Fix To Topic Page Links

This PR fixes and issue with links to local topic pages.

In MonoGame our Markdown documentation does stuff like this:
```
The [Pipeline Tool](pipeline.md) is used to organize and define content for use with MonoGame. 
```
This results in links which work even when browsing or editing the docs from the GitHub UI:

![github](https://cloud.githubusercontent.com/assets/103522/3941516/38465056-252f-11e4-9974-1de5396da947.png)

Later in the config.xml we do this to add that file into the TOC:
```
<topic id="Pipeline" name="Pipeline" filename="pipeline.md"/>
``` 
Note we use `id="Pipeline"` here and that the filename does not match the id.  This is important because it means our URLs end up looking nice like this:

http://www.monogame.net/documentation/?page=Pipeline

The problem is that when generating docs it would resolve links assuming that the topic id was the same as the filename.  So in our case it would not find the reference and process like the link was to an external url and ultimately generate a bad URL.

This PR fixes it to do an additional lookup for a matching topic filename solving our case.