After cloning:
# create symlink to .(g)vimrc
cd ~
ln -s ~/.vim/.vimrc ~/.vimrc
ln -s ~/.vim/.gvimrc ~/.gvimrc
# init submodules
git submodule update --init
To update plugins run:
git submodule foreach git pull origin master
Use :Helptags command to generate help tags for all bundled plugins after cloning or updating.