When I have .gitignore data/* and run git clean -fd, the data folder and all its content files are deleted.
What I want is to delete all unrevisioned files in a git repo while excluding all ignored files (i.e. DON'T delete gitignored files). What could I do?
Git normally doesn't clean ignored files unless the -x flag is specified, but strangely it cleans out when configured as you did (folder/*).
As @VonC pointed out, you should change your .gitignore-file to ignore the directory (data/) rather than its contents (data/*).
It's a subtle difference, but it matters to git.