Feature/seqware 1242 integration tests

This is a pull request for various improvements for the integration tests which morphed into various fixes to the command-line tools as they were exposed including the AttributeAnnotator which had major flaws in its implementation. 

I'm cutting this off here because the branch is becoming too large.

Fixes include:
Trivial fixes to command-line tools (Workflow Launcher, BundleManager)
Attribute Annotator 
   Fixes: (cascading deletion behaviour, non-duplicate behaviour, inability to annotate processings without a populated update_tstmp) Affects database and hibernate layer
   New feature: File annotation
Integration tests: Allow some extended integration tests that do not require Pegasus/Condor/SGE to run without the extITs profile