fix: address twenty-first round of Copilot PR review feedback

- Fix _create_pack helper for command type: use commands/ subdir and
  file path for template_type='command' instead of always templates/
- Cache registry and manifests in reconcile loop: compute
  list_by_priority() once and reuse resolver._get_manifest() cache
  to avoid O(commands*presets) YAML loads
- Use line-based frontmatter splitter: scan for --- on its own line
  to avoid false matches on --- inside YAML values, consistent with
  integrations/base.py approach
- Fix PS1 stderr capture: redirect to temp file instead of 2>&1 pipe
  which could merge stderr into stdout and break stratResult parsing

Author: mnriem

scripts/powershell/common.ps1

@@ -423,7 +423,7 @@ function Resolve-TemplateContent {
                     try {
                         # Use Python to parse YAML manifest for strategy and file path
                         $pyArgs = if ($pyCmd.Count -gt 1) { $pyCmd[1..($pyCmd.Count-1)] } else { @() }
-                        $pyStderr = $null
+                        $pyStderrFile = [System.IO.Path]::GetTempFileName()
                         $stratResult = & $pyCmd[0] @pyArgs -c @"
 import sys
 try:
@@ -442,20 +442,17 @@ try:
     print('replace\t')
 except Exception:
     print('replace\t')
-"@ $manifest $TemplateName 2>&1 | ForEach-Object {
-                            if ($_ -is [System.Management.Automation.ErrorRecord]) {
-                                $pyStderr = $_.ToString()
-                            } else { $_ }
-                        }
+"@ $manifest $TemplateName 2>$pyStderrFile
                         if ($stratResult) {
                             $parts = $stratResult.Trim() -split "`t", 2
                             $strategy = $parts[0].ToLowerInvariant()
                             if ($parts.Count -gt 1 -and $parts[1]) { $manifestFilePath = $parts[1] }
                         }
                         # Warn only when PyYAML is explicitly missing
-                        if ($pyStderr -and $pyStderr -match 'yaml_missing') {
+                        if ((Test-Path $pyStderrFile) -and (Get-Content $pyStderrFile -Raw -ErrorAction SilentlyContinue) -match 'yaml_missing') {
                             Write-Warning "PyYAML not available; composition strategies in $manifest may be ignored"
                         }
+                        Remove-Item $pyStderrFile -Force -ErrorAction SilentlyContinue
                     } catch {
                         $strategy = 'replace'
                     }

src/specify_cli/presets.py

@@ -638,6 +638,10 @@ def _reconcile_composed_commands(self, command_names: List[str]) -> None:
         resolver = PresetResolver(self.project_root)
         registrar = CommandRegistrar()
 
+        # Cache registry and manifests outside the loop to avoid
+        # repeated filesystem reads for each command name.
+        presets_by_priority = list(PresetRegistry(self.presets_dir).list_by_priority()) if self.presets_dir.exists() else []
+
         for cmd_name in command_names:
             layers = resolver.collect_all_layers(cmd_name, "command")
             if not layers:
@@ -655,15 +659,11 @@ def _reconcile_composed_commands(self, command_names: List[str]) -> None:
                 top_path = top_layer["path"]
                 # Try to find which preset owns this layer
                 registered = False
-                for pack_id, _meta in PresetRegistry(self.presets_dir).list_by_priority():
+                for pack_id, _meta in presets_by_priority:
                     pack_dir = self.presets_dir / pack_id
                     if top_path.is_relative_to(pack_dir):
-                        manifest_path = pack_dir / "preset.yml"
-                        if manifest_path.exists():
-                            try:
-                                manifest = PresetManifest(manifest_path)
-                            except PresetValidationError:
-                                continue
+                        manifest = resolver._get_manifest(pack_dir)
+                        if manifest:
                             for tmpl in manifest.templates:
                                 if tmpl.get("name") == cmd_name and tmpl.get("type") == "command":
                                     self._register_for_non_skill_agents(
@@ -694,14 +694,10 @@ def _reconcile_composed_commands(self, command_names: List[str]) -> None:
 
                 # Write to the highest-priority preset's .composed dir
                 registered = False
-                for pack_id, _meta in PresetRegistry(self.presets_dir).list_by_priority():
+                for pack_id, _meta in presets_by_priority:
                     pack_dir = self.presets_dir / pack_id
-                    manifest_path = pack_dir / "preset.yml"
-                    if not manifest_path.exists():
-                        continue
-                    try:
-                        manifest = PresetManifest(manifest_path)
-                    except PresetValidationError:
+                    manifest = resolver._get_manifest(pack_dir)
+                    if not manifest:
                         continue
                     for tmpl in manifest.templates:
                         if tmpl.get("name") == cmd_name and tmpl.get("type") == "command":
@@ -2445,20 +2441,24 @@ def resolve_content(
         def _split_frontmatter(text: str) -> tuple:
             """Return (frontmatter_block_with_fences, body) or (None, text).
 
-            Detects frontmatter by the presence of ``---`` fences rather than
-            whether the parsed YAML has keys, so empty frontmatter blocks
-            (``---\\n---``) are also stripped.
+            Uses line-based fence detection (fence must be ``---`` on its
+            own line) to avoid false matches on ``---`` inside YAML values.
             """
-            if not text.startswith("---"):
+            lines = text.splitlines(keepends=True)
+            if not lines or lines[0].rstrip("\r\n") != "---":
                 return None, text
-            end = text.find("---", 3)
-            if end == -1:
+
+            fence_end = -1
+            for i, line in enumerate(lines[1:], start=1):
+                if line.rstrip("\r\n") == "---":
+                    fence_end = i
+                    break
+
+            if fence_end == -1:
                 return None, text
-            fm_block = text[:end + 3]
-            body = text[end + 3:]
-            # Remove only the single newline after the closing fence
-            if body.startswith("\n"):
-                body = body[1:]
+
+            fm_block = "".join(lines[:fence_end + 1]).rstrip("\n")
+            body = "".join(lines[fence_end + 1:])
             return fm_block, body
 
         if is_command:

tests/test_presets.py

@@ -3746,8 +3746,13 @@ def _create_pack(temp_dir, valid_pack_data, pack_id, content,
     tmpl_entry = {
         "type": template_type,
         "name": template_name,
-        "file": f"templates/{template_name}.md" if template_type != "script" else f"scripts/{template_name}.sh",
     }
+    if template_type == "script":
+        tmpl_entry["file"] = f"scripts/{template_name}.sh"
+    elif template_type == "command":
+        tmpl_entry["file"] = f"commands/{template_name}.md"
+    else:
+        tmpl_entry["file"] = f"templates/{template_name}.md"
     if strategy != "replace":
         tmpl_entry["strategy"] = strategy
     pack_data["provides"] = {"templates": [tmpl_entry]}
@@ -3761,6 +3766,10 @@ def _create_pack(temp_dir, valid_pack_data, pack_id, content,
         subdir = pack_dir / "scripts"
         subdir.mkdir(exist_ok=True)
         (subdir / f"{template_name}.sh").write_text(content)
+    elif template_type == "command":
+        subdir = pack_dir / "commands"
+        subdir.mkdir(exist_ok=True)
+        (subdir / f"{template_name}.md").write_text(content)
     else:
         subdir = pack_dir / "templates"
         subdir.mkdir(exist_ok=True)