fix: address second round of Copilot review feedback

1. Ensure .mdc frontmatter on existing files — upsert_context_section()
   now checks for missing YAML frontmatter on .mdc files during updates
   (not just creation), so pre-existing Cursor files get alwaysApply.

2. Guard against context_file=None — use 'or ""' instead of a default
   arg so explicit null values in init-options.json don't cause a
   TypeError in str.replace().

3. Clean up .mdc files on removal — remove_context_section() treats
   files containing only the Speckit-generated frontmatter block as
   empty, deleting them rather than leaving orphaned frontmatter.

Author: mnriem

src/specify_cli/agents.py

@@ -364,7 +364,7 @@ def resolve_skill_placeholders(
         body = body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", agent_name)
 
         # Resolve __CONTEXT_FILE__ from init-options
-        context_file = init_opts.get("context_file", "")
+        context_file = init_opts.get("context_file") or ""
         body = body.replace("__CONTEXT_FILE__", context_file)
 
         return CommandRegistrar.rewrite_project_relative_paths(body)

src/specify_cli/integrations/base.py

@@ -450,6 +450,10 @@ def upsert_context_section(
                     new_content = content + "\n" + section
                 else:
                     new_content = section
+
+            # Ensure .mdc files have required YAML frontmatter
+            if ctx_path.suffix == ".mdc" and not new_content.startswith("---\n"):
+                new_content = "---\nalwaysApply: true\n---\n\n" + new_content
         else:
             ctx_path.parent.mkdir(parents=True, exist_ok=True)
             # Cursor .mdc files require YAML frontmatter to be loaded
@@ -497,6 +501,13 @@ def remove_context_section(self, project_root: Path) -> bool:
 
         new_content = content[:start_idx] + content[end_of_marker:]
 
+        # For .mdc files, also strip Speckit-generated frontmatter
+        if ctx_path.suffix == ".mdc":
+            stripped = new_content.strip()
+            if stripped in ("", "---\nalwaysApply: true\n---"):
+                ctx_path.unlink()
+                return True
+
         if not new_content.strip():
             ctx_path.unlink()
         else: