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- CodeGraph now indexes nested repositories that git records as gitlinks, so a workspace built by stacking several repos inside one another indexes completely from a single `codegraph init` at the top. When a repo contains another git repo that was `git add`ed into it — so git tracks it as a `160000` "commit" pointer rather than a folder of files — or a submodule that isn't an active, initialized submodule in your checkout, that nested repo's source used to be skipped entirely: indexing the top level stopped at the nested repo's boundary and pulled in only the outer repo's own files, so a stacked-repo project came up nearly empty (one report saw ~10 files indexed at the root). CodeGraph now descends into each such nested repo that has a real working tree on disk and indexes it as its own embedded repository, recursively, so every layer of a stacked workspace is covered. Active submodules (already handled) and plain untracked nested clones are unchanged; a nested repo under a dependency directory such as `vendor/` or `node_modules/` stays excluded; and a submodule with nothing checked out on disk is correctly left alone rather than reported as empty. Thanks @ofergr and @kun-yx for the reports. (#1031, #1033)
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- CodeGraph no longer shows a misleading "different git working tree" warning when you work inside a submodule (or other nested repo) of a workspace you indexed at its root. Because indexing a workspace now pulls in its submodules and embedded clones, a query run from inside one correctly resolves up to the workspace's single index — but it was still warning that the results came from "a different working tree" and suggesting you run `codegraph init -i`, which would have split the submodule back out into its own separate index and undone the unified view. CodeGraph now recognizes that the nested repo's code is already part of the workspace index and stays quiet. The warning still appears for a genuine git worktree — a second checkout of the *same* repository on another branch, which really does have its own uncommitted symbols — since that's the case it exists for. (#1031, #1033)
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+- On Windows, CodeGraph's background server now shuts down cleanly instead of occasionally aborting with a crash error. When the indexed project contained a nested repository (a submodule or embedded clone), stopping the server could race the file watcher's teardown and exit with a Windows crash code rather than a clean exit. Shutdown now lets that teardown finish first, so the server stops cleanly and promptly. (Windows only; other platforms were unaffected.) (#1033)
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Colby Mchenry