Javadocs, bug fixes, few enchancements, logging

Technical description:
- Javadoc'd most of the classes for developers to use. Addresses #6
- Added support for custom main loop sleep times
- Fixed a bug when the server would not allow clients to connect by
default
- Fixed a bug when the server would progress the client through
authentication even if the server was not accepting clients
- Removed some methods that duplicated other methods
- Switched a few APIs to public and a few to protected
- Revamped the Logging system, now exports log files. Addresses #3