fix(mcp): fail fast on a second direct-mode writer per project (#1740) (#1744)

Concurrent CODEGRAPH_NO_DAEMON / in-process fallback serve --mcp instances
each started a FileWatcher and contended on codegraph.lock until auto-sync
degraded. Add an exclusive .codegraph/writer.pid lock held by the daemon or
the single direct writer; a second writer exits with actionable guidance.
Daemon mode still multiplexes N proxies onto one writer.

Co-authored-by: Colby McHenry <colbymchenry@users.noreply.github.com>
This commit is contained in:
Colby Mchenry
2026-09-07 23:56:52 -05:00
committed by GitHub
co-authored by Colby McHenry
parent df435d50d1
commit 7440d2c475
8 changed files with 467 additions and 0 deletions
+4
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@@ -135,6 +135,10 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
### Fixes
#### MCP / indexing
- **A second `codegraph serve --mcp` on the same project no longer silently kills auto-sync (#1740).** Direct mode (`CODEGRAPH_NO_DAEMON=1` or proxy→in-process fallback) now takes an exclusive `.codegraph/writer.pid` lock; a second writer exits immediately with guidance to stop the other server or unset `CODEGRAPH_NO_DAEMON` so clients share the daemon. The shared daemon already multiplexes N clients onto one watcher — this closes the same-OS dual-direct gap the docs warned about for Windows/WSL but did not guard.
#### Screens, links and navigation
- **Where the app goes after login is a fork, not two always-es.** A navigation whose destination comes back from a helper — `router.replace(await resolvePostLoginRoute())` over `return (await hasSeenWelcome(…)) ? '/home/' : '/welcome/'` — drew both screens with no condition, reading as if the welcome screen always shows. The two arms share a line, and only a column can tell them apart; each synthesized edge now carries its literal's own position, so the guard reader says which arm it is: `WHEN await hasSeenWelcome(…)` → home, and its negation → welcome. And the scan starts at the helper's body, so a literal-union return type — `Promise<'/welcome/' | '/home/'>`, whose routes are string literals too, written first — no longer stands in for the navigation itself. Re-index after upgrading to pick the positions up.
+2
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@@ -944,6 +944,8 @@ Framework routing is validated the same way, on a canonical app per framework: E
**MCP server not connecting** — Your agent starts the server itself, so you don't launch it by hand. Make sure the project is initialized and indexed (`codegraph status`) and that the path in your MCP config is correct. If it still won't connect, re-run `codegraph install` to rewrite the config.
**Two `codegraph serve --mcp` on one project fight over the index / auto-sync stops** — CodeGraph allows one live MCP *writer* per project (the shared background daemon, or a single direct-mode process). Extra clients should proxy to that daemon. If you set `CODEGRAPH_NO_DAEMON=1`, run only one `serve --mcp` for that project; a second instance exits with a clear writer-lock error (see `writer.pid` under `.codegraph/`). Prefer leaving the daemon enabled so multiple MCP hosts share one watcher.
**MCP tool calls fail with `Transport closed` while `codegraph status`/`sync` are healthy** — almost always WSL2 with the project on a Windows drive (a `/mnt/c` or `/mnt/d` path), where the local socket CodeGraph uses to share one background server across sessions is unreliable. CodeGraph now falls back to serving the session in-process instead of dropping the connection, but if you still hit it, set `CODEGRAPH_NO_DAEMON=1` in your MCP server's environment to skip the shared server entirely (each session runs in its own process). Moving the project onto the Linux-native filesystem (e.g. under `~/` instead of `/mnt/`) restores the shared server.
**Missing symbols** — The MCP server auto-syncs on save (wait a couple seconds). Run `codegraph sync` manually if needed. Check that the file's language is supported and isn't inside a `.gitignore`d or default-excluded directory (e.g. `node_modules`, `dist`).
+128
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@@ -0,0 +1,128 @@
/**
* Issue #1740 concurrent direct-mode serve --mcp must fail fast on the
* second writer instead of silently degrading auto-sync.
