Related for secret handling tools like secretspec and varlock (https://varlock.dev), there's no way to securely hand claude code sensitive env vars for use with MCP. While it will do env var replacement in your MCP config, there's not really an easy way to set those vars. If using the cli you can wrap the `claude` command (bit awkward), but when running the desktop app, there is nothing.
I opened an issue here - https://github.com/anthropics/claude-code/issues/88757 - please chime in!