Put ontologies in an ontologies folder

[rjyounes]

The gist root directory is mostly nicely partitioned, and I propose that we make it one step cleaner by putting the ontologies (there are 5 so far and others may be coming) into their own ontologies directory. In my client projects I typically go one level deeper, using models/ontologies alongside models/taxonomies and whatever we want to call controlled datasets that aren't taxonomies. We already have one of the latter in gistMediaTypes.ttl.

Is it also possible to move bundle.yaml to tools? Not sure if this would have any adverse affects when running onto_tool.

[rjyounes]

This gets even worse in the release package, though of course the structure of the package doesn't have to be the same as the repository structure.

[rjyounes]

DECISION: Yes.

[rjyounes]

Includes both the repository and the release package; the latter requires updates to bundle.yaml.

[rjyounes]

@kchastain703 to follow up with @Jamie-SA about any implications for upload/download/import.