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If you staged the directory of a removed submodule, a nested repository or a worktree inside the repo, git added it as an embedded repository: a gitlink without an entry in .gitmodules. For a removed submodule, this brings it back in a broken state. git warns about it, but lazygit didn't show the warning. Staging all files did the same to every such directory. Disable staging a selection that contains one of these, and disable staging all files if that would stage one. The disabled reason tells you how to get rid of it. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>