Add Java Doc comments to all classes

```
Go through the code and add Java Doc comments throughout the code so that
javadoc files can be built on the project.

This is a very low priority, only to be worked on if your stuck on
something and want to feel like your getting something done

```

Original issue reported on code.google.com by `darkbird44@gmail.com` on 13 Mar 2007 at 3:29
