fix: resolve configuration file corruption and data loss issues

Root cause: MCPServerConfig model was rejecting host-specific fields and
configuration writing was overwriting existing servers instead of merging.

Critical fixes:
1. **Allow host-specific fields**: Changed MCPServerConfig.Config.extra from
   'forbid' to 'allow' to support Gemini's cwd, timeout, trust fields
2. **Preserve existing servers**: Modified write_configuration to merge new
   servers with existing ones instead of complete replacement
3. **Enhanced JSON validation**: Added JSON verification after write to
   prevent invalid output with missing brackets
4. **Improved error handling**: Better cleanup and error reporting for
   JSON serialization failures

Resolves Issue 1: Configuration File Corruption and Data Loss
- ✅ Existing mcpServers configuration preserved (no data loss)
- ✅ Valid JSON output with proper structure
- ✅ Host-specific fields (cwd, timeout, trust) supported

Tested: All MCP CLI tests pass (100% success rate)
Verified: Configuration merge preserves existing servers while adding new ones

Author: LittleCoinCoin

hatch/mcp_host_config/models.py

@@ -101,7 +101,7 @@ def is_remote_server(self) -> bool:
 
     class Config:
         """Pydantic configuration."""
-        extra = "forbid"  # Prevent additional fields for strict validation
+        extra = "allow"  # Allow additional fields for host-specific extensions
         json_encoders = {
             Path: str
         }

hatch/mcp_host_config/strategies.py

@@ -458,21 +458,35 @@ def write_configuration(self, config: HostConfiguration, no_backup: bool = False
                 except Exception:
                     pass
 
-            # Convert MCPServerConfig objects to dict
-            servers_dict = {}
+            # 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
             for name, server_config in config.servers.items():
-                servers_dict[name] = server_config.model_dump(exclude_none=True)
-            
-            # Update configuration
-            existing_config[self.get_config_key()] = servers_dict
+                existing_servers[name] = server_config.model_dump(exclude_none=True)
+
+            # Update configuration with merged servers
+            existing_config[self.get_config_key()] = existing_servers
 
-            # Write atomically
+            # Write atomically with enhanced error handling
             temp_path = config_path.with_suffix('.tmp')
-            with open(temp_path, 'w') as f:
-                json.dump(existing_config, f, indent=2)
-            
-            temp_path.replace(config_path)
-            return True
+            try:
+                with open(temp_path, 'w') as f:
+                    json.dump(existing_config, f, indent=2, ensure_ascii=False)
+
+                # Verify the JSON is valid by reading it back
+                with open(temp_path, 'r') as f:
+                    json.load(f)  # This will raise an exception if JSON is invalid
+
+                # Only replace if verification succeeds
+                temp_path.replace(config_path)
+                return True
+            except Exception as json_error:
+                # Clean up temp file on JSON error
+                if temp_path.exists():
+                    temp_path.unlink()
+                logger.error(f"JSON serialization/verification failed: {json_error}")
+                raise
 
         except Exception as e:
             logger.error(f"Failed to write Gemini configuration: {e}")