Claude Desktop on Windows switched to being a WindowsApp which means that it's filesystem is now virtualized. A recent build has an escaped bug where it is trying to read the claude_desktop_config.json config file from the virtualized file system where it wouldn't be found effectively breaking access to MCP tools.

People keep reporting this issue against the Claude Code repo and they keep closing the bug because it technically is Claude Desktop, not Claude Code. There is no public place to submit this kind of issue.