Remove unused submodules directories.

Running `rake install`, runs the `:submodule_init` task, which in turn runs the following command:

    git submodule update --init --recursive

This fails with the following couple of errors (separately):

    No submodule mapping found in .gitmodules for path 'vim/bundle/mattn-zencoding-vim'
    No submodule mapping found in .gitmodules for path 'vim/bundle/skwp-vim-indexed-search'

This was introduced by 3d60f721dd53e7f5414d11004c749784efc74f64 which removed the 'mattn/zencoding-vim' and 'skwp/vim-indexed-search' submodules from the `.gitmodules`.