}
+
+/**
+ * Whether `projectRoot` is inside a git working tree. Returns false if git
+ * isn't installed or the path isn't a repo.
+ */
+export function isGitRepo(projectRoot: string): boolean {
+  try {
+    const out = execFileSync('git', ['rev-parse', '--is-inside-work-tree'], {
+      cwd: projectRoot,
+      encoding: 'utf8',
+      stdio: ['ignore', 'pipe', 'ignore'],
+    }).trim();
+    return out === 'true';
+  } catch {
+    return false;
+  }
+}
+
+/**
+ * Resolve the git hooks directory for a project, honoring `core.hooksPath`
+ * and git worktrees. Returns an absolute path, or null when not a repo.
+ */
+function gitHooksDir(projectRoot: string): string | null {
+  try {
+    const out = execFileSync('git', ['rev-parse', '--git-path', 'hooks'], {
+      cwd: projectRoot,
+      encoding: 'utf8',
+      stdio: ['ignore', 'pipe', 'ignore'],
+    }).trim();
+    if (!out) return null;
+    return path.isAbsolute(out) ? out : path.resolve(projectRoot, out);
+  } catch {
+    return null;
+  }
+}
+
+/** The shell snippet (between markers) injected into each hook. */
+function markerBlock(): string {
+  return [
+    MARKER_BEGIN,
+    '# Keeps the CodeGraph index fresh while the live file watcher is off',
+    '# (e.g. WSL2 /mnt drives). Runs in the background so it never blocks git.',
+    '# Managed by codegraph; remove with `codegraph uninit` or delete this block.',
+    'if command -v codegraph >/dev/null 2>&1; then',
+    '  ( codegraph sync >/dev/null 2>&1 & ) >/dev/null 2>&1',
+    'fi',
+    MARKER_END,
+  ].join('\n');
+}
+
+/** Remove our marker block (and the marker lines) from hook content. */
+function stripMarkerBlock(content: string): string {
+  const lines = content.split('\n');
+  const kept: string[] = [];
+  let inBlock = false;
+  for (const line of lines) {
+    const trimmed = line.trim();
+    if (trimmed === MARKER_BEGIN) { inBlock = true; continue; }
+    if (trimmed === MARKER_END) { inBlock = false; continue; }
+    if (!inBlock) kept.push(line);
+  }
+  return kept.join('\n');
+}
+
+/** Whether a hook body is just a shebang / blank lines (i.e. only ever ours). */
+function isEffectivelyEmpty(content: string): boolean {
+  return content
+    .split('\n')
+    .map((l) => l.trim())
+    .every((l) => l.length === 0 || l.startsWith('#!'));
+}
+
+function chmodExecutable(file: string): void {
+  try {
+    fs.chmodSync(file, 0o755);
+  } catch {
+    /* chmod is a no-op / unsupported on some platforms (e.g. Windows) */
+  }
+}
+
+/**
+ * Install (or update) the CodeGraph sync hooks in a git repository.
+ * Idempotent: re-running replaces our marker block rather than duplicating
