Reduced the size of the mindboggle repo by removing files.

java -jar /desk/bfg-1.11.8.jar  -b 1M mindboggle.git
java -jar /desk/bfg-1.11.8.jar --delete-folders 'build' mindboggle.git
git filter-branch -f --prune-empty -d /desk/tmp --index-filter 'git rm -rf --cached --ignore-unmatch *.sql.gz *.sql *.pyc *.jpg *.png *.gz *.zip *.tar *zip *.jpeg *.vtk *.gif *.html' --tag-name-filter cat -- --all
git reflog expire --expire=now --all
git gc --prune=now --aggressive
git push

... all within a bare clone:
git clone --mirror git@github.com:binarybottle/mindboggle.git

... and after accounting for all branches:
for branch in   remotes/origin/br-zernike
  remotes/origin/debian
  remotes/origin/gh-pages
  remotes/origin/ohinds-realignment; do     git branch --track  ; done

https://www.kernel.org/pub/software/scm/git/docs/git-filter-branch.html