Hey, thanks for the feature request. It’s a great suggestion.
The team is working on improving MCP tool management, including issues with settings persistence. There’s a known issue with the allowlist not saving permissions: MCP Allowlist doesn't work, also can't be edited
Your request to support configuration via mcp.json makes sense, especially for servers with a large number of tools. The options you suggested (enabledTools, wildcards, toolConfig) are well thought out and cover different use cases.
The team is looking into improvements in this area.