Clean up some code a bit and fix SimplePacketManager

I didn't change very much, other than creating Javadoc comments, but this mainly focuses on ```SimplePacketManager```, so here's what I changed there:

- I made [a modification to ```ExtensionRegistry``` in protobuf's Java API](https://github.com/rmsy/Protobuf-extended/blob/master/java/src/main/java/com/google/protobuf/ExtensionRegistry.java#L219), which is used in ```SimplePacketManager``` to get all of a ```Message```'s extensions (and thus Protobuf-extended is [also a dependency](https://github.com/rmsy/Protobuf-Packet/blob/master/pom.xml#L22))
- I modified ```build()``` to use varargs (so that multiple ```Message```s can be set at a time)

I'm not going to go into much more detail in the description because it's hard for me to visualize my changes without having them in front of me, so I'll just make line comments (which will show up inline on the discussion tab, anyway).

Thanks.