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

Author: Copilot

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}")

src/specify_cli/agent_pack.py

@@ -222,6 +222,22 @@ def agent_dir(self, project_path: Path) -> Path:
         """Return the agent's top-level directory inside the project."""
         return project_path / self.manifest.commands_dir.split("/")[0]
 
+    def finalize_setup(self, project_path: Path) -> None:
+        """Record all files in the agent directory for tracked teardown.
+
+        This must be called **after** the full init pipeline has finished
+        writing files (commands, context files, etc.) into the agent
+        directory.  It scans ``self.manifest.commands_dir`` and records
+        every file with its SHA-256 hash so that :meth:`teardown` can
+        detect user modifications.
+        """
+        if not self.manifest.commands_dir:
+            return
+        commands_dir = project_path / self.manifest.commands_dir
+        if commands_dir.is_dir():
+            installed = [p for p in commands_dir.rglob("*") if p.is_file()]
+            record_installed_files(project_path, self.manifest.id, installed)
+
 
 # ---------------------------------------------------------------------------
 # Installed-file tracking

src/specify_cli/core_pack/agents/agy/bootstrap.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
 
 
 class Agy(AgentBootstrap):
@@ -16,9 +16,6 @@ def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -
         """Install Antigravity agent files into the project."""
         commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
         commands_dir.mkdir(parents=True, exist_ok=True)
-        # Record installed files for tracked teardown
-        installed = [p for p in commands_dir.rglob("*") if p.is_file()]
-        record_installed_files(project_path, self.manifest.id, installed)
 
     def teardown(self, project_path: Path, *, force: bool = False) -> None:
         """Remove Antigravity agent files from the project.

src/specify_cli/core_pack/agents/amp/bootstrap.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
 
 
 class Amp(AgentBootstrap):
@@ -16,9 +16,6 @@ def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -
         """Install Amp agent files into the project."""
         commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
         commands_dir.mkdir(parents=True, exist_ok=True)
-        # Record installed files for tracked teardown
-        installed = [p for p in commands_dir.rglob("*") if p.is_file()]
-        record_installed_files(project_path, self.manifest.id, installed)
 
     def teardown(self, project_path: Path, *, force: bool = False) -> None:
         """Remove Amp agent files from the project.

src/specify_cli/core_pack/agents/auggie/bootstrap.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
 
 
 class Auggie(AgentBootstrap):
@@ -16,9 +16,6 @@ def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -
         """Install Auggie CLI agent files into the project."""
         commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
         commands_dir.mkdir(parents=True, exist_ok=True)
-        # Record installed files for tracked teardown
-        installed = [p for p in commands_dir.rglob("*") if p.is_file()]
-        record_installed_files(project_path, self.manifest.id, installed)
 
     def teardown(self, project_path: Path, *, force: bool = False) -> None:
         """Remove Auggie CLI agent files from the project.

src/specify_cli/core_pack/agents/bob/bootstrap.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
 
 
 class Bob(AgentBootstrap):
@@ -16,9 +16,6 @@ def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -
         """Install IBM Bob agent files into the project."""
         commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
         commands_dir.mkdir(parents=True, exist_ok=True)
-        # Record installed files for tracked teardown
-        installed = [p for p in commands_dir.rglob("*") if p.is_file()]
-        record_installed_files(project_path, self.manifest.id, installed)
 
     def teardown(self, project_path: Path, *, force: bool = False) -> None:
         """Remove IBM Bob agent files from the project.

src/specify_cli/core_pack/agents/claude/bootstrap.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
 
 
 class Claude(AgentBootstrap):
@@ -16,9 +16,6 @@ def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -
         """Install Claude Code agent files into the project."""
         commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
         commands_dir.mkdir(parents=True, exist_ok=True)
-        # Record installed files for tracked teardown
-        installed = [p for p in commands_dir.rglob("*") if p.is_file()]
-        record_installed_files(project_path, self.manifest.id, installed)
 
     def teardown(self, project_path: Path, *, force: bool = False) -> None:
         """Remove Claude Code agent files from the project.

src/specify_cli/core_pack/agents/codebuddy/bootstrap.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
 
 
 class Codebuddy(AgentBootstrap):
@@ -16,9 +16,6 @@ def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -
         """Install CodeBuddy agent files into the project."""
         commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
         commands_dir.mkdir(parents=True, exist_ok=True)
-        # Record installed files for tracked teardown
-        installed = [p for p in commands_dir.rglob("*") if p.is_file()]
-        record_installed_files(project_path, self.manifest.id, installed)
 
     def teardown(self, project_path: Path, *, force: bool = False) -> None:
         """Remove CodeBuddy agent files from the project.

src/specify_cli/core_pack/agents/codex/bootstrap.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
 
 
 class Codex(AgentBootstrap):
@@ -16,9 +16,6 @@ def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -
         """Install Codex CLI agent files into the project."""
         commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
         commands_dir.mkdir(parents=True, exist_ok=True)
-        # Record installed files for tracked teardown
-        installed = [p for p in commands_dir.rglob("*") if p.is_file()]
-        record_installed_files(project_path, self.manifest.id, installed)
 
     def teardown(self, project_path: Path, *, force: bool = False) -> None:
         """Remove Codex CLI agent files from the project.

src/specify_cli/core_pack/agents/copilot/bootstrap.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
+from specify_cli.agent_pack import AgentBootstrap, remove_tracked_files
 
 
 class Copilot(AgentBootstrap):
@@ -16,9 +16,6 @@ def setup(self, project_path: Path, script_type: str, options: Dict[str, Any]) -
         """Install GitHub Copilot agent files into the project."""
         commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
         commands_dir.mkdir(parents=True, exist_ok=True)
-        # Record installed files for tracked teardown
-        installed = [p for p in commands_dir.rglob("*") if p.is_file()]
-        record_installed_files(project_path, self.manifest.id, installed)
 
     def teardown(self, project_path: Path, *, force: bool = False) -> None:
         """Remove GitHub Copilot agent files from the project.