Add Javadocs

[willkroboth]

All the developer-facing methods used to make AddOns should have appropriate Javadocs written for them. Everything that is explained in the various markdown documentation files should get Javadocs, as well as any other methods and classes that might be useful for AddOn developers.

[willkroboth]

Largely addressed by 324bfee, though as new classes and methods are added and updated, this issue will of course need continuous work.