SBOL 2->3 converter: post-creation fix-up of links

[bbartley]

The current approach for converting SBOL2 -> SBOL3 compliant URIs results in broken links.

For example, here is a broken link in this intermediate test file currently being used as the expected SBOL3:
https://github.com/SynBioDex/SBOL-utilities/blob/develop/test/test_files/sbol_3to2_implementation_compliant.nt#L6

Perhaps an important design decision here is:
Do we update all SBOL2 URIs that reference objects either internal or external to the Document (probably using some kind of regex pattern matching)?
or
Do we update only SBOL2 URIs that reference other objects internal the Document (probably using some kind of lookup table)?

[jakebeal]

We should only ever update URIs that reference objects internal to the Document.
Objects outside of the document, by definition we cannot know if it's been converted.

[jakebeal]

The plan that @bbartley has for tackling this is to do triple-surgery with the aid of a hashtable at the end of conversion. Every object of a triple will be checked against the hash table for mapping to a new identity.

The only case in which this will produce a behavior other than an identity update per the description above, is the case where somebody has abused a text field to fill it with a URI that matches the identity of an object in the document.

If that is the case, the text field will also be updated, and we are considering that to be a feature rather than a bug.