fix: address seventh round of Copilot PR review feedback

- Strip frontmatter from command layers during composition: parse each
  layer into (frontmatter, body), compose bodies only, then reattach
  the highest-priority frontmatter to avoid leaking YAML metadata
- Filter disabled presets in bash resolve_template and
  resolve_template_content: skip presets with enabled=false
- Filter disabled presets in PowerShell Resolve-Template and
  Resolve-TemplateContent: add Where-Object enabled filter to match
  Python resolver behavior

Author: mnriem

scripts/bash/common.sh

@@ -321,7 +321,8 @@ try:
         data = json.load(f)
     presets = data.get('presets', {})
     for pid, meta in sorted(presets.items(), key=lambda x: x[1].get('priority', 10)):
-        print(pid)
+        if meta.get('enabled', True) is not False:
+            print(pid)
 except Exception:
     sys.exit(1)
 " 2>/dev/null); then
@@ -408,7 +409,8 @@ try:
         data = json.load(f)
     presets = data.get('presets', {})
     for pid, meta in sorted(presets.items(), key=lambda x: x[1].get('priority', 10)):
-        print(pid)
+        if meta.get('enabled', True) is not False:
+            print(pid)
 except Exception:
     sys.exit(1)
 " 2>/dev/null); then

scripts/powershell/common.ps1

@@ -330,6 +330,7 @@ function Resolve-Template {
                 $presets = $registryData.presets
                 if ($presets) {
                     $sortedPresets = $presets.PSObject.Properties |
+                        Where-Object { $null -eq $_.Value.enabled -or $_.Value.enabled -ne $false } |
                         Sort-Object { if ($null -ne $_.Value.priority) { $_.Value.priority } else { 10 } } |
                         ForEach-Object { $_.Name }
                 }
@@ -402,6 +403,7 @@ function Resolve-TemplateContent {
                 $presets = $registryData.presets
                 if ($presets) {
                     $sortedPresets = $presets.PSObject.Properties |
+                        Where-Object { $null -eq $_.Value.enabled -or $_.Value.enabled -ne $false } |
                         Sort-Object { if ($null -ne $_.Value.priority) { $_.Value.priority } else { 10 } } |
                         ForEach-Object { $_.Name }
                 }

src/specify_cli/presets.py

@@ -2346,11 +2346,41 @@ def resolve_content(
         if content is None:
             return None
 
+        # For command composition, strip frontmatter from each layer to avoid
+        # leaking YAML metadata into the composed body. The highest-priority
+        # layer's frontmatter will be reattached at the end.
+        is_command = template_type == "command"
+        top_frontmatter_text = None
+
+        def _strip_frontmatter(text: str) -> tuple:
+            """Return (frontmatter_text_with_fences, body) or (None, text)."""
+            if not text.startswith("---"):
+                return None, text
+            end = text.find("---", 3)
+            if end == -1:
+                return None, text
+            fm_block = text[:end + 3]
+            body = text[end + 3:].strip()
+            return fm_block, body
+
+        if is_command:
+            fm, body = _strip_frontmatter(content)
+            if fm:
+                top_frontmatter_text = fm
+                content = body
+
         # Apply composition layers from bottom to top
         for layer in reversed_layers[start_idx:]:
             layer_content = layer["path"].read_text(encoding="utf-8")
             strategy = layer["strategy"]
 
+            if is_command:
+                fm, layer_body = _strip_frontmatter(layer_content)
+                layer_content = layer_body
+                # Track the highest-priority frontmatter seen
+                if fm:
+                    top_frontmatter_text = fm
+
             if strategy == "replace":
                 content = layer_content
             elif strategy == "prepend":
@@ -2371,4 +2401,8 @@ def resolve_content(
                     )
                 content = layer_content.replace(placeholder, content)
 
+        # Reattach the highest-priority frontmatter for commands
+        if is_command and top_frontmatter_text:
+            content = top_frontmatter_text + "\n\n" + content
+
         return content