fix(dev): overwrite server config in mcp host rather than merging

Writing to the server config would originally (65e32cd) merge the new server configurations with existing ones.
Effectively making it and "append" only writing operation preventing to use this api for removing server configurations (overriding everything).
By default, we expect the MCPHostConfig passed to the `write_configuration` to be perfect.

- Only in Gemini strategy, because the change was originally operated only there.

Author: LittleCoinCoin

hatch/mcp_host_config/strategies.py

@@ -444,29 +444,27 @@ def write_configuration(self, config: HostConfiguration, no_backup: bool = False
         config_path = self.get_config_path()
         if not config_path:
             return False
-        
+
         try:
             # Ensure parent directory exists
             config_path.parent.mkdir(parents=True, exist_ok=True)
-            
-            # Read existing configuration to preserve other settings
+
+            # Read existing configuration to preserve non-MCP settings
             existing_config = {}
             if config_path.exists():
                 try:
                     with open(config_path, 'r') as f:
                         existing_config = json.load(f)
                 except Exception:
                     pass
-            
-            # Preserve existing servers and add/update new ones
-            existing_servers = existing_config.get(self.get_config_key(), {})
 
-            # Convert MCPServerConfig objects to dict and merge with existing
+            # Convert MCPServerConfig objects to dict (REPLACE, don't merge)
+            servers_dict = {}
             for name, server_config in config.servers.items():
-                existing_servers[name] = server_config.model_dump(exclude_none=True)
+                servers_dict[name] = server_config.model_dump(exclude_none=True)
 
-            # Update configuration with merged servers
-            existing_config[self.get_config_key()] = existing_servers
+            # Update configuration with new servers (preserves non-MCP settings)
+            existing_config[self.get_config_key()] = servers_dict
 
             # Write atomically with enhanced error handling
             temp_path = config_path.with_suffix('.tmp')