Sped up py transform and rdf generation by not precomputing visible nodes and calling eval on nonprecompiled code

Created Neighbor interface to enable discovering nodes by hnodeids from
a given node
Precompiled the transform code call and used set on the interpreter
instead of exec to add variables to the python workspace
Optimizred collectNodes
Speed ups
Reset workspace between batches of offline rdf generation

Refactored out some commonality between the rdf generators.

Cleaned up some exception handling (not every import needs to be able
to throw a SQLException)
Replaced regex in normalizeURI with a hand coded replacement method

Also, we don't rebuild the URI unless we find a problem.
cleaning warnings and merge local research branch
Merge branch 'development' of github.com:InformationIntegrationGroup/Web-Karma into pytransform_speedup

need pytransform command checking for adding new columns
Add some error checking to AddColumnCommand
Fixed a reinitialization bug for offline database rdf generation
ArrayList fixes for speedup
Optimized Semantic Type Suggestion

Now disabled in offline rdf generation

Only compute suggestions on single column when we add columns instead
of whole table.

Optimized sampling of examples for semantic types.

Fixed issue with unsetting semantic type when no semantic type is set.
Replaced toCharArray to charAt

toCharArray makes a copy.
Tentative fix for out of order json
solve utf-8 problem
solve conflict between head and remote branch
Merge remote-tracking branch 'upstream/development' into development
Prevent duplicate Transformation tags from being appended to py transform command

o SubmitPyTransformationCommand and processed by
Worksheet2RMLJenaModelParser
decode the python script output to utf-8
Lots of refactoring

maybe all for naught.
move research code to local package