*/
import { afterEach, beforeEach, describe, expect, it } from 'vitest';
import { ChildProcessWithoutNullStreams, spawn } from 'child_process';
import * as fs from 'fs';
import * as os from 'os';
import * as path from 'path';
import { CodeGraph } from '../src';
import { getWriterPidPath } from '../src/mcp/writer-lock';
const BIN = path.resolve(__dirname, '../dist/bin/codegraph.js');
function sleep(ms: number): Promise<void> {
return new Promise((r) => setTimeout(r, ms));
}
function spawnMcp(
cwd: string,
env: NodeJS.ProcessEnv,
): { child: ChildProcessWithoutNullStreams; getStderr: () => string } {
const child = spawn(process.execPath, [BIN, 'serve', '--mcp'], {
cwd,
stdio: ['pipe', 'pipe', 'pipe'],
env: { ...process.env, ...env },
}) as ChildProcessWithoutNullStreams;
child.on('error', () => {});
child.stdin.on('error', () => {});
let stderr = '';
child.stderr.on('data', (c: Buffer) => { stderr += c.toString('utf8'); });
child.stdout.on('data', () => {});
return { child, getStderr: () => stderr };
}
describe('issue #1740 — direct-mode writer lock', () => {
let tempDir: string;
let realRoot: string;
const children: ChildProcessWithoutNullStreams[] = [];
beforeEach(async () => {
tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'cg1740-mcp-'));
realRoot = fs.realpathSync(tempDir);
fs.mkdirSync(path.join(realRoot, 'src'));
fs.writeFileSync(path.join(realRoot, 'src/a.ts'), 'export function a() { return 1; }\n');
const cg = await CodeGraph.init(realRoot);
await cg.indexAll();
cg.close();
});
afterEach(async () => {
for (const c of children) {
try { c.kill('SIGTERM'); } catch { /* ignore */ }
}
children.length = 0;
await sleep(300);
try { fs.rmSync(tempDir, { recursive: true, force: true }); } catch { /* ignore */ }
});
it('second CODEGRAPH_NO_DAEMON serve --mcp exits with writer-lock error', async () => {
const env = {
CODEGRAPH_NO_DAEMON: '1',
CODEGRAPH_MCP_DEBUG: '1',
CODEGRAPH_NO_WATCHDOG: '1',
CODEGRAPH_STARTUP_HANDSHAKE_TIMEOUT_MS: '0',
// Avoid wasm --liftoff-only re-exec so lock.pid matches the spawned pid.
CODEGRAPH_NO_RELAUNCH: '1',
CODEGRAPH_WASM_RELAUNCHED: '1',
};
const first = spawnMcp(realRoot, env);
children.push(first.child);
const lockPath = getWriterPidPath(realRoot);
const deadline = Date.now() + 10000;
while (Date.now() < deadline && !fs.existsSync(lockPath)) {
await sleep(50);
}
expect(fs.existsSync(lockPath)).toBe(true);
expect(first.child.exitCode).toBeNull();
const second = spawnMcp(realRoot, env);
children.push(second.child);
const code = await new Promise<number | null>((resolve) => {
const timer = setTimeout(() => resolve(second.child.exitCode), 10000);
second.child.on('close', (c) => {
clearTimeout(timer);
resolve(c);
});
});
expect(code).toBe(1);
expect(second.getStderr()).toMatch(/writer lock held/i);
expect(second.getStderr()).toMatch(/CODEGRAPH_NO_DAEMON/);
expect(first.child.exitCode).toBeNull();
const lock = JSON.parse(fs.readFileSync(lockPath, 'utf8')) as { pid: number };
expect(lock.pid).toBe(first.child.pid);
}, 20000);
it('default daemon mode still allows two proxies to share one writer', async () => {
const env = {
CODEGRAPH_MCP_LOG_ATTACH: '1',
CODEGRAPH_NO_WATCHDOG: '1',
CODEGRAPH_STARTUP_HANDSHAKE_TIMEOUT_MS: '0',
CODEGRAPH_NO_RELAUNCH: '1',
CODEGRAPH_WASM_RELAUNCHED: '1',
};
const a = spawnMcp(realRoot, env);
const b = spawnMcp(realRoot, env);
children.push(a.child, b.child);
const lockPath = getWriterPidPath(realRoot);
const deadline = Date.now() + 15000;
while (Date.now() < deadline && !fs.existsSync(lockPath)) {
await sleep(50);
}
expect(fs.existsSync(lockPath)).toBe(true);
await sleep(1000);
expect(a.child.exitCode).toBeNull();
expect(b.child.exitCode).toBeNull();
const lock = JSON.parse(fs.readFileSync(lockPath, 'utf8')) as { pid: number; mode: string };
expect(lock.mode).toBe('daemon');
expect(lock.pid).not.toBe(a.child.pid);
expect(lock.pid).not.toBe(b.child.pid);
}, 25000);
});
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@@ -0,0 +1,87 @@
/**
* Project writer lock (#1740) unit coverage for acquire / re-entrant /
* stale-dead-pid / live-holder refusal.
