When the indexed root is a directory an enclosing git repo ignores,
`git ls-files --directory` collapses the whole cwd to a single literal
`./` entry. That sentinel reached the `ignore` matcher, which rejects it
("path should be a `path.relative()`d string, but got "./""), aborting
buildScopeIgnore — the one ignore-building call in FileWatcher.start().
So the MCP daemon's startWatching() threw, was caught as "Failed to open
project", and auto-sync never started: the index silently went stale
until a manual `codegraph sync` (CODEGRAPH_NO_DAEMON=1 was the only
workaround).
Filter the `./`/`.` self-entry wherever we consume `--directory` output
(listIgnoredDirs + the untracked-dir loop in discoverEmbeddedRepoRoots).
Semantically correct, not just a crash guard: `./` means "the whole cwd",
never a nested repo to recurse into.
Not platform-specific (reported on Codex/Windows, reproduced on macOS):
the trigger is git state, not the OS.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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