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Address code review: setup() now only creates directories, while finalize_setup() (on base class) scans the agent's commands_dir for all files and records them. This ensures files are tracked after the full init pipeline has written them, not before. - Add AgentBootstrap.finalize_setup() that scans commands_dir - Remove premature record_installed_files() from all 25 setup() methods - agent_switch calls finalize_setup() after setup() completes - Update test helper to match new pattern Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com> Agent-Logs-Url: https://github.com/github/spec-kit/sessions/779eabf6-21d5-428b-9f01-dd363df4c84a