It seems as there are files in the git repo with CRLF line endings, which causes changes by non-Windows users to show up as the entire file has changed (as the line ending will be converted to LF. This will also happen for Windows users with recommended git settings (core.autocrlf=true).
This is not good as it makes it difficult to see what was actually changed.

The git repo needs to be normalized on line endings (LF). Also, a .gitattributes file should be added to prevent the same problem from happen again.

See:
https://help.github.com/articles/dealing-with-line-endings
http://adaptivepatchwork.com/2012/03/01/mind-the-end-of-your-line/