YADR comes with a dead simple plugin manager that just uses vundles and submodules, without any fancy config files.
Add a plugin
yav -u https://github.com/airblade/vim-rooter
Delete a plugin
ydv -u airblade/vim-rooter
The aliases (yav=yadr vim-add-plugin), (ydp=yadr vim-delete-plugin) and (yuv=yadr vim-update-all-plugins) live in the aliases file. You can then commit the change. It's good to have your own fork of this project to do that.