fix: only use materialized command output for the active stack row

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: nicolehaugen <10600161+nicolehaugen@users.noreply.github.com>

Author: Copilot

src/specify_cli/artifacts/__init__.py

@@ -429,6 +429,8 @@ def _derive_source_path(
     project_root: Path,
     kind: ArtifactKind,
     name: str,
+    *,
+    active: bool,
 ) -> str | None:
     """Return the repo-relative concrete file backing a preset/extension layer.
 
@@ -437,6 +439,11 @@ def _derive_source_path(
     (``preset_id``/``pack_dir`` or ``extension_id``/``extension_dir``)
     alongside ``lookupId``; core and project rows intentionally do not produce
     a source path here.
+
+    The tracked materialized agent output is shared by every stack row that
+    contributed the same command name, so it only reflects the winning
+    (``active``) row's content. Lower ``replace``/``merge`` rows must report
+    their own installed pack file instead of that shared output.
     """
     lookup_id = layer.get("lookupId", "")
     layer_kind = layer_kind_from_lookup_id(lookup_id)
@@ -447,7 +454,7 @@ def _derive_source_path(
         from ..presets import PresetRegistry
 
         metadata = PresetRegistry(project_root / ".specify" / "presets").get(pack_id)
-        if kind == "command":
+        if kind == "command" and active:
             materialized = _materialized_command_source_path(
                 project_root, metadata, name, source="preset"
             )
@@ -460,7 +467,7 @@ def _derive_source_path(
         from ..extensions import ExtensionRegistry
 
         metadata = ExtensionRegistry(project_root / ".specify" / "extensions").get(extension_id)
-        if kind == "command":
+        if kind == "command" and active:
             materialized = _materialized_command_source_path(
                 project_root, metadata, name, source="extension"
             )
@@ -471,8 +478,9 @@ def _derive_source_path(
         # artifact contract's perspective, so their sourcePath stays null.
         return None
 
-    # Non-command preset/extension layers, and command layers without a tracked
-    # materialized agent output, report the installed pack file from the raw
+    # Non-active command layers, non-command preset/extension layers, and
+    # active command layers without a tracked materialized agent output all
+    # report the installed pack file from the raw
     # PresetResolver.collect_all_layers() row's concrete ``path`` key.
     path = layer.get("path")
     if isinstance(path, Path):
@@ -547,7 +555,7 @@ def _build_stack(
             hidden = idx > first_replace_idx
 
         layer_kind, source_id, lookup_id = _public_layer_shape(layer)
-        source_path = _derive_source_path(layer, project_root, kind, name)
+        source_path = _derive_source_path(layer, project_root, kind, name, active=active)
 
         if layer_kind == PROJECT_OVERRIDE_LAYER:
             rows.append(

tests/test_artifact_command.py

@@ -743,6 +743,86 @@ def test_list_json_rows_include_stack(self, spec_kit_project: Path, monkeypatch:
         info = json.loads(info_result.stdout)
         assert row["stack"] == info["stack"]
 
+    def test_hidden_command_layer_source_path_is_own_pack_file(
+        self, spec_kit_project: Path
+    ):
+        """A hidden (non-active) command row must not report the winner's
+        shared materialized agent output as its ``sourcePath``.
+
+        Both presets below register the same command name and the same
+        agent skill name, so the tracked materialized output is a single
+        shared file. Only the active (winning) row may report that shared
+        file; the hidden loser row must report its own installed pack file.
+        """
+        pack_low = install_preset(
+            spec_kit_project,
+            "aaa-low-priority-preset",
+            {
+                "commands": [
+                    {
+                        "name": "speckit.compliance.plan",
+                        "file": "commands/speckit.compliance.plan.md",
+                        "description": "Loser",
+                    }
+                ]
+            },
+            priority=20,
+        )
+        (pack_low / "commands").mkdir()
+        (pack_low / "commands" / "speckit.compliance.plan.md").write_text(
+            "---\ndescription: Loser\n---\nloser body\n", encoding="utf-8"
+        )
+        PresetRegistry(spec_kit_project / ".specify" / "presets").update(
+            "aaa-low-priority-preset",
+            {"registered_skills": {"copilot": ["speckit-compliance-plan"]}},
+        )
+
+        pack_high = install_preset(
+            spec_kit_project,
+            "zzz-high-priority-preset",
+            {
+                "commands": [
+                    {
+                        "name": "speckit.compliance.plan",
+                        "file": "commands/speckit.compliance.plan.md",
+                        "description": "Winner",
+                    }
+                ]
+            },
+            priority=5,
+        )
+        (pack_high / "commands").mkdir()
+        (pack_high / "commands" / "speckit.compliance.plan.md").write_text(
+            "---\ndescription: Winner\n---\nwinner body\n", encoding="utf-8"
+        )
+        PresetRegistry(spec_kit_project / ".specify" / "presets").update(
+            "zzz-high-priority-preset",
+            {"registered_skills": {"copilot": ["speckit-compliance-plan"]}},
+        )
+
+        skill_file = (
+            spec_kit_project
+            / ".github"
+            / "skills"
+            / "speckit-compliance-plan"
+            / "SKILL.md"
+        )
+        skill_file.parent.mkdir(parents=True)
+        skill_file.write_text("---\nname: speckit-compliance-plan\n---\n", encoding="utf-8")
+
+        info = ArtifactCatalog(spec_kit_project).get_artifact_info("speckit.compliance.plan")
+        stack = info["stack"]
+        assert stack[0]["active"] is True
+        assert stack[0]["sourcePath"] == ".github/skills/speckit-compliance-plan/SKILL.md"
+
+        hidden_rows = [layer for layer in stack if layer["active"] is False]
+        assert hidden_rows
+        for row in hidden_rows:
+            assert row["sourcePath"] != stack[0]["sourcePath"]
+            assert row["sourcePath"] == (
+                ".specify/presets/aaa-low-priority-preset/commands/speckit.compliance.plan.md"
+            )
+
     def test_list_json_stack_source_path_contract(
         self, spec_kit_project: Path, monkeypatch: pytest.MonkeyPatch
     ):