*/
import { afterEach, describe, expect, it } from 'vitest';
import * as fs from 'fs';
import * as os from 'os';
import * as path from 'path';
import {
decodeWriterLockInfo,
getWriterPidPath,
releaseWriterLock,
tryAcquireWriterLock,
writerLockHeldMessage,
} from '../src/mcp/writer-lock';
describe('writer lock (#1740)', () => {
let dir: string;
afterEach(() => {
if (dir) {
releaseWriterLock(dir);
try { fs.rmSync(dir, { recursive: true, force: true }); } catch { /* ignore */ }
}
});
function makeProject(): string {
dir = fs.mkdtempSync(path.join(os.tmpdir(), 'cg1740-lock-'));
fs.mkdirSync(path.join(dir, '.codegraph'), { recursive: true });
return dir;
}
it('acquires and releases writer.pid', () => {
const root = makeProject();
const r = tryAcquireWriterLock(root, 'direct');
expect(r.kind).toBe('acquired');
expect(fs.existsSync(getWriterPidPath(root))).toBe(true);
const info = decodeWriterLockInfo(fs.readFileSync(getWriterPidPath(root), 'utf8'));
expect(info?.pid).toBe(process.pid);
expect(info?.mode).toBe('direct');
releaseWriterLock(root);
expect(fs.existsSync(getWriterPidPath(root))).toBe(false);
});
it('is re-entrant for the same pid', () => {
const root = makeProject();
expect(tryAcquireWriterLock(root, 'daemon').kind).toBe('acquired');
const again = tryAcquireWriterLock(root, 'fallback');
expect(again.kind).toBe('acquired');
releaseWriterLock(root);
});
it('reports taken when a live foreign pid holds the lock', () => {
const root = makeProject();
// Use our own pid first, then overwrite with a fake live-looking pid by
// writing a pid that is alive: process.pid of this test — simulate foreign
// by writing a different alive pid. On Linux, PID 1 is almost always alive.
fs.writeFileSync(
getWriterPidPath(root),
JSON.stringify({ pid: 1, mode: 'direct', startedAt: Date.now() }) + '\n',
{ flag: 'wx' },
);
const r = tryAcquireWriterLock(root, 'direct');
expect(r.kind).toBe('taken');
if (r.kind === 'taken') {
expect(r.existing?.pid).toBe(1);
const msg = writerLockHeldMessage(r.existing, r.pidPath);
expect(msg).toMatch(/writer lock held/i);
expect(msg).toMatch(/CODEGRAPH_NO_DAEMON/);
expect(msg).toMatch(/daemon stop/);
}
});
it('clears a stale dead-pid lock and acquires', () => {
const root = makeProject();
// Pick a pid that is extremely unlikely to be alive.
const deadPid = 2147483646;
fs.writeFileSync(
getWriterPidPath(root),
JSON.stringify({ pid: deadPid, mode: 'direct', startedAt: Date.now() }) + '\n',
);
const r = tryAcquireWriterLock(root, 'direct');
expect(r.kind).toBe('acquired');
releaseWriterLock(root);
});
});
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@@ -55,6 +55,7 @@ import {
getDaemonSocketPath,
} from './daemon-paths';
import { CodeGraphPackageVersion } from './version';
import { releaseWriterLock, tryAcquireWriterLock, writerLockHeldMessage } from './writer-lock';
import { registerDaemon, deregisterDaemon } from './daemon-registry';
/** Default idle linger after the last client disconnects. */
@@ -204,6 +205,16 @@ export class Daemon {
* listening the daemon then sticks around until idle/shutdown.
