Internal links are not smart enough about cross-file linking.
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There are two main problems with internal linking as it works now:

1. The links are resolved relative to the directory of the file being processed
   when they should be resolved relative to the root output directory.
   
   For example, consider ``@org id1`` defined in ``dir/file1.src``, then
   referenced in ``dir/file2.src`` in this manner: ``[link](jlp://id1``. The
   url written in ``dir/file2.html`` is ``dir/file1.html#id1``. However, when
   the page is viewed, this url is interpreted relative to the directory of the
   current page. So if the docs live at ``file:///docs`` then the url will
   resolve to ``file:///docs/dir/dir/file1.src#id1`` instead of
   ``file:///docs/dir/file1.html#id1``.

2. The links do substitute the ``html`` suffix to the file names in place of the
   files' suffixes. In the above example note that the actual urls end in
   ``.src`` like the original input files, but the expected url ends in
   ``.html``.

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Created:  2011-09-08
Resolved: 2011-09-09
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