fix: address sixteenth round of Copilot PR review feedback

- Remove dead has_composition branch in resolve_content: after the
  top-replace early return, the top layer is guaranteed non-replace
  so the any() check was always true
- Fix CLI composition chain base labeling: compute effective base index
  using same logic as resolve_content (last consecutive replace from
  bottom before first non-replace) instead of always labeling i==0
- Support extension manifest file paths in collect_all_layers: when
  convention lookup fails for commands, parse extension.yml to find
  the actual file path, enabling composition onto extension commands
  that use non-convention filenames

Author: mnriem

src/specify_cli/__init__.py

@@ -2612,12 +2612,20 @@ def preset_resolve(
         if has_composition:
             console.print("    [dim]Final output is composed from multiple preset layers; the path above is the highest-priority contributing layer.[/dim]")
             console.print("\n  [bold]Composition chain:[/bold]")
-            for i, layer in enumerate(reversed(layers)):
+            # Compute the effective base: the last consecutive replace layer
+            # from the bottom before the first non-replace (same logic as
+            # PresetResolver.resolve_content).
+            reversed_display = list(reversed(layers))
+            effective_base_idx = 0
+            for idx, lyr in enumerate(reversed_display):
+                if lyr["strategy"] == "replace":
+                    effective_base_idx = idx
+                else:
+                    break
+            for i, layer in enumerate(reversed_display):
                 strategy_label = layer["strategy"]
-                if strategy_label == "replace":
-                    # Only mark the effective base (the one composition builds on)
-                    if i == 0:
-                        strategy_label = "base"
+                if strategy_label == "replace" and i == effective_base_idx:
+                    strategy_label = "base"
                 console.print(f"    {i + 1}. [{strategy_label}] {layer['source']} → {layer['path']}")
     else:
         # No layers found — fall back to resolve_with_source for non-composition cases

src/specify_cli/presets.py

@@ -2320,7 +2320,25 @@ def _find_in_subdirs(base_dir: Path) -> Optional[Path]:
             ext_dir = self.extensions_dir / ext_id
             if not ext_dir.is_dir():
                 continue
+            # Try convention-based lookup first
             candidate = _find_in_subdirs(ext_dir)
+            # If not found and this is a command, check extension manifest
+            if candidate is None and template_type == "command":
+                ext_manifest_path = ext_dir / "extension.yml"
+                if ext_manifest_path.exists():
+                    try:
+                        from .extensions import ExtensionManifest
+                        ext_manifest = ExtensionManifest(ext_manifest_path)
+                        for cmd in ext_manifest.commands:
+                            if cmd.get("name") == template_name:
+                                cmd_file = cmd.get("file")
+                                if cmd_file:
+                                    c = ext_dir / cmd_file
+                                    if c.exists():
+                                        candidate = c
+                                break
+                    except Exception:
+                        pass
             if candidate:
                 if ext_meta:
                     version = ext_meta.get("version", "?")
@@ -2395,13 +2413,6 @@ def resolve_content(
         if layers[0]["strategy"] == "replace":
             return layers[0]["path"].read_text(encoding="utf-8")
 
-        # Check if any layer uses a non-replace strategy
-        has_composition = any(layer["strategy"] != "replace" for layer in layers)
-
-        if not has_composition:
-            # Pure replacement — just read the highest-priority file
-            return layers[0]["path"].read_text(encoding="utf-8")
-
         # Composition: build content bottom-up (lowest priority first)
         # Start from the lowest-priority "replace" layer as the base,
         # then apply composition layers on top.