fix: address Copilot PR review comments (round 2)

- Fix init --preset error masking: distinguish "not found" from real errors
- Fix bash resolve_template: skip hidden dirs in extensions (match Python/PS)
- Fix temp dir leaks in tests: use temp_dir fixture instead of mkdtemp
- Fix self-test catalog entry: add note that it's local-only (no download_url)
- Fix Windows path issue in resolve_with_source: use Path.relative_to()
- Fix skill restore path: use project's .specify/templates/commands/ not source tree
- Add encoding="utf-8" to all file read/write in agents.py
- Update test to set up core command templates for skill restoration

presets/catalog.json

@@ -5,11 +5,12 @@
   "presets": {
     "self-test": {
       "name": "Self-Test Preset",
-      "description": "A preset that overrides all core templates for testing purposes",
+      "description": "A preset that overrides all core templates for testing purposes. Install with --dev from the repo.",
       "author": "github",
       "version": "1.0.0",
       "repository": "https://github.com/github/spec-kit",
       "license": "MIT",
+      "note": "This preset is bundled with the repo and intended for local testing only. Install via: specify preset add --dev presets/self-test",
       "requires": {
         "speckit_version": ">=0.1.0"
       },

scripts/bash/common.sh

@@ -213,6 +213,8 @@ except Exception:
     if [ -d "$ext_dir" ]; then
         for ext in "$ext_dir"/*/; do
             [ -d "$ext" ] || continue
+            # Skip hidden directories (e.g. .backup, .cache)
+            case "$(basename "$ext")" in .*) continue;; esac
             local candidate="$ext/templates/${template_name}.md"
             [ -f "$candidate" ] && echo "$candidate" && return 0
         done

src/specify_cli/__init__.py

@@ -1600,17 +1600,21 @@ def init(
                         preset_manager.install_from_directory(local_path, speckit_ver)
                     else:
                         preset_catalog = PresetCatalog(project_path)
-                        try:
-                            zip_path = preset_catalog.download_pack(preset)
-                            preset_manager.install_from_zip(zip_path, speckit_ver)
-                            # Clean up downloaded ZIP to avoid cache accumulation
-                            try:
-                                zip_path.unlink(missing_ok=True)
-                            except OSError:
-                                # Best-effort cleanup; failure to delete is non-fatal
-                                pass
-                        except PresetError:
+                        pack_info = preset_catalog.get_pack_info(preset)
+                        if not pack_info:
                             console.print(f"[yellow]Warning:[/yellow] Preset '{preset}' not found in catalog. Skipping.")
+                        else:
+                            try:
+                                zip_path = preset_catalog.download_pack(preset)
+                                preset_manager.install_from_zip(zip_path, speckit_ver)
+                                # Clean up downloaded ZIP to avoid cache accumulation
+                                try:
+                                    zip_path.unlink(missing_ok=True)
+                                except OSError:
+                                    # Best-effort cleanup; failure to delete is non-fatal
+                                    pass
+                            except PresetError as preset_err:
+                                console.print(f"[yellow]Warning:[/yellow] Failed to install preset '{preset}': {preset_err}")
                 except Exception as preset_err:
                     console.print(f"[yellow]Warning:[/yellow] Failed to install preset: {preset_err}")
 

src/specify_cli/agents.py

@@ -301,7 +301,7 @@ class CommandRegistrar:
             if not source_file.exists():
                 continue
 
-            content = source_file.read_text()
+            content = source_file.read_text(encoding="utf-8")
             frontmatter, body = self.parse_frontmatter(content)
 
             frontmatter = self._adjust_script_paths(frontmatter)
@@ -318,7 +318,7 @@ class CommandRegistrar:
                 raise ValueError(f"Unsupported format: {agent_config['format']}")
 
             dest_file = commands_dir / f"{cmd_name}{agent_config['extension']}"
-            dest_file.write_text(output)
+            dest_file.write_text(output, encoding="utf-8")
 
             if agent_name == "copilot":
                 self.write_copilot_prompt(project_root, cmd_name)
@@ -327,7 +327,7 @@ class CommandRegistrar:
 
