removed code to load ontologies
Close printWriter after generating RDF
Merge branch 'development' into load_r2rml_from_url
Remove all warnings.
Better logging of modeling commands.
Fix typo in error message.
Better logging
Make sure we initialize data structures in OntologyCache
Added ability to set manual alignment to true in ModelingConfiguration

RdfGenerator by default sets manual alignment to true.
Make sure ManualAlignment isn't overwritten in ModelingConfiguration
Merge branch 'load_r2rml_from_url' into development