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There is no need to put askbot and the bits of your site into the same repository even if you want to pull askbot from the repo.

For example - you can "pip-install" askbot into the virtual environment in the source form:

virtualenv env --no-site-packages
source env/bin/activate
pip install -e git+git://
askbot-setup #and continue as in the manual

This way you will get:

mysite/ #and other project files
    env #with all the virtualenv files

Now if you want to create a git repo for your deployment:

git init
echo env > .gitignore
git add .gitignore
git add
git commit -m 'my initial commit'
#then you can add a remote repo and push to your main backup repository

Now you will have askbot inside the env/src in an independent repository, which will be ignored together with all the environment files from your site repo.