I have a seperate folder with the git checkout, then use symlinks to connect the actual dotfile locations. I think the author may have alluded to the same thing:
> I can quickly clone the git repository and fire up my bootstrap script to wire all the symlinks, aliases and scripts
Though personally I don't use symlinks for my scripts (only my dotfiles) - for my scripts I simply add my git checkout to my $PATH
This is what I tend to do, along with a script that runs all the required install (rpm/apt generally) and stow commands for everything I use.
It does mean I have to update it whenever I add a new application to my default setup, or an application/tool has a new configuration layout. But those are pretty rare.
