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- setup() returns List[Path] of installed files so CLI can record them - finalize_setup() accepts agent_files + extension_files for combined tracking - Install manifest categorises files: agent_files and extension_files - get_tracked_files() returns (agent_files, extension_files) split - remove_tracked_files() accepts explicit files dict for CLI-driven teardown - agent_switch checks for modifications BEFORE teardown and prompts user - _reregister_extension_commands() returns List[Path] of created files - teardown() accepts files parameter to receive explicit file lists - All 25 bootstraps updated with new signatures - 5 new tests: categorised manifest, get_tracked_files, explicit file teardown, extension file modification detection Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com> Agent-Logs-Url: https://github.com/github/spec-kit/sessions/32e470fc-6bf5-453c-bf6c-79a8521efa56