0.47 mostly fixes this. However only when a .cursorignore is present.
According to the docs, Cursor should ignore a set of default files (which includes .env) but only for indexing and stuff mentioned in .gitignore. I think this is still a mayor problem.
Without a specific .cursorignore it means opening a repository for the first time might be dangerous… Basically you would need inject a basic ignore file for every project on your device (or somehow set it up globally, which I tried to find) before starting cursor within that folder.
Nice to see this improved, but come on…