Improve database creation code
This applies to new database creation, database changes through ontology updates, and creation of graph databases.
Refactor database creation code with some improvements
- Simpler code in finding out the ontology updates and the database changes resulting from there. Now this is the result of simpler and easier to follow operations.
- Greater guarantees at the supported kinds of ontology changes, and support for more changes previously unsupported
- It's no longer necessary to change nrl:lastModified to have ontology changes detected
- The gvdb dependency has been dropped
- Less code, more tests, and better coverage for these paths