Proposed Dataset API changes

[namedgraph]

The Dataset is quite weird and assumes that standalone Graphs have identifiers, which will be phased out (#2537). For example, adding a named graph to a Dataset looks like this:

g = Graph(identifier=URIRef("urn:named_graph"))
g.add((..., ... ,...))
...
d = Dataset()
d.add_graph(g)

Moreover, Dataset uses the term context when referring to named graphs. I think it should be phased out as well.
If in doubt, I suggest just copying Jena's Dataset API.

My suggestions for Dataset:

• add add_named_graph(uri: IdentifiedNode, graph: Graph) method
• add has_named_graph(uri: IdentifiedNode) method
• add remove_named_graph(uri: IdentifiedNode) method
• add replace_named_graph(uri: IdentifiedNode, graph: Graph)) method
• add graphs() method as an alias for contexts()
• add default_graph property as an alias for default_context
• add get_named_graph as an alias for get_graph
• deprecate graph(graph) method
• deprecate remove_graph(graph) method
• deprecate contexts() method

Using IdentifiedNode as a super-interface for URIRef and BNode (since both are allowed as graph names in RDF 1.1).

The above example would become something like this after these changes:

g = Graph()
g.add((..., ... ,...))
...
d = Dataset()
d.add_named_graph(URIRef("urn:named_graph"), g)

[namedgraph]

Also aligns with #2446 and #2407

[namedgraph]

It also looks like a simple Graph.add(self, g: Graph) method is missing 🤷‍♂️ There's only __add__.

[nicholascar]

I support all of the proposals in this discussion. This has been a long-time coming - we've noticed these things for years - but have never done anything about these and they still hurt u - @edmondchuc is battling with datasets in a current project.

I suggest we also remove the ConjunctiveGraph class and fold any differences it has with Dataset into Dataset constructor parameters.

[namedgraph]

I don't think ConjunctiveGraph has to go -- as I understand, it provides a "union graph" which most triplestores support. But Dataset probably does not need to extend it.