Issue with migration scripts and local files

[dylan-sa]

One use case for the migration scripts is to run them over local ontology/vocabulary files to capture updates. Our README points out limited support for named graphs when the scripts are run over local files using onto-tool. Since named graphs are used in queries/action/default, running these queries over local files generates the following error (as expected):

raise Exception(
Exception: You performed a query operation requiring a dataset (i.e. ConjunctiveGraph), but operating currently on a single graph.

Commenting out the minus {named graph pattern} portion of these queries gets them to work. I think the queries in this directory will still work well when run from a triplestore, but I wonder if we can find a way to better accommodate the local file use case. This might just be adding some additional notes to the README or queries.

See also #1140.

[rjyounes]

Implement as documentation updates along with #1140.