add missing javadocs and copyright headers.
fix some stream reading test code.
Change API for getting all plugin resources of a specific type
to a map instead of a flat list so that versions for a resource
are grouped together. Also changed active filter to be a
parameter instead of a separate call with a separate signature.
Changing some of the terminology. You now stage a resource instead
of activating it, and each resource has a status which is inactive,
staged, active, or unstaged.