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If a commit that you check out or pull removes a submodule, git leaves the submodule's directory behind, and git status reports it as an untracked directory. The files panel shows that directory with a file below it that has no name. Discarding the directory shows an error, even though the directory is gone afterwards. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>