Move file recording to finalize_setup() — called after init pipeline writes files

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

src/specify_cli/__init__.py

@@ -2604,6 +2604,8 @@ def agent_switch(
         new_bootstrap = load_bootstrap(resolved.path, resolved.manifest)
         console.print(f"  [dim]Setting up {agent_id}...[/dim]")
         new_bootstrap.setup(project_path, script_type, options)
+        # Record all installed files for tracked teardown
+        new_bootstrap.finalize_setup(project_path)
         console.print(f"  [green]✓[/green] {agent_id} installed")
     except AgentPackError as exc:
         console.print(f"[red]Error setting up {agent_id}:[/red] {exc}")