             for alias in cmd_info.get("aliases", []):
                 alias_file = commands_dir / f"{alias}{agent_config['extension']}"
-                alias_file.write_text(output)
+                alias_file.write_text(output, encoding="utf-8")
                 if agent_name == "copilot":
                     self.write_copilot_prompt(project_root, alias)
                 registered.append(alias)
@@ -345,7 +345,7 @@ class CommandRegistrar:
         prompts_dir = project_root / ".github" / "prompts"
         prompts_dir.mkdir(parents=True, exist_ok=True)
         prompt_file = prompts_dir / f"{cmd_name}.prompt.md"
-        prompt_file.write_text(f"---\nagent: {cmd_name}\n---\n")
+        prompt_file.write_text(f"---\nagent: {cmd_name}\n---\n", encoding="utf-8")
 
     def register_commands_for_all_agents(
         self,

src/specify_cli/presets.py

@@ -565,9 +565,8 @@ class PresetManager:
 
         from . import SKILL_DESCRIPTIONS
 
-        # Locate core command templates
-        script_dir = Path(__file__).parent.parent.parent  # up from src/specify_cli/
-        core_templates_dir = script_dir / "templates" / "commands"
+        # Locate core command templates from the project's installed templates
+        core_templates_dir = self.project_root / ".specify" / "templates" / "commands"
 
         for skill_name in skill_names:
             # Derive command name from skill name (speckit-specify -> specify)
@@ -1458,20 +1457,29 @@ class PresetResolver:
         if str(self.presets_dir) in resolved_str and self.presets_dir.exists():
             registry = PresetRegistry(self.presets_dir)
             for pack_id, _metadata in registry.list_by_priority():
-                if f"/{pack_id}/" in resolved_str:
+                pack_dir = self.presets_dir / pack_id
+                try:
+                    resolved.relative_to(pack_dir)
                     meta = registry.get(pack_id)
                     version = meta.get("version", "?") if meta else "?"
                     return {
                         "path": resolved_str,
                         "source": f"{pack_id} v{version}",
                     }
+                except ValueError:
+                    continue
 
-        if str(self.extensions_dir) in resolved_str and self.extensions_dir.exists():
+        if self.extensions_dir.exists():
             for ext_dir in sorted(self.extensions_dir.iterdir()):
-                if ext_dir.is_dir() and f"/{ext_dir.name}/" in resolved_str:
+                if not ext_dir.is_dir() or ext_dir.name.startswith("."):
+                    continue
+                try:
+                    resolved.relative_to(ext_dir)
                     return {
                         "path": resolved_str,
                         "source": f"extension:{ext_dir.name}",
                     }
+                except ValueError:
+                    continue
 
         return {"path": resolved_str, "source": "core"}

tests/test_presets.py

@@ -499,15 +499,15 @@ class TestPresetManager:
         manager = PresetManager(project_dir)
         assert manager.get_pack("nonexistent") is None
 
-    def test_check_compatibility_valid(self, pack_dir):
+    def test_check_compatibility_valid(self, pack_dir, temp_dir):
         """Test compatibility check with valid version."""
-        manager = PresetManager(Path(tempfile.mkdtemp()))
+        manager = PresetManager(temp_dir)
         manifest = PresetManifest(pack_dir / "preset.yml")
         assert manager.check_compatibility(manifest, "0.1.5") is True
 
-    def test_check_compatibility_invalid(self, pack_dir):
+    def test_check_compatibility_invalid(self, pack_dir, temp_dir):
         """Test compatibility check with invalid specifier."""
-        manager = PresetManager(Path(tempfile.mkdtemp()))
+        manager = PresetManager(temp_dir)
         manifest = PresetManifest(pack_dir / "preset.yml")
         manifest.data["requires"]["speckit_version"] = "not-a-specifier"
         with pytest.raises(PresetCompatibilityError, match="Invalid version specifier"):
@@ -1678,6 +1678,11 @@ class TestPresetSkills:
 
         (project_dir / ".claude" / "commands").mkdir(parents=True, exist_ok=True)
 
+        # Set up core command template in the project so restoration works
+        core_cmds = project_dir / ".specify" / "templates" / "commands"
+        core_cmds.mkdir(parents=True, exist_ok=True)
+        (core_cmds / "specify.md").write_text("---\ndescription: Core specify command\n---\n\nCore specify body\n")
+
         manager = PresetManager(project_dir)
         SELF_TEST_DIR = Path(__file__).parent.parent / "presets" / "self-test"
         manager.install_from_directory(SELF_TEST_DIR, "0.1.5")