I just did 24 hours of this hell. I re-cloned the repositories, destroyed the applications, repacked, cropped ... as many as 9 yards.
It turned out that I had a .txt file of ~ 250 MB in size, which, although I deleted it from my main branch, was still present in my local (as well as in github) cache.
I checked this page and accidentally found my answer here:
https://help.github.com/articles/remove-sensitive-data
.txt doc/, , .
git filter-branch --index-filter 'git rm --cached --ignore-unmatch doc/US.txt'
, , - , 13.