Git lets you ignore those files by assuming they are unchanged.

Ignoring versioned files

This is done by running the git update-index --assume-unchanged path/to/file.txt command. Once marking a file as such, git will completely ignore any changes on that file; they will not show up when running git status or git diff, nor will they ever be committed.

To make git track the file again, simply run 

git update-index --no-assume-unchanged path/to/file.txt.

https://help.github.com/articles/ignoring-files

To get a list of dir's/files that are assume-unchanged run this:

git ls-files -v|grep '^h'