feat(gen-owl): type a permissible value by the classes it instantiates

[jdsika]

Summary

Fixes # — no issue covers this.

A permissible value can be an instance of a class defined in another schema: an open vocabulary declares the class (Category), and an extension contributes named individuals of it. The metamodel states exactly this with instantiates on the permissible value — "An element in another schema which this element instantiates" — but gen-owl ignored it. Its slot URI is linkml:instantiates, which add_metadata skips, so the individual was typed only with the enum's own class. A validator checking sh:class vocab:LicenseCategory then rejects the value, although the schema says it is one.

Each instantiates value of a permissible value with an IRI now becomes an rdf:type of that IRI:

enums:
  LinkCategory:
    implements: [owl:NamedIndividual]
    permissible_values:
      isLicense:
        meaning: ex:isLicense
        instantiates: [vocab:LicenseCategory]

ex:isLicense a owl:NamedIndividual, ex:LinkCategory, vocab:LicenseCategory .
ex:LinkCategory owl:oneOf ( ex:isLicense ... ) .

• The enum still closes its own class with owl:oneOf; the instantiated class stays open, so other schemas can keep adding members.
• Literal permissible values have no node to type, so instantiates is ignored with a warning, as meaning already is.

Without this, the only ways to type such individuals are a global --default-permissible-value-type (one class for every value of every enum) or an enum is_a, which must name another enum.

How was this tested?

• New test_permissible_value_instantiates_types_the_value: single and multiple instantiates, the value keeps owl:NamedIndividual and the enum class, the enum's owl:oneOf is unchanged, a value without instantiates gets no extra type, and the instantiated class gets no owl:oneOf.
• New test_permissible_value_instantiates_ignored_on_literal: no type triple and a warning.
• pytest tests/linkml/test_generators/test_owlgen.py -m "not kroki" — 99 passed, 3 skipped.
• ruff check and ruff format --check (0.11.13) clean.

Areas of uncertainty

• Default owl:Class permissible values. A class value that instantiates a class is typed by it too, which is metaclass punning — the same reading instantiates has for classes elsewhere in the metamodel. Not restricted to individuals, because the metamodel does not restrict it.

Checklist

• My code follows the contributor guidelines
• I have added tests that prove my fix/feature works
• Existing tests pass locally with my changes

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