As I stated earlier this morning, I LOVE your plugin. There are 2 types of links that don't get followed correctly. Hopefully, linking to files in the filesystem and to internal links in the document are both something you feel should be addressed:

(1)Internal links such as

Jump to: [top](#top) ... [today](#today) ... [thisweek](#thisweek) ... [deferred](#deferred) ...[bottom](#bottom)
...
<a name="today"></a>
...
<a name="deferred"></a>

and also links to separate md files such as

* See [Comcast Issues](./Comcast.md)