fix: align resolve() with manifest file paths and match extension context_note

- Update resolve() preset tier to consult manifest file paths before
  convention-based lookup, matching collect_all_layers behavior
- Use exact extension context_note format matching extensions.CommandRegistrar
- Update test to declare template in manifest (authoritative manifest)

Author: mnriem

src/specify_cli/presets.py

@@ -747,11 +747,10 @@ def _reconcile_composed_commands(self, command_names: List[str]) -> None:
                                     if c.get("name") == cmd_name
                                 ]
                                 if matching_cmds:
-                                    ext_name = ext_manifest.data.get("extension", {}).get("name", ext_id)
                                     registrar.register_commands_for_non_skill_agents(
                                         matching_cmds, ext_id, ext_dir,
                                         self.project_root,
-                                        context_note=f"Extension: {ext_name} ({ext_id})",
+                                        context_note=f"\n<!-- Extension: {ext_id} -->\n<!-- Config: .specify/extensions/{ext_id}/ -->\n",
                                     )
                                     registered = True
                             except Exception:
@@ -2432,13 +2431,27 @@ def resolve(
             registry = PresetRegistry(self.presets_dir)
             for pack_id, _metadata in registry.list_by_priority():
                 pack_dir = self.presets_dir / pack_id
-                for subdir in subdirs:
-                    if subdir:
-                        candidate = pack_dir / subdir / f"{template_name}{ext}"
-                    else:
-                        candidate = pack_dir / f"{template_name}{ext}"
-                    if candidate.exists():
-                        return candidate
+                # Check manifest file path first
+                manifest = self._get_manifest(pack_dir)
+                if manifest:
+                    for tmpl in manifest.templates:
+                        if (tmpl.get("name") == template_name
+                                and tmpl.get("type") == template_type):
+                            file_path = tmpl.get("file")
+                            if file_path:
+                                candidate = pack_dir / file_path
+                                if candidate.exists():
+                                    return candidate
+                            break
+                # Convention-based fallback (only when manifest doesn't list this template)
+                else:
+                    for subdir in subdirs:
+                        if subdir:
+                            candidate = pack_dir / subdir / f"{template_name}{ext}"
+                        else:
+                            candidate = pack_dir / f"{template_name}{ext}"
+                        if candidate.exists():
+                            return candidate
 
         # Priority 3: Extension-provided templates (sorted by priority — lower number wins)
         for _priority, ext_id, _metadata in self._get_all_extensions_by_priority():

tests/test_presets.py

@@ -2886,17 +2886,28 @@ def test_enable_not_installed(self, project_dir):
         assert result.exit_code == 1, result.output
         assert "not installed" in result.output.lower()
 
-    def test_disabled_preset_excluded_from_resolution(self, project_dir, pack_dir):
+    def test_disabled_preset_excluded_from_resolution(self, project_dir, temp_dir, valid_pack_data):
         """Test that disabled presets are excluded from template resolution."""
-        # Install preset with a template
+        # Install preset with a template declared in the manifest
+        pack_data = {**valid_pack_data}
+        pack_data["preset"] = {**valid_pack_data["preset"], "id": "test-pack", "name": "Test"}
+        pack_data["provides"] = {
+            "templates": [{
+                "type": "template",
+                "name": "test-template",
+                "file": "templates/test-template.md",
+            }]
+        }
+        pack_dir = temp_dir / "test-pack"
+        pack_dir.mkdir(exist_ok=True)
+        with open(pack_dir / "preset.yml", "w") as f:
+            yaml.dump(pack_data, f)
+        (pack_dir / "templates").mkdir(exist_ok=True)
+        (pack_dir / "templates" / "test-template.md").write_text("# Template from test-pack")
+
         manager = PresetManager(project_dir)
         manager.install_from_directory(pack_dir, "0.1.5")
 
-        # Create a template in the preset directory
-        preset_template = project_dir / ".specify" / "presets" / "test-pack" / "templates" / "test-template.md"
-        preset_template.parent.mkdir(parents=True, exist_ok=True)
-        preset_template.write_text("# Template from test-pack")
-
         resolver = PresetResolver(project_dir)
 
         # Template should be found when enabled