fix: Address invalid JSON field in installation suite

- Separate SuperClaude metadata from Claude Code settings.json
- Create .superclaude-metadata.json for framework-specific data
- Fix JSON validation issues with settings management
- Update all components to use proper metadata storage
- Maintain compatibility with Claude Code settings format
- Add migration support for existing installations

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

setup/components/mcp.py

@@ -131,8 +131,8 @@ class MCPComponent(Component):
         """Get files to install (none for MCP component)"""
         return []
     
-    def get_settings_modifications(self) -> Dict[str, Any]:
-        """Get settings modifications"""
+    def get_metadata_modifications(self) -> Dict[str, Any]:
+        """Get metadata modifications for MCP component"""
         return {
             "components": {
                 "mcp": {
@@ -148,6 +148,11 @@ class MCPComponent(Component):
             }
         }
     
+    def get_settings_modifications(self) -> Dict[str, Any]:
+        """Get settings.json modifications (now only Claude Code compatible settings)"""
+        # Return empty dict as we don't modify Claude Code settings
+        return {}
+    
     def _check_mcp_server_installed(self, server_name: str) -> bool:
         """Check if MCP server is already installed"""
         try:
@@ -292,13 +297,27 @@ class MCPComponent(Component):
                         self.logger.error(f"Required MCP server {server_name} failed to install")
                         return False
             
-            # Update settings.json
+            # Update metadata
             try:
-                settings_mods = self.get_settings_modifications()
-                self.settings_manager.update_settings(settings_mods)
-                self.logger.info("Updated settings.json with MCP component registration")
+                # Add component registration to metadata
+                self.settings_manager.add_component_registration("mcp", {
+                    "version": "3.0.0",
+                    "category": "integration",
+                    "servers_count": len(self.mcp_servers)
+                })
+                
+                # Add MCP configuration to metadata
+                metadata = self.settings_manager.load_metadata()
+                metadata["mcp"] = {
+                    "enabled": True,
+                    "servers": list(self.mcp_servers.keys()),
+                    "auto_update": False
+                }
+                self.settings_manager.save_metadata(metadata)
+                
+                self.logger.info("Updated metadata with MCP component registration")
             except Exception as e:
-                self.logger.error(f"Failed to update settings.json: {e}")
+                self.logger.error(f"Failed to update metadata: {e}")
                 return False
             
             # Verify installation
@@ -347,13 +366,18 @@ class MCPComponent(Component):
                 if self._uninstall_mcp_server(server_name):
                     uninstalled_count += 1
             
-            # Update settings.json to remove MCP component
+            # Update metadata to remove MCP component
             try:
                 if self.settings_manager.is_component_installed("mcp"):
                     self.settings_manager.remove_component_registration("mcp")
-                    self.logger.info("Removed MCP component from settings.json")
+                    # Also remove MCP configuration from metadata
+                    metadata = self.settings_manager.load_metadata()
+                    if "mcp" in metadata:
+                        del metadata["mcp"]
+                        self.settings_manager.save_metadata(metadata)
+                    self.logger.info("Removed MCP component from metadata")
             except Exception as e:
-                self.logger.warning(f"Could not update settings.json: {e}")
+                self.logger.warning(f"Could not update metadata: {e}")
             
             self.logger.success(f"MCP component uninstalled ({uninstalled_count} servers removed)")
             return True
@@ -401,12 +425,18 @@ class MCPComponent(Component):
                     self.logger.error(f"Error updating MCP server {server_name}: {e}")
                     failed_servers.append(server_name)
             
-            # Update settings
+            # Update metadata
             try:
-                settings_mods = self.get_settings_modifications()
-                self.settings_manager.update_settings(settings_mods)
+                # Update component version in metadata
+                metadata = self.settings_manager.load_metadata()
+                if "components" in metadata and "mcp" in metadata["components"]:
+                    metadata["components"]["mcp"]["version"] = target_version
+                    metadata["components"]["mcp"]["servers_count"] = len(self.mcp_servers)
+                if "mcp" in metadata:
+                    metadata["mcp"]["servers"] = list(self.mcp_servers.keys())
+                self.settings_manager.save_metadata(metadata)
             except Exception as e:
-                self.logger.warning(f"Could not update settings.json: {e}")
+                self.logger.warning(f"Could not update metadata: {e}")
             
             if failed_servers:
                 self.logger.warning(f"Some MCP servers failed to update: {failed_servers}")
@@ -423,9 +453,9 @@ class MCPComponent(Component):
         """Validate MCP component installation"""
         errors = []
         
-        # Check settings.json registration
+        # Check metadata registration
         if not self.settings_manager.is_component_installed("mcp"):
-            errors.append("MCP component not registered in settings.json")
+            errors.append("MCP component not registered in metadata")
             return False, errors
         
         # Check version matches