Add rdfs:isDefinedBy to instances during bundling

[rjyounes]

Currently this is not getting added to instances. It requires use of the all value for the definedBy action, but I don't currently see a way to invoke that in the config file (as opposed to on the commandline with the other subcommands like export).

@sa-bpelakh Please advise - is there a way to do this? If not, we need an update to onto_tool.

[rjyounes]

Requires onto_tool updates: semanticarts/ontology-toolkit#138.

But probably these should be defined by the gistReferenceData ontology, not gistCore. So we'd need to add and maintain them manually. This point requires some discussion.