Cleanup and documentation

- Made fields final where applicable.
- Added throws statements where missing.
- Added missing annotations suppress unchecked (Aspect).
- renamed local variables hiding fields
- documentation for almost everything.
- lots of formatting, whitespaces, newlines, ...

I didn't get around to finish all of the EntitySystems, but those will come later.
Also didn't remove the private field docu yet, no time, but I bulk reformatted field documentation to be one liners.

Please review for any errors and such.