Treat pathogen as a bundle
Improve install script to handle Bundles

Can now specify vim plugin bundles as short forms. Eg.:
- tpope/vim-pathogen - goes to github.com/tpope/vim-pathogen.git
- vimwiki - goes to github.com/vim-scripts/vimwiki.git
- any other form is not modified and passed straight through

Can also specify the transport mechanism to use when installing bundles.
This has no impact when updating bundles, since these will use the
remote url specified in the git repo.

Can also specify not to update existing bundles with a command line
switch.