Provenance creation updates and fixes for 'With' keyword functionality.

Fixes for provenance creation with the 'with' operator. Note that 'testConceptualModelBindingWithTraitDRL' is failing. If there should be 5 Activities created, there is only 4 now. I'm not sure what the 5th one woule be.
Merge pull request #7 from kevinpeterson/0.6.x

Provenance creation updates and fixes for 'With' keyword functionality.
Fix provenance extraction