Add installed-file tracking with SHA-256 hashes for safe agent teardown

Setup records installed files and their SHA-256 hashes in
.specify/agent-manifest-<agent_id>.json. Teardown uses the manifest
to remove only individual files (never directories). If any tracked
file was modified since installation, teardown requires --force.

- Add record_installed_files(), check_modified_files(), remove_tracked_files()
  and AgentFileModifiedError to agent_pack.py
- Update all 25 bootstrap modules to use file-tracked setup/teardown
- Add --force flag to 'specify agent switch'
- Add 11 new tests for file tracking (record, check, remove, force,
  directory preservation, deleted-file handling, manifest structure)

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/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
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Agy(AgentBootstrap):
@@ -16,10 +16,15 @@ class Agy(AgentBootstrap):
         """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) -> None:
-        """Remove Antigravity agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Antigravity agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Amp(AgentBootstrap):
@@ -16,18 +16,15 @@ class Amp(AgentBootstrap):
         """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) -> None:
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
         """Remove Amp agent files from the project.
 
-        Only removes the commands/ subdirectory — preserves other .agents/
-        content (e.g. Codex skills/) which shares the same parent directory.
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
         """
-        import shutil
-        commands_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
-        if commands_dir.is_dir():
-            shutil.rmtree(commands_dir)
-        # Remove .agents/ only if now empty
-        agents_dir = project_path / self.AGENT_DIR
-        if agents_dir.is_dir() and not any(agents_dir.iterdir()):
-            agents_dir.rmdir()
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Auggie(AgentBootstrap):
@@ -16,10 +16,15 @@ class Auggie(AgentBootstrap):
         """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) -> None:
-        """Remove Auggie CLI agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Auggie CLI agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Bob(AgentBootstrap):
@@ -16,10 +16,15 @@ class Bob(AgentBootstrap):
         """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) -> None:
-        """Remove IBM Bob agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove IBM Bob agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Claude(AgentBootstrap):
@@ -16,10 +16,15 @@ class Claude(AgentBootstrap):
         """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) -> None:
-        """Remove Claude Code agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Claude Code agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Codebuddy(AgentBootstrap):
@@ -16,10 +16,15 @@ class Codebuddy(AgentBootstrap):
         """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) -> None:
-        """Remove CodeBuddy agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove CodeBuddy agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Codex(AgentBootstrap):
@@ -16,18 +16,15 @@ class Codex(AgentBootstrap):
         """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) -> None:
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
         """Remove Codex CLI agent files from the project.
 
-        Only removes the skills/ subdirectory — preserves other .agents/
-        content (e.g. Amp commands/) which shares the same parent directory.
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
         """
-        import shutil
-        skills_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
-        if skills_dir.is_dir():
-            shutil.rmtree(skills_dir)
-        # Remove .agents/ only if now empty
-        agents_dir = project_path / self.AGENT_DIR
-        if agents_dir.is_dir() and not any(agents_dir.iterdir()):
-            agents_dir.rmdir()
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Copilot(AgentBootstrap):
@@ -16,18 +16,15 @@ class Copilot(AgentBootstrap):
         """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) -> None:
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
         """Remove GitHub Copilot agent files from the project.
 
-        Only removes the agents/ subdirectory — preserves other .github
-        content (workflows, issue templates, etc.).
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
         """
-        import shutil
-        agents_dir = project_path / self.AGENT_DIR / self.COMMANDS_SUBDIR
-        if agents_dir.is_dir():
-            shutil.rmtree(agents_dir)
-        # Also clean up companion .github/prompts/ if empty
-        prompts_dir = project_path / self.AGENT_DIR / "prompts"
-        if prompts_dir.is_dir() and not any(prompts_dir.iterdir()):
-            prompts_dir.rmdir()
+        remove_tracked_files(project_path, self.manifest.id, force=force)

