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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)