fix: address ninth round of Copilot PR review feedback

- Add top-replace short-circuit in PowerShell Resolve-TemplateContent:
  return top layer directly when its strategy is replace, matching
  Python and bash resolver behavior
- Reconcile skills after install: call _reconcile_skills() for affected
  command names so SKILL.md files reflect the actual priority winner
- Promote _collect_all_layers to public collect_all_layers: the method
  is used by the CLI (preset resolve command), so it should be a public
  API rather than a private helper

Author: mnriem

scripts/powershell/common.ps1

@@ -498,6 +498,12 @@ except Exception:
 
     if ($layerPaths.Count -eq 0) { return $null }
 
+    # If the top (highest-priority) layer is replace, it wins entirely —
+    # lower layers are irrelevant regardless of their strategies.
+    if ($layerStrategies[0] -eq 'replace') {
+        return (Get-Content $layerPaths[0] -Raw)
+    }
+
     # Check if any layer uses a non-replace strategy
     $hasComposition = $false
     foreach ($s in $layerStrategies) {

src/specify_cli/__init__.py

@@ -2596,7 +2596,7 @@ def preset_resolve(
         raise typer.Exit(1)
 
     resolver = PresetResolver(project_root)
-    layers = resolver._collect_all_layers(template_name)
+    layers = resolver.collect_all_layers(template_name)
     result = resolver.resolve_with_source(template_name)
 
     if layers:

src/specify_cli/presets.py

@@ -624,7 +624,7 @@ def _reconcile_composed_commands(self, command_names: List[str]) -> None:
         registrar = CommandRegistrar()
 
         for cmd_name in command_names:
-            layers = resolver._collect_all_layers(cmd_name, "command")
+            layers = resolver.collect_all_layers(cmd_name, "command")
             if not layers:
                 continue
 
@@ -770,7 +770,7 @@ def _reconcile_skills(self, command_names: List[str]) -> None:
 
         resolver = PresetResolver(self.project_root)
         for cmd_name in command_names:
-            layers = resolver._collect_all_layers(cmd_name, "command")
+            layers = resolver.collect_all_layers(cmd_name, "command")
             if not layers:
                 continue
 
@@ -1258,6 +1258,9 @@ def install_from_directory(
         ]
         if cmd_names:
             self._reconcile_composed_commands(cmd_names)
+            # Also reconcile skills so SKILL.md files reflect the actual
+            # winning command layer, not just the last-installed preset.
+            self._reconcile_skills(cmd_names)
 
         return manifest
 
@@ -2162,7 +2165,7 @@ def resolve_with_source(
 
         return {"path": resolved_str, "source": "core"}
 
-    def _collect_all_layers(
+    def collect_all_layers(
         self,
         template_name: str,
         template_type: str = "template",
@@ -2318,7 +2321,7 @@ def resolve_content(
         Returns:
             Composed content string, or None if not found
         """
-        layers = self._collect_all_layers(template_name, template_type)
+        layers = self.collect_all_layers(template_name, template_type)
         if not layers:
             return None
 

tests/test_presets.py

@@ -3541,7 +3541,7 @@ class TestCollectAllLayers:
     def test_single_core_layer(self, project_dir):
         """Test collecting layers with only core template."""
         resolver = PresetResolver(project_dir)
-        layers = resolver._collect_all_layers("spec-template")
+        layers = resolver.collect_all_layers("spec-template")
         assert len(layers) == 1
         assert layers[0]["source"] == "core"
         assert layers[0]["strategy"] == "replace"
@@ -3554,7 +3554,7 @@ def test_layers_include_presets(self, project_dir, temp_dir, valid_pack_data):
         manager.install_from_directory(pack_dir, "0.1.5")
 
         resolver = PresetResolver(project_dir)
-        layers = resolver._collect_all_layers("spec-template")
+        layers = resolver.collect_all_layers("spec-template")
         assert len(layers) == 2
         # Highest priority first
         assert "test-pack" in layers[0]["source"]
@@ -3575,7 +3575,7 @@ def test_layers_order_matches_priority(self, project_dir, temp_dir, valid_pack_d
             manager.install_from_directory(p, "0.1.5", priority=prio)
 
         resolver = PresetResolver(project_dir)
-        layers = resolver._collect_all_layers("spec-template")
+        layers = resolver.collect_all_layers("spec-template")
         assert len(layers) == 3  # pack-hi, pack-lo, core
         assert "pack-hi" in layers[0]["source"]
         assert "pack-lo" in layers[1]["source"]
@@ -3604,7 +3604,7 @@ def test_layers_read_strategy_from_manifest(self, project_dir, temp_dir, valid_p
         manager.install_from_directory(pack_dir, "0.1.5")
 
         resolver = PresetResolver(project_dir)
-        layers = resolver._collect_all_layers("spec-template")
+        layers = resolver.collect_all_layers("spec-template")
         # Preset layer should have strategy=append
         assert layers[0]["strategy"] == "append"
         # Core layer should be replace
@@ -3675,7 +3675,7 @@ def test_remove_restores_lower_priority_command(
         # The low-priority preset's command should still be present
         # in the resolution stack
         resolver = PresetResolver(project_dir)
-        layers = resolver._collect_all_layers("speckit.specify", "command")
+        layers = resolver.collect_all_layers("speckit.specify", "command")
         assert len(layers) >= 1
         assert "lo-preset" in layers[0]["source"]