Installation

git clone https://github.com/gontcharovd/neovim.git ~/.config/neovim
cd ~/.config/neovim
git submodule update --init

Add modules

git submodule add https://github.com/instant-markdown/vim-instant-markdown.git pack/plugins/start/vim-instant-markdown

Update all plugins

git submodule update --remote --merge

Removing a plugin and its git submodule

Delete the relevant section from the .gitmodules file.
Stage the .gitmodules changes git add .gitmodules.
Delete the relevant section from .git/config.
Run git rm --cached path_to_submodule.
Run rm -rf .git/modules/path_to_submodule.
Commit git commit -m "Removed submodule "
Delete the now untracked submodule files rm -rf path_to_submodule