fix: address nineteenth round of Copilot PR review feedback

- Keep non-skill agent reconciliation: reconciliation uses
  register_commands_for_non_skill_agents to avoid overwriting formatted
  SKILL.md content; _unregister_skills restores core/extension skills
  and _reconcile_skills handles lower-priority preset skills
- Show composition error in CLI resolve: when has_composition is true,
  call resolve_content() and warn if composition cannot produce output
  (no base layer) instead of showing a misleading 'resolved' path

Author: mnriem

src/specify_cli/__init__.py

@@ -2610,7 +2610,12 @@ def preset_resolve(
             and any(layer["strategy"] != "replace" for layer in layers)
         )
         if has_composition:
-            console.print("    [dim]Final output is composed from multiple preset layers; the path above is the highest-priority contributing layer.[/dim]")
+            # Verify composition is actually possible
+            composed = resolver.resolve_content(template_name)
+            if composed is None:
+                console.print("    [yellow]Warning: composition cannot produce output (no base layer with 'replace' strategy)[/yellow]")
+            else:
+                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]")
             # Compute the effective base: the last consecutive replace layer
             # from the bottom before the first non-replace (same logic as

src/specify_cli/presets.py

@@ -772,10 +772,12 @@ def _register_for_non_skill_agents(
         source_id: str,
         source_dir: Path,
     ) -> None:
-        """Register commands for all non-skill agents.
+        """Register commands for all agents during reconciliation.
 
-        Used during reconciliation to avoid overwriting properly formatted
-        SKILL.md files that were written by _register_skills().
+        Uses the non-skill registrar for command agents, then relies on
+        _reconcile_skills() (called separately) to properly format SKILL.md
+        files for skill-based agents. This avoids overwriting properly
+        formatted SKILL.md content with raw command file content.
         """
         registrar.register_commands_for_non_skill_agents(
             commands, source_id, source_dir, self.project_root