Remove pathogen to install as submodule.
Install pathogen.vim as submodule.
Configure .vimrc for pathogen.
Install vim-pandoc.
Update README how to install submodules.
Set runtimepath for pathogen to work.
Change submodules to keep working tree clean.

See [Nils' Haldenwang's post](http://www.nils-haldenwang.de/frameworks-and-tools/git/how-to-ignore-changes-in-git-submodules).
Set tab and space settings.