+ * it, and any user-authored hook content is preserved.
+ */
+export function installGitSyncHook(
+  projectRoot: string,
+  hooks: GitHookName[] = DEFAULT_SYNC_HOOKS,
+): GitHookResult {
+  const hooksDir = gitHooksDir(projectRoot);
+  if (!hooksDir) {
+    return { installed: [], hooksDir: null, skipped: 'not a git repository' };
+  }
+
+  try {
+    fs.mkdirSync(hooksDir, { recursive: true });
+  } catch {
+    return { installed: [], hooksDir, skipped: 'could not access the git hooks directory' };
+  }
+
+  const block = markerBlock();
+  const installed: GitHookName[] = [];
+
+  for (const hook of hooks) {
+    const file = path.join(hooksDir, hook);
+    let content: string;
+
+    if (fs.existsSync(file)) {
+      // Strip any prior block, then re-append the current one.
+      const base = stripMarkerBlock(fs.readFileSync(file, 'utf8')).replace(/\s*$/, '');
+      content = base.length > 0
+        ? `${base}\n\n${block}\n`
+        : `#!/bin/sh\n${block}\n`;
+    } else {
+      content = `#!/bin/sh\n${block}\n`;
+    }
+
+    fs.writeFileSync(file, content);
+    chmodExecutable(file);
+    installed.push(hook);
+  }
+
+  return { installed, hooksDir };
+}
+
+/**
+ * Remove the CodeGraph sync hooks. Strips only our marker block; deletes the
+ * hook file entirely when nothing but a shebang remains, otherwise rewrites
+ * the user's content untouched.
+ */
+export function removeGitSyncHook(
+  projectRoot: string,
+  hooks: GitHookName[] = DEFAULT_SYNC_HOOKS,
+): GitHookResult {
+  const hooksDir = gitHooksDir(projectRoot);
+  if (!hooksDir) {
+    return { installed: [], hooksDir: null, skipped: 'not a git repository' };
+  }
+
+  const removed: GitHookName[] = [];
+
+  for (const hook of hooks) {
+    const file = path.join(hooksDir, hook);
+    if (!fs.existsSync(file)) continue;
+
+    const original = fs.readFileSync(file, 'utf8');
+    if (!original.includes(MARKER_BEGIN)) continue;
+
+    const stripped = stripMarkerBlock(original);
+    if (isEffectivelyEmpty(stripped)) {
+      fs.unlinkSync(file);
+    } else {
+      fs.writeFileSync(file, `${stripped.replace(/\s*$/, '')}\n`);
+      chmodExecutable(file);
+    }
+    removed.push(hook);
+  }
+
+  return { installed: removed, hooksDir };
+}
+
+/** Whether any CodeGraph sync hook is currently installed. */
+export function isSyncHookInstalled(
+  projectRoot: string,
+  hooks: GitHookName[] = DEFAULT_SYNC_HOOKS,
+): boolean {
+  const hooksDir = gitHooksDir(projectRoot);
+  if (!hooksDir) return false;
+  return hooks.some((hook) => {
+    const file = path.join(hooksDir, hook);
+    return fs.existsSync(file) && fs.readFileSync(file, 'utf8').includes(MARKER_BEGIN);
+  });
+}

