fix(mcp): prevent "Transport closed" from a stray daemon-socket error (#974) (#983)

The client-facing MCP proxy could exit with "Transport closed" when its
connection to the shared daemon hit a socket 'error' with no listener
attached — common on WSL2 /mnt (DrvFs), where AF_UNIX is flaky. The global
fatal handler turned that uncaughtException into process.exit(1), which the
MCP client saw as a bare transport close even though the index was healthy.

proxy.ts now keeps an 'error' listener on the daemon socket for its whole
life (and skips a socket destroyed in the connect window), so a stray error
degrades to the existing in-process fallback instead of crashing. daemon.ts
releases the lockfile it acquired when it fails to bind, so the next launch
doesn't spin on a stale lock (the duplicate serve --mcp pileup).

No default behavior change for anyone; WSL /mnt users who still hit trouble
can set CODEGRAPH_NO_DAEMON=1 to skip the shared daemon entirely. Validated
on macOS (unit + live serve probe) and Linux (Docker, --init): 64/64 across
the daemon/socket/lifecycle suites, incl. real AF_UNIX.

Closes #974

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

CHANGELOG.md

@@ -12,6 +12,8 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 ### Fixes
 
 - CodeGraph respects your `.gitignore` again when looking for nested git repositories. A directory you've gitignored — a `resource/` or `.repos/` folder of cloned reference projects, a large vendored data dir — is no longer walked into and indexed: version 1.0.0 started searching inside *every* gitignored directory for embedded git repos and pulling them all in, which could multiply a graph many times over and slow indexing to a crawl on a multi-gigabyte folder of clones, even though you'd explicitly excluded it. Indexing the repos inside a gitignored directory is now opt-in — add an `includeIgnored` list to a `codegraph.json` at your repo root, e.g. `{ "includeIgnored": ["packages/", "services/"] }`, to index the embedded repos under the directories you name. The "super-repo of independent clones" layout from 1.0.0 still works, just declared explicitly. Nested repos you *haven't* gitignored (untracked clones) are indexed as before, and a project without this layout is unaffected. (#970, #976, #622)
+- The MCP server no longer drops out with `Transport closed` when its connection to the shared background server hits a transient socket error. To serve all your editor/agent sessions from a single index, CodeGraph runs one shared background server they reach over a local socket; a stray error on that socket while a session was connecting used to take the whole server process down, so your agent saw a bare `Transport closed` even though `codegraph status` and `codegraph sync` were perfectly healthy. Now such an error is handled gracefully — the session falls back to serving itself in-process instead of crashing. This is most common on WSL2 when your project lives on a Windows drive (a `/mnt/c` or `/mnt/d` path), where that socket is flaky; if you still hit problems there, set `CODEGRAPH_NO_DAEMON=1` to skip the shared server entirely and run each session in its own process. Affects Codex and any other MCP client. (#974)
+- A shared background server that can't bind its socket now cleans up its own lock file before exiting, instead of leaving a stale lock that the next launch trips over — which previously could let duplicate `serve --mcp` processes pile up for the same project. (#974)
 
 
 ## [1.1.0] - 2026-06-23