title: vim-pathogen is ignoring 'after' directory
body: <p>I am using this <a href="https://github.com/Yggdroot/indentLine" rel="nofollow noreferrer">plugin</a> which only ships with 'after' directory, containing 'plugin' and 'syntax'  directories.</p>
  
  <p><a href="https://github.com/tpope/vim-pathogen/blob/master/autoload/pathogen.vim#L118" rel="nofollow noreferrer">Here</a>, it looks like the 'after' directory is added to run time path as well. </p>
  
  <p>If I manually move the 'plugin' and 'syntax' directories to the bundles/indentLine root the plugin works, the commands are recognized. </p>
  
  <p>Any suggestions on what's going wrong? How do I debug? How do I add print statements in there?</p>
  
  <p>EDIT: I am going to clarify this a little more.</p>
  
  <p>I have a directory layout ~/.vim/bundles. All of my plugins that are from gitrepos are here, so you are looking at something like - </p>
  
  <p>Output:</p>
  
  <pre><code>~/.vim/bundle
  |-- nerdtree
  |   |-- syntax
  |   `-- plugin
  |-- indentLine
  |   `-- after
  |       `-- syntax
  |       `-- plugin
  `-- vim-surround
      |-- syntax
      `-- plugin
  </code></pre>
  
  <p>scriptnames includes nerdtree and vim-surround. However, indentLine doesn't show up in scriptnames. If I move the "syntax" and "plugin" directories from "indentLine\after" into the "indentLine" directory, then indentLine shows up in <code>:scriptnames</code> as well.</p>
  
  <p>Basically, the <code>:indentLines\after</code> directory is not looked into for plugins.</p>