src/sync/index.ts

@@ -6,8 +6,20 @@
  *
  * Components:
  * - FileWatcher: Debounced fs.watch that auto-triggers sync on file changes
+ * - Watch policy: decides when the watcher must be disabled (e.g. WSL2 /mnt)
+ * - Git sync hooks: opt-in commit/merge/checkout hooks when watching is off
  * - Content hashing for change detection (in extraction module)
  * - Incremental reindexing (in extraction module)
  */
 
 export { FileWatcher, WatchOptions } from './watcher';
+export { watchDisabledReason, detectWsl } from './watch-policy';
+export {
+  installGitSyncHook,
+  removeGitSyncHook,
+  isSyncHookInstalled,
+  isGitRepo,
+  DEFAULT_SYNC_HOOKS,
+  type GitHookName,
+  type GitHookResult,
+} from './git-hooks';

src/sync/watch-policy.ts

@@ -0,0 +1,104 @@
+/**
+ * Watch Policy
+ *
+ * Decides whether the live file watcher should run for a given project.
+ *
+ * Native recursive `fs.watch` is pathologically slow on WSL2 `/mnt/*`
+ * drives (NTFS exposed over the 9p/drvfs bridge): setting up the recursive
+ * watch walks the directory tree, and every readdir/stat crosses the
+ * Windows boundary. Inside an MCP server this stalls the event loop during
+ * startup long enough to blow past host handshake timeouts (opencode's 30s),
+ * so the tools never appear. See issue #199.
+ *
+ * This module centralizes the on/off decision so the watcher, the MCP
+ * server (for diagnostics), and the installer all agree.
+ */
+
+import * as fs from 'fs';
+import { normalizePath } from '../utils';
+
+let wslChecked = false;
+let wslValue = false;
+
+/**
+ * Detect whether the current process is running under WSL (Windows
+ * Subsystem for Linux). Result is cached after the first call.
+ *
+ * Checks the WSL-specific env vars first (no I/O), then falls back to
+ * `/proc/version`, which contains "microsoft" on WSL kernels.
+ */
+export function detectWsl(): boolean {
+  if (wslChecked) return wslValue;
+  wslChecked = true;
+
+  if (process.platform !== 'linux') {
+    wslValue = false;
+    return wslValue;
+  }
+  if (process.env.WSL_DISTRO_NAME || process.env.WSL_INTEROP) {
+    wslValue = true;
+    return wslValue;
+  }
+  try {
+    const version = fs.readFileSync('/proc/version', 'utf8').toLowerCase();
+    wslValue = version.includes('microsoft') || version.includes('wsl');
+  } catch {
+    wslValue = false;
+  }
+  return wslValue;
+}
+
+/**
+ * True for WSL Windows-drive mounts like `/mnt/c` or `/mnt/d/project`.
+ * Deliberately matches only single-letter drive mounts, so genuinely fast
+ * Linux mounts such as `/mnt/wsl/...` are not flagged.
+ */
+function isWindowsDriveMount(projectRoot: string): boolean {
+  return /^\/mnt\/[a-z](\/|$)/i.test(normalizePath(projectRoot));
+}
+
+/**
+ * Inputs that can be overridden in tests so the decision is deterministic
+ * without touching real env vars or `/proc/version`.
+ */
+export interface WatchProbe {
+  /** Defaults to `process.env`. */
+  env?: NodeJS.ProcessEnv;
+  /** Defaults to `detectWsl()`. */
+  isWsl?: boolean;
+}
+
+/**
+ * Decide whether the file watcher should be disabled for a project, and why.
+ *
+ * Returns a short human-readable reason when watching should be skipped, or
+ * `null` when it should run normally.
+ *
+ * Precedence (first match wins):
+ *  1. `CODEGRAPH_NO_WATCH=1`    → off  (explicit opt-out always wins)
+ *  2. `CODEGRAPH_FORCE_WATCH=1` → on   (overrides auto-detection)
+ *  3. WSL2 + `/mnt/*` drive     → off  (recursive fs.watch is too slow; #199)
+ */
+export function watchDisabledReason(projectRoot: string, probe: WatchProbe = {}): string | null {
+  const env = probe.env ?? process.env;
+
+  if (env.CODEGRAPH_NO_WATCH === '1') {
+    return 'CODEGRAPH_NO_WATCH=1 is set';
+  }
+  if (env.CODEGRAPH_FORCE_WATCH === '1') {
+    return null;
+  }
+
+  const isWsl = probe.isWsl ?? detectWsl();
+  if (isWsl && isWindowsDriveMount(projectRoot)) {
+    return 'project is on a WSL2 /mnt/ drive, where recursive fs.watch is too slow to be reliable';
+  }
+
+  return null;
+}
+
+/** Test-only: reset the cached WSL detection. */
+export function __resetWslCacheForTests(): void {
+  wslChecked = false;
+  wslValue = false;
+}

src/sync/watcher.ts

@@ -13,6 +13,7 @@ import { CodeGraphConfig } from '../types';
 import { shouldIncludeFile } from '../extraction';
 import { logDebug, logWarn } from '../errors';
 import { normalizePath } from '../utils';
+import { watchDisabledReason } from './watch-policy';
 
 /**
  * Options for the file watcher
@@ -82,6 +83,16 @@ export class FileWatcher {
     if (this.watcher) return true; // Already watching
     this.stopped = false;
 
+    // Some environments make recursive fs.watch unusable — most notably WSL2
+    // /mnt/ drives, where setup blocks long enough to break MCP startup
+    // handshakes (issue #199). Skip watching there; callers fall back to
+    // manual `codegraph sync` or the git sync hooks.
+    const disabledReason = watchDisabledReason(this.projectRoot);
+    if (disabledReason) {
+      logDebug('File watcher disabled', { reason: disabledReason, projectRoot: this.projectRoot });
+      return false;
+    }
+
     try {
       this.watcher = fs.watch(
         this.projectRoot,