Indexing a super-repo now descends into its submodules and gitlinked clones, so
a query run from inside one resolves up to the parent's unified index — whose
graph DOES contain that nested repo's files. But the git-worktree-mismatch
warning still fired, telling the agent the results were from "a different working
tree" and to run `codegraph init -i` — which would split the submodule back into
its own index and undo the unified view. A false positive carrying harmful advice.
Distinguish a genuine borrowed worktree (the SAME repository on a different
branch — shares a git common dir with the index root) from a submodule/embedded
clone (a DIFFERENT repository — its own common dir), and suppress the warning
only for the latter. Add gitCommonDir() for the check. The issue-#155 linked-worktree
case is unchanged.
Verified end-to-end: the warning no longer fires for a submodule-rooted MCP
session and still fires for a real linked worktree. Edit-sync (manual sync +
the live watcher) keeps the nested repo's files current on both macOS and Linux
(active-submodule and bare-gitlink shapes), so suppressing the warning is safe.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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