fix(agents): remove empty skill parent dir on unregister (#2017)

When unregistering a SKILL.md-based command (claude, codex, kimi, agy),
the SKILL.md file was unlinked but the now-empty parent directory
(e.g. .claude/skills/speckit-myext-run/) was left behind. After unlinking
the file, attempt rmdir on the parent — a best-effort cleanup that is
silently ignored if the directory is non-empty or already gone.

Add test_unregister_skill_removes_parent_directory to cover this.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: iamaeroplane

src/specify_cli/agents.py

@@ -553,6 +553,14 @@ def unregister_commands(
                 cmd_file = commands_dir / f"{output_name}{agent_config['extension']}"
                 if cmd_file.exists():
                     cmd_file.unlink()
+                    # For SKILL.md agents the file lives in a subdirectory
+                    # (e.g. .claude/skills/speckit-foo/SKILL.md). Remove the
+                    # now-empty parent directory so no orphaned dirs remain.
+                    if agent_config["extension"] == "/SKILL.md":
+                        try:
+                            cmd_file.parent.rmdir()
+                        except OSError:
+                            pass  # not empty or already gone — leave it
 
                 if agent_name == "copilot":
                     prompt_file = project_root / ".github" / "prompts" / f"{cmd_name}.prompt.md"

tests/test_extensions.py

@@ -1262,6 +1262,21 @@ def test_unregister_commands_for_codex_skills_uses_mapped_names(self, project_di
         assert not (skills_dir / "speckit-specify" / "SKILL.md").exists()
         assert not (skills_dir / "speckit-shortcut" / "SKILL.md").exists()
 
+    def test_unregister_skill_removes_parent_directory(self, project_dir):
+        """Removing a SKILL.md-based command also removes the empty parent directory."""
+        skills_dir = project_dir / ".agents" / "skills"
+        (skills_dir / "speckit-myext-run").mkdir(parents=True)
+        (skills_dir / "speckit-myext-run" / "SKILL.md").write_text("body")
+
+        registrar = CommandRegistrar()
+        registrar.unregister_commands(
+            {"codex": ["speckit.myext.run"]},
+            project_dir,
+        )
+
+        assert not (skills_dir / "speckit-myext-run" / "SKILL.md").exists()
+        assert not (skills_dir / "speckit-myext-run").exists()
+
     def test_register_commands_for_all_agents_distinguishes_codex_from_amp(self, extension_dir, project_dir):
         """A Codex project under .agents/skills should not implicitly activate Amp."""
         skills_dir = project_dir / ".agents" / "skills"