*/
async start(): Promise<DaemonStartResult> {
// #1740: claim the project writer lock before opening/watching so a
// concurrent direct-mode serve --mcp cannot start a second watcher.
const writer = tryAcquireWriterLock(this.projectRoot, 'daemon');
if (writer.kind === 'taken') {
const msg = writerLockHeldMessage(writer.existing, writer.pidPath);
process.stderr.write(`[CodeGraph daemon] ${msg}\n`);
this.cleanupLockfile();
throw new Error(msg);
}
// Engine init is deliberately backgrounded — see #172. The first session
// to land waits on `ensureInitialized` either way, and unloaded sessions
// (cross-project tool calls only) shouldn't pay any open cost.
@@ -498,6 +509,7 @@ export class Daemon {
}
private cleanupLockfile(): void {
releaseWriterLock(this.projectRoot);
try {
if (fs.existsSync(this.pidPath)) {
// Only remove if it still belongs to us — another daemon may have
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@@ -16,6 +16,7 @@ import type CodeGraph from '../index';
import { resolveServerRoot } from '../directory';
import { watchDisabledReason } from '../sync';
import { ToolHandler } from './tools';
import { releaseWriterLock, tryAcquireWriterLock, writerLockHeldMessage } from './writer-lock';
import { QueryPool, resolvePoolSize } from './query-pool';
// Lazy-load the heavy CodeGraph chain (sqlite + query/graph/context layers) OFF
@@ -67,6 +68,8 @@ export class MCPEngine {
// bounded but shouldn't run on every tool call in the no-default state.
private lastRetrySubScanAt = 0;
private watcherStarted = false;
/** Set when this engine holds writer.pid (#1740). */
private writerLockRoot: string | null = null;
private opts: Required<MCPEngineOptions>;
private closed = false;
// Off-loop read-tool pool (daemon mode only). Created lazily once the default
@@ -203,6 +206,10 @@ export class MCPEngine {
stop(): void {
if (this.closed) return;
this.closed = true;
if (this.writerLockRoot) {
releaseWriterLock(this.writerLockRoot);
this.writerLockRoot = null;
}
// Detach + terminate the worker pool first so no tool call routes to a
// worker mid-teardown; outstanding pool calls resolve with graceful guidance.
this.toolHandler.setQueryPool(null);
@@ -278,6 +285,24 @@ export class MCPEngine {
private startWatching(): void {
if (!this.cg || this.watcherStarted || !this.opts.watch) return;
// #1740: only one live watcher/writer per project. Daemon and startDirect
// usually already hold writer.pid (re-entrant for this pid). Proxy
// in-process fallback acquires here; if another writer holds it, skip the
// watcher so we never contend on codegraph.lock until auto-sync degrades.
const lockRoot = this.projectPath;
if (lockRoot) {
const writer = tryAcquireWriterLock(lockRoot, 'fallback');
if (writer.kind === 'taken') {
const msg = writerLockHeldMessage(writer.existing, writer.pidPath);
process.stderr.write(
`[CodeGraph MCP] File watcher not started — ${msg}\n`
);
this.watcherStarted = true;
return;
}
this.writerLockRoot = lockRoot;
}
const disabledReason = watchDisabledReason(this.projectPath ?? process.cwd());
if (disabledReason) {
process.stderr.write(
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@@ -48,6 +48,7 @@ import {
tryAcquireDaemonLock,
} from './daemon';
import { connectWithHello, runLocalHandshakeProxy } from './proxy';
import { releaseWriterLock, tryAcquireWriterLock, writerLockHeldMessage } from './writer-lock';
import { getDaemonSocketCandidates, probeDaemonIdentity } from './daemon-paths';
import { getTelemetry } from '../telemetry';
import { checkForUpdateInBackground } from '../upgrade/update-check';
@@ -252,6 +253,8 @@ export class MCPServer {
// Idempotency guard for stop().
