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-initialize.test.ts

@@ -23,6 +23,14 @@ function spawnServer(cwd: string): ChildProcessWithoutNullStreams {
   return spawn(process.execPath, [BIN, 'serve', '--mcp'], {
     cwd,
     stdio: ['pipe', 'pipe', 'pipe'],
+    // Pin to direct (in-process) mode. #172 is a contract about the in-process
+    // server's init ordering — the "File watcher active" log this test observes
+    // is emitted in-process. In daemon mode the watcher runs in the detached
+    // daemon (logging to .codegraph/daemon.log, not the child's stderr); the
+    // same response-before-init guarantee lives in the shared session code and
+    // is covered by mcp-daemon.test.ts. Direct mode also avoids leaking a
+    // detached daemon from this suite.
+    env: { ...process.env, CODEGRAPH_NO_DAEMON: '1' },
   }) as ChildProcessWithoutNullStreams;
 }