To set up the dotfiles on a new system and init all submodules:

$ git clone --bare https://github.com/patrickbr/dotfiles.git $HOME/.dotfiles
$ cd
$ git --git-dir=$HOME/.dotfiles/ --work-tree=$HOME checkout
$ git --git-dir=$HOME/.dotfiles/ --work-tree=$HOME submodule update --recursive --init

You might run into conflicts when files are already existing. In this case, delete them manually and repeat the checkout. You can also run git --git-dir=$HOME/.dotfiles/ --work-tree=$HOME checkout -f to overwrite existing files. You could also commit them locally and merge them...

To use the .bashrc_gen, you could do something like this at the end of your .bashrc:

if [ -f $HOME/.bashrc_gen ]; then
    . $HOME/.bashrc_gen
fi

Following an idea from this thread on Hackernews, you can set up an alias for the git invocation. For example:

$ echo "alias dotfiles='/usr/bin/git --git-dir=$HOME/.dotfiles/ --work-tree=$HOME'" >> ~/.bashrc

After sourcing your .bashrc, you can now do this:

$ dotfiles status
$ dotfiles add ~/.somecfg
$ dotfiles commit -m 'add some cfg'