Sounds horrible. Just let me open a folder without it being a project or having to use a script to clean up stuff (wtf?).
I don't see this as a lot different than MacOS spraying .DS_STORE files everywhere. It's not a big deal to add to .gitignore, but it does leave a fingerprint. It's just that tries to determine reasonable defaults if the path doesn't exist instead of Netbeans/Eclipse/whatever forcing you to pick them with a wizard if you want any of the "real" features to work.