fix(presets): resolve() honors manifest-declared file: for installed presets

src/specify_cli/presets/__init__.py

@@ -2676,6 +2676,34 @@ def resolve(
             registry = PresetRegistry(self.presets_dir)
             for pack_id, _metadata in registry.list_by_priority():
                 pack_dir = self.presets_dir / pack_id
+                # The preset manifest is authoritative: if it declares this
+                # template with an explicit ``file:``, resolve to that path —
+                # and do NOT fall back to convention when it's missing, to
+                # avoid masking typos or picking up an undeclared file. Only
+                # when the manifest is absent or doesn't list this template do
+                # we use the convention-based subdir lookup. Mirrors
+                # collect_all_layers()/resolve_content() so resolve() and
+                # resolve_with_source() agree with them instead of returning
+                # the core template (or a stray convention file).
+                manifest_file_path = None
+                manifest_found_entry = False
+                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):
+                            manifest_file_path = tmpl.get("file")
+                            manifest_found_entry = True
+                            break
+                if manifest_file_path:
+                    manifest_candidate = pack_dir / manifest_file_path
+                    if manifest_candidate.exists():
+                        return manifest_candidate
+                    # Declared file missing: skip this pack's convention fallback.
+                    continue
+                if manifest_found_entry:
+                    # Manifest lists the template without a file: nothing here.
+                    continue
                 for subdir in subdirs:
                     if subdir:
                         candidate = pack_dir / subdir / f"{template_name}{ext}"

tests/test_presets.py

@@ -884,6 +884,84 @@ def test_resolve_pack_takes_priority_over_core(self, project_dir, pack_dir):
         assert result is not None
         assert "Custom Spec Template" in result.read_text()
 
+    def _install_pack_with_manifest_file(self, project_dir, *, extra_file=False):
+        """Create a pack whose manifest declares a NON-convention file: path.
+
+        Returns the pack dir under the project. The declared file lives at
+        custom/spec.md (not the convention templates/spec-template.md).
+        """
+        presets_dir = project_dir / ".specify" / "presets"
+        pack_dir = presets_dir / "mypack"
+        (pack_dir / "custom").mkdir(parents=True)
+        (pack_dir / "custom" / "spec.md").write_text(
+            "# Manifest-declared Spec\n", encoding="utf-8"
+        )
+        if extra_file:
+            # An undeclared convention-path file the manifest points away from.
+            (pack_dir / "templates").mkdir()
+            (pack_dir / "templates" / "spec-template.md").write_text(
+                "# Stray Convention Spec\n", encoding="utf-8"
+            )
+        manifest = {
+            "schema_version": "1.0",
+            "preset": {
+                "id": "mypack",
+                "name": "My Pack",
+                "version": "1.0.0",
+                "description": "declares a non-convention file path",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "templates": [
+                    {
+                        "type": "template",
+                        "name": "spec-template",
+                        "file": "custom/spec.md",
+                        "strategy": "replace",
+                    }
+                ]
+            },
+        }
+        with open(pack_dir / "preset.yml", "w") as f:
+            yaml.dump(manifest, f)
+        PresetRegistry(presets_dir).add(
+            "mypack", {"version": "1.0.0", "priority": 10}
+        )
+        return pack_dir
+
+    def test_resolve_uses_manifest_declared_file_path(self, project_dir):
+        """resolve() must honor a manifest-declared non-convention file: path.
+
+        Previously the tier-2 loop was convention-only, so it returned the
+        core template and resolve_with_source() misattributed source='core',
+        diverging from collect_all_layers()/resolve_content().
+        """
+        pack_dir = self._install_pack_with_manifest_file(project_dir)
+        resolver = PresetResolver(project_dir)
+
+        result = resolver.resolve("spec-template")
+        assert result == pack_dir / "custom" / "spec.md"
+        assert "Manifest-declared Spec" in result.read_text()
+
+        sourced = resolver.resolve_with_source("spec-template")
+        assert sourced is not None
+        assert "mypack" in sourced["source"]
+        # resolve() must agree with collect_all_layers()'s top layer.
+        layers = resolver.collect_all_layers("spec-template")
+        assert Path(layers[0]["path"]) == pack_dir / "custom" / "spec.md"
+
+    def test_resolve_manifest_file_wins_over_undeclared_convention_file(
+        self, project_dir
+    ):
+        """A stray convention-path file must not shadow the manifest's file:."""
+        pack_dir = self._install_pack_with_manifest_file(
+            project_dir, extra_file=True
+        )
+        resolver = PresetResolver(project_dir)
+        result = resolver.resolve("spec-template")
+        assert result == pack_dir / "custom" / "spec.md"
+        assert "Manifest-declared Spec" in result.read_text()
+
     def test_resolve_override_takes_priority_over_pack(self, project_dir, pack_dir):
         """Test that overrides take priority over installed packs."""
         # Install the pack