src/specify_cli/core_pack/agents/cursor-agent/bootstrap.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class CursorAgent(AgentBootstrap):
@@ -16,10 +16,15 @@ class CursorAgent(AgentBootstrap):
         """Install Cursor 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) -> None:
-        """Remove Cursor agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Cursor agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Gemini(AgentBootstrap):
@@ -16,10 +16,15 @@ class Gemini(AgentBootstrap):
         """Install Gemini 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) -> None:
-        """Remove Gemini CLI agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Gemini CLI agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Iflow(AgentBootstrap):
@@ -16,10 +16,15 @@ class Iflow(AgentBootstrap):
         """Install iFlow 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) -> None:
-        """Remove iFlow CLI agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove iFlow CLI agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Junie(AgentBootstrap):
@@ -16,10 +16,15 @@ class Junie(AgentBootstrap):
         """Install Junie 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) -> None:
-        """Remove Junie agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Junie agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Kilocode(AgentBootstrap):
@@ -16,10 +16,15 @@ class Kilocode(AgentBootstrap):
         """Install Kilo 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) -> None:
-        """Remove Kilo Code agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Kilo Code agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Kimi(AgentBootstrap):
@@ -16,10 +16,15 @@ class Kimi(AgentBootstrap):
         """Install Kimi 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) -> None:
-        """Remove Kimi Code agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Kimi Code agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

src/specify_cli/core_pack/agents/kiro-cli/bootstrap.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class KiroCli(AgentBootstrap):
@@ -16,10 +16,15 @@ class KiroCli(AgentBootstrap):
         """Install Kiro 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) -> None:
-        """Remove Kiro CLI agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Kiro CLI agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Opencode(AgentBootstrap):
@@ -16,10 +16,15 @@ class Opencode(AgentBootstrap):
         """Install opencode 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) -> None:
-        """Remove opencode agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove opencode agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Pi(AgentBootstrap):
@@ -16,10 +16,15 @@ class Pi(AgentBootstrap):
         """Install Pi Coding Agent 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) -> None:
-        """Remove Pi Coding Agent agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Pi Coding Agent agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Qodercli(AgentBootstrap):
@@ -16,10 +16,15 @@ class Qodercli(AgentBootstrap):
         """Install Qoder 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) -> None:
-        """Remove Qoder CLI agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Qoder CLI agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Qwen(AgentBootstrap):
@@ -16,10 +16,15 @@ class Qwen(AgentBootstrap):
         """Install Qwen 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) -> None:
-        """Remove Qwen Code agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Qwen Code agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Roo(AgentBootstrap):
@@ -16,10 +16,15 @@ class Roo(AgentBootstrap):
         """Install Roo 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) -> None:
-        """Remove Roo Code agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Roo Code agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Shai(AgentBootstrap):
@@ -16,10 +16,15 @@ class Shai(AgentBootstrap):
         """Install SHAI 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) -> None:
-        """Remove SHAI agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove SHAI agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Tabnine(AgentBootstrap):
@@ -16,18 +16,15 @@ class Tabnine(AgentBootstrap):
         """Install Tabnine 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) -> None:
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
         """Remove Tabnine CLI agent files from the project.
 
-        Removes the agent/ subdirectory under .tabnine/ to preserve
-        any other Tabnine configuration.
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
         """
-        import shutil
-        agent_subdir = project_path / self.AGENT_DIR
-        if agent_subdir.is_dir():
-            shutil.rmtree(agent_subdir)
-        # Remove .tabnine/ only if now empty
-        tabnine_dir = project_path / ".tabnine"
-        if tabnine_dir.is_dir() and not any(tabnine_dir.iterdir()):
-            tabnine_dir.rmdir()
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Trae(AgentBootstrap):
@@ -16,10 +16,15 @@ class Trae(AgentBootstrap):
         """Install Trae 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) -> None:
-        """Remove Trae agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Trae agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Vibe(AgentBootstrap):
@@ -16,10 +16,15 @@ class Vibe(AgentBootstrap):
         """Install Mistral Vibe 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) -> None:
-        """Remove Mistral Vibe agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Mistral Vibe agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)

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

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Any, Dict
 
-from specify_cli.agent_pack import AgentBootstrap
+from specify_cli.agent_pack import AgentBootstrap, record_installed_files, remove_tracked_files
 
 
 class Windsurf(AgentBootstrap):
@@ -16,10 +16,15 @@ class Windsurf(AgentBootstrap):
         """Install Windsurf 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) -> None:
-        """Remove Windsurf agent files from the project."""
-        import shutil
-        agent_dir = project_path / self.AGENT_DIR
-        if agent_dir.is_dir():
-            shutil.rmtree(agent_dir)
+    def teardown(self, project_path: Path, *, force: bool = False) -> None:
+        """Remove Windsurf agent files from the project.
+
+        Only removes individual tracked files — directories are never
+        deleted.  Raises ``AgentFileModifiedError`` if any tracked file
+        was modified and *force* is ``False``.
+        """
+        remove_tracked_files(project_path, self.manifest.id, force=force)