fix: harden daemon and large-index recovery paths (#1562)

* fix: harden indexing recovery and daemon liveness

* test: cover daemon and recovery review gaps

* test: pin that a failure marker never blocks a later successful parse (#1557 retry-discard guard)

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

---------

Co-authored-by: danusha2345 <ewidusoc498@gmail.com>
Co-authored-by: Colby McHenry <me@colbymchenry.com>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

src/mcp/daemon-paths.ts

@@ -29,6 +29,7 @@
  */
 
 import * as crypto from 'crypto';
+import * as net from 'net';
 import * as os from 'os';
 import * as path from 'path';
 import { getCodeGraphDir } from '../directory';
@@ -101,6 +102,55 @@ export interface DaemonLockInfo {
   startedAt: number;
 }
 
+/**
+ * Verify that the process named by a lockfile is the CodeGraph daemon serving
+ * its socket. A bare PID liveness probe is insufficient because OSes reuse PIDs
+ * after an OOM/SIGKILL (#1553).
+ */
+export function probeDaemonIdentity(info: DaemonLockInfo, timeoutMs = 1_000): Promise<boolean> {
+  if (!Number.isInteger(info.pid) || info.pid <= 0 || !info.socketPath) return Promise.resolve(false);
+  return new Promise<boolean>((resolve) => {
+    let socket: net.Socket;
+    let buffer = '';
+    let done = false;
+    const finish = (ok: boolean) => {
+      if (done) return;
+      done = true;
+      clearTimeout(timer);
+      socket.destroy();
+      resolve(ok);
+    };
+    const timer = setTimeout(() => finish(false), timeoutMs);
+    timer.unref?.();
+    try {
+      socket = net.createConnection(info.socketPath);
+    } catch {
+      clearTimeout(timer);
+      resolve(false);
+      return;
+    }
+    socket.setEncoding('utf8');
+    socket.on('data', (chunk) => {
+      buffer += String(chunk);
+      if (buffer.length > 4096) return finish(false);
+      const newline = buffer.indexOf('\n');
+      if (newline < 0) return;
+      try {
+        const hello = JSON.parse(buffer.slice(0, newline)) as Record<string, unknown>;
+        finish(
+          hello.protocol === 1 &&
+          hello.pid === info.pid &&
+          (info.version === 'unknown' || hello.codegraph === info.version)
+        );
+      } catch {
+        finish(false);
+      }
+    });
+    socket.on('error', () => finish(false));
+    socket.on('close', () => finish(false));
+  });
+}
+
 /**
  * Serialize a {@link DaemonLockInfo} for writing to the pidfile. JSON for
  * human readability — operators occasionally `cat` this when debugging.