Use the project install file. The installer will backup the old nvim directory (if present) with a date stamp
git clone https://github.com/fergusb/nvim.git ~/.config/nvim
cd ~/.comfig/nvim/
./install
cd ~/.config/nvim/
git submodule init
git submodule update
Note: for pyflakes or jedi to work correctly, use:
git submodule update --init --recursive
cd ~/.config/nvim/
mkdir bundle
git submodule add https://github.com/fergusb/nvim-foo.git bundle/foo
git submodule foreach git pull origin master
git submodule update
" vim:ft=mkd