deprecated class cleanup

[brandonnodnarb]

While performing the sanity checks for the 3.5 release, ROBOT was throwing warnings about deprecated classes still being in hierarchies (paraphrasing).

As such, all deprecated classes should be removed from any hierarchies; only a subclass of owl:thing.
Should they also be detached from any non-annotation properties?

And as a followup --- Given the modular nature of SWEET, should there be a deprecated.ttl file (or similar) specifically to house deprecated classes?

related to #192