private stopped = false;
private mode: 'unstarted' | 'direct' | 'proxy' | 'daemon' = 'unstarted';
/** Project root whose writer.pid we hold in direct mode (#1740); released on stop. */
private writerLockRoot: string | null = null;
constructor(projectPath?: string) {
this.projectPath = projectPath || null;
@@ -329,6 +332,10 @@ export class MCPServer {
stop(): void {
if (this.stopped) return;
this.stopped = true;
if (this.writerLockRoot) {
releaseWriterLock(this.writerLockRoot);
this.writerLockRoot = null;
}
if (this.ppidWatchdog) {
clearInterval(this.ppidWatchdog);
this.ppidWatchdog = null;
@@ -358,6 +365,20 @@ export class MCPServer {
if (reason && process.env.CODEGRAPH_MCP_DEBUG) {
process.stderr.write(`[CodeGraph MCP] Direct mode: ${reason}.\n`);
}
// #1740: refuse a second direct writer on an initialized project. Daemon
// mode multiplexes clients; direct mode is single-writer-per-project.
const writerRoot = resolveDaemonRoot(this.projectPath);
if (writerRoot) {
const writer = tryAcquireWriterLock(writerRoot, 'direct');
if (writer.kind === 'taken') {
const msg = writerLockHeldMessage(writer.existing, writer.pidPath);
process.stderr.write(`[CodeGraph MCP] ${msg}\n`);
process.exit(1);
}
this.writerLockRoot = writerRoot;
}
this.engine = new MCPEngine();
const transport = new StdioTransport();
this.session = new MCPSession(transport, this.engine, {
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@@ -0,0 +1,188 @@
/**
* Project writer lock (#1740).
*
* At most one long-lived MCP *writer* (shared daemon OR direct-mode /
* in-process engine that owns the FileWatcher) may serve a given project.
* The shared daemon already multiplexes N stdio proxies onto one writer; this
* lock closes the same-OS gap where two direct-mode `serve --mcp` processes
* (via `CODEGRAPH_NO_DAEMON=1` or proxyin-process fallback) each start a
* watcher, contend on `codegraph.lock`, and degrade auto-sync.
*
* Deliberately separate from `daemon.pid`: proxies probe the daemon socket
* and may clear a live pid that has no socket. A direct-mode holder must not
* look like a daemon. `writer.pid` is only about "who owns live auto-sync".
*/
import * as fs from 'fs';
import * as path from 'path';
import { getCodeGraphDir } from '../directory';
/** Signal-0 liveness (EPERM ⇒ alive). Local copy to avoid a daemon↔writer cycle. */
function isProcessAlive(pid: number): boolean {
try {
process.kill(pid, 0);
return true;
} catch (err: unknown) {
const e = err as NodeJS.ErrnoException;
if (e.code === 'EPERM') return true;
return false;
}
}
/** Absolute path to the writer pid lockfile for `projectRoot`. */
export function getWriterPidPath(projectRoot: string): string {
let root = projectRoot;
try { root = fs.realpathSync(projectRoot); } catch { /* keep lexical */ }
return path.join(getCodeGraphDir(root), 'writer.pid');
}
/** Structured contents of the writer pidfile. */
export interface WriterLockInfo {
pid: number;
/** `direct` | `daemon` | `fallback` — for actionable error text only. */
mode: string;
startedAt: number;
}
export type WriterAcquireResult =
| { kind: 'acquired'; pidPath: string; info: WriterLockInfo }
| { kind: 'taken'; existing: WriterLockInfo | null; pidPath: string };
function encode(info: WriterLockInfo): string {
return JSON.stringify(info) + '\n';
}
export function decodeWriterLockInfo(raw: string): WriterLockInfo | null {
try {
const parsed = JSON.parse(raw.trim()) as Partial<WriterLockInfo>;
if (typeof parsed.pid !== 'number' || typeof parsed.mode !== 'string') return null;
return {
pid: parsed.pid,
mode: parsed.mode,
startedAt: typeof parsed.startedAt === 'number' ? parsed.startedAt : 0,
};
} catch {
return null;
}
}
/**
* Atomically create `writer.pid` (link-into-place, O_EXCL fallback). If held
* by a dead PID, clear and retry once. Does not steal from a live holder.
