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Discarding a nested repository deletes its directory like that of any untracked file. If the repository keeps its git dir in its directory, this deletes all of its history, and nothing said so. The directory of a removed submodule keeps its git dir elsewhere, but it may have changes that aren't committed. Check for both before discarding. If anything would be lost, list it and ask for confirmation. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>