I encrypt lots of things. I use the following: To encrypt directories cryptsetup and encfs on linux, dmg on mac, geli on freebsd and git-crypt with private bitbucket repos for docs that I'd like to have a history log (commits).

I think that in your case, you could take a look at git-crypt, but make sure you understand what is encrypted and what is not. Also make sure you don't push before git-crypt lock. A bash prompt changing colours might be handy.