It's possible those files became modified as a result of the game updating.
Some teams will clone/commit the whole scaffold and/or java project, but that can have many negative side-effects, like these. If the game client modifies files that are commited to your repo as a function of updating the game, git won't know the difference. It will just look like a file has changed. Similarly, if IDE project files are commited and somebody edits them (Or the IDE does), git wont know the difference and will show the diff as a modified file. Committing any of these things and pushing up changes can risk major merge conflicts with other players, as well as causing weird IDE behavior if multiple contributors use the same IDE but configured differently.
I'd say the cleanest way to support multiple IDEs is to commit only your team's src files to the repo. If your repo consists only of what's in your
src/team folder, then it can be cloned into any players scaffold running whatever IDE configured how they choose and should most likely cause no conflicts/issues.