Add an editable git checkout to your deploy/pip_packages.txt:
-e git+https://github.com/aptivate/cmsbootstrap.git@2ccf433e101ec9e7eef7ccc4a6c16cc8c5eb59f6#egg=cmsbootstrap
Run deploy/bootstrap.py.
Make changes to the editable code, for example:
echo 'test {}' >> django/website/.ve/src/cmsbootstrap/cmsbootstrap/static/sass/cmsbootstrap.scss
Touch pip_packages.txt and run bootstrap again:
touch deploy/pip_packages.txt
deploy/bootstrap.py
Check what happened to your change:
grep test django/website/.ve/src/cmsbootstrap/cmsbootstrap/static/sass/cmsbootstrap.scss
And it's gone!
Silently blowing away changes to an editable repo is not cool.