Unclear It is not clear what the extra copy of the settings is used for or whether it changes anything a user sees.
Plugins can bring MCP servers, which are add-on services that give Claude extra tools. Some run as a local program on your machine (stdio servers). For these, Claude Code used to produce only the fully filled-in settings. It now also keeps a second copy taken before the server's environment variables are finalised. Plugin MCP servers reached over the network (SSE or HTTP) now go through an extra processing step when plugins are listed.
You set up plugin MCP servers the same way as before. This changes how Claude Code handles their settings behind the scenes.
It is not clear what the extra copy of the settings is used for or whether it changes anything a user sees.