Whitespace has ended up being a horrible pain for me while using git.
git config apply.whitespace=strip
If you are going to turn on those settings, you need to schedule a day where ALL source code in your project gets its whitespace uniformly stripped, by running a script, or by saving every file from an editor that will perform the strip on save. Then, all future commits will be policed by the settings, so all should be well going forward.