Intellij IDEA And Its Config Files of Pain

I believe you are doing it wrong.

I do not version control my IntelliJ project files, at least with Maven you don't need them in your VCS, if, and only IF I need to checkout a new copy into another computer I just re-create the project from the pom files. and I believe same may be true with Gradle, lets be realistic how often you change computers that you need to keep your project files with you?

IDE project files do not belong in the repo. They are a detail of the IDE that you choose to use.