atomspace: add API for managing incoming set

It will be both faster, and more generally useful, to track
the incoming set locally, instead of in the atomtable.  This
provides an API for doing this.
atomsapce: Use make_shared instead of new
atomspace: remove obsolete addRealAtom()
atomspace: remove the deprecated clone() method

...it should never have been added in the first place. oh well.
atomspace bugfix: validate atom type
atomspace: revert to crazy atom remove behaviour
cython test fix for invalid atom types
Merge pull request #320 from linas/atomspace

Atomspace twerking