Hey, this is expected behavior, not something specific to NixOS. Right now the CLI cursor-agent and the IDE store chat history separately. The CLI writes to ~/.cursor/chats, and the IDE keeps transcripts inside the workspace state at ~/.cursor/projects/<project>/agent-transcripts/.... They don’t sync with each other on any OS.
No need to open a separate thread. This is basically a feature request, and there’s already a good one: Sync Cursor chats across workspaces Sync Cursor chats across workspaces. You can add your use case there and like it to help it get more attention.
As for the original XDG_CONFIG_HOME bug, it’s been reported internally. I’ll reply here once there’s an update on the fix.