Note I have studied the git-is-very-very-slow question, but in their case the reason was big binary files - while in my repository there is PHP/JS/HTML/CSS only code (no binaries) and the biggest file in the repository is around 800 KB.
I've changed one file (a few lines), then
git add .
git commit -m "msg"
git push origin master
git pull origin master
The problem was in
EmberJS app directory. It contained
bower_components directories which kept third-party libraries used by
GruntJS to build my JS and CSS assets.
Each of these contained many files and directories.. considering that the dependency tree contained hundreds of libraries of size varying from small (few files) to big fat (many files).
After removing these directories and ignoring them, the git repository works fast again.