Put ~/.vim first in &rtp and ~/.vim/after last.

The paths ~/.vim and ~/.vim/after where hardcoded so this might be an
*NIX only solution.

Could close #244.

autoload/vundle/config.vim

@@ -81,6 +81,10 @@ func! s:rtp_add_a()
   let appends = join(paths, '/after,').'/after'
   exec 'set rtp^='.fnameescape(prepends)
   exec 'set rtp+='.fnameescape(appends)
+  set rtp-=~/.vim
+  set rtp^=~/.vim
+  set rtp-=~/.vim/after
+  set rtp+=~/.vim/after
 endf
 
 func! s:rtp_rm(dir) abort