feat(mcp): share one serve --mcp per project across MCP clients (#411)

One shared, detached daemon per project root: every `codegraph serve --mcp` is a thin stdio<->socket proxy (Unix socket / Windows named pipe) to it, so N agents in one repo share a single file watcher, SQLite connection, and tree-sitter warm-up instead of N copies. The daemon outlives any single session and reaps via client-refcount + idle timeout; `CODEGRAPH_NO_DAEMON=1` opts out.

Hardened during review: detached-process lifecycle (preserves the #277 watchdog via the proxy; the daemon no longer orphans on host SIGKILL), atomic lockfile + pid-verified stale-clear (no double-daemon on concurrent startup), realpath root canonicalization. Validated on macOS, Linux (Docker - 3x fewer inotify watches for 3 agents), and Windows (named pipes); A/B confirms byte-identical tool output vs direct mode. Closes #411.

Co-Authored-By: Colby McHenry <me@colbymchenry.com>
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

__tests__/mcp-ppid-watchdog.test.ts

@@ -103,7 +103,12 @@ describe.skipIf(process.platform === 'win32')('MCP PPID watchdog (#277)', () =>
       stdinHolder.unref();
       const child = spawn(process.execPath, [${JSON.stringify(BIN)}, 'serve', '--mcp'], {
         stdio: [stdinHolder.stdout, 'ignore', stderrFd],
-        env: { ...process.env, CODEGRAPH_PPID_POLL_MS: '200' },
+        // Pin to direct (in-process) mode: this test targets the in-process
+        // server's PPID watchdog (#277). The detached-daemon/proxy watchdog is
+        // covered separately in mcp-daemon.test.ts ("daemon survives the first
+        // client dying"). Without this the spawned process becomes a proxy and
+        // also spawns a detached daemon that would outlive the test.
+        env: { ...process.env, CODEGRAPH_PPID_POLL_MS: '200', CODEGRAPH_NO_DAEMON: '1' },
         detached: true,
       });
       child.unref();