[jdsika