*/
export function tryAcquireWriterLock(
projectRoot: string,
mode: string,
): WriterAcquireResult {
const pidPath = getWriterPidPath(projectRoot);
fs.mkdirSync(path.dirname(pidPath), { recursive: true });
const info: WriterLockInfo = {
pid: process.pid,
mode,
startedAt: Date.now(),
};
const attempt = (): WriterAcquireResult => {
const tmp = `${pidPath}.${process.pid}.tmp`;
let acquired = false;
try {
fs.writeFileSync(tmp, encode(info), { mode: 0o600 });
try {
fs.linkSync(tmp, pidPath);
acquired = true;
} catch (err: unknown) {
if ((err as NodeJS.ErrnoException).code === 'EEXIST') {
// taken
} else {
// No hard links — O_EXCL create.
try {
const fd = fs.openSync(pidPath, 'wx', 0o600);
try {
fs.writeSync(fd, encode(info));
acquired = true;
} finally {
fs.closeSync(fd);
}
} catch (e2: unknown) {
if ((e2 as NodeJS.ErrnoException).code !== 'EEXIST') throw e2;
}
}
}
} finally {
try { fs.unlinkSync(tmp); } catch { /* ignore */ }
}
if (acquired) return { kind: 'acquired', pidPath, info };
let existing: WriterLockInfo | null = null;
try {
existing = decodeWriterLockInfo(fs.readFileSync(pidPath, 'utf8'));
} catch { /* unreadable */ }
return { kind: 'taken', existing, pidPath };
};
let result = attempt();
if (result.kind === 'taken' && result.existing && result.existing.pid === process.pid) {
// Same process already holds it (daemon acquired before engine watch).
return { kind: 'acquired', pidPath: result.pidPath, info: result.existing };
}
if (result.kind === 'taken') {
const existing = result.existing;
if (!existing || existing.pid <= 0 || !isProcessAlive(existing.pid)) {
// Stale — clear (pid-verified) and retry once.
try {
const raw = fs.readFileSync(pidPath, 'utf8');
const cur = decodeWriterLockInfo(raw);
if (!cur || cur.pid === existing?.pid) {
if (!cur || cur.pid <= 0 || !isProcessAlive(cur.pid)) {
fs.unlinkSync(pidPath);
}
}
} catch { /* ENOENT ok */ }
result = attempt();
}
}
return result;
}
/** Release if we still own the lock (pid match). */
export function releaseWriterLock(projectRoot: string): void {
const pidPath = getWriterPidPath(projectRoot);
try {
if (!fs.existsSync(pidPath)) return;
const info = decodeWriterLockInfo(fs.readFileSync(pidPath, 'utf8'));
if (info && info.pid === process.pid) {
fs.unlinkSync(pidPath);
}
} catch { /* best-effort */ }
}
/** Read current lock without acquiring. */
export function readWriterLock(projectRoot: string): WriterLockInfo | null {
const pidPath = getWriterPidPath(projectRoot);
try {
return decodeWriterLockInfo(fs.readFileSync(pidPath, 'utf8'));
} catch {
return null;
}
}
/**
* Actionable message when another live process owns the writer lock (#1740).
*/
export function writerLockHeldMessage(
existing: WriterLockInfo | null,
pidPath: string,
): string {
const who = existing && existing.pid > 0
? `PID ${existing.pid} (${existing.mode || 'unknown'} mode)`
: 'another process';
return (
'CodeGraph writer lock held by ' + who + '. ' +
'Only one live MCP writer may serve a project (auto-sync / index). ' +
'Stop the other server (codegraph daemon stop if a shared daemon, or end the other MCP session), ' +
'or unset CODEGRAPH_NO_DAEMON so additional clients proxy to the shared daemon. ' +
'If this is stale, delete ' + pidPath
);
}