Option to preserve keywords with the bel_upgrade executable

[abargnesi]

The bel_upgrade will replace namespace keywords, but not annotation keywords. This is inconsistent and doesn't provide user control.

By default bel_upgrade should replace keywords as defined by the --changelog option. The user can provide a --preserve-annotation-keywords and --preserve-namespace-keywords to maintain keywords in the BEL document.

[ncatlett]

Note that the current handling of the namespace and annotation keywords differs in part due to how they are used. The annotation keywords are (in part) noting the type of annotation (Species, Disease, Cell, Cell Line, etc.) that for namespace values is captured with the BEL function (protein, pathology, biological process, etc.). Ultimately, we want to associate both annotation types (e.g., Disease) and prefixes/vocabulary references (e.g. DO/Disease Ontology) with an Annotation.