With .gitattributes we can force all java files etc to have linux file endings.

I am experimenting with this in the optaplanner repository:
https://github.com/droolsjbpm/optaplanner/commit/40dca629262568d5e5abb379655d0ea65aef19a6

If it works well, we'll want to compile a good overall .gitattributes file and commit it to all droolsjbpm repositories.

During the refactor to .gitattributes, execute this script to detect and fix all previous errors:
https://help.github.com/articles/dealing-with-line-endings#re-normalizing-a-repository

Important:
In OptaPlanner we just committed the file without "fixing all previous errors". It turned out we had 2.
The person who adds the .gitattributes file doesn't get a problem, but other people who clone a new repository
get immediate modifications to incorrect files. This is a PITA.
So after the commit .gitattributes files, all previous errors need to be fixed for and verified by doing a new clone and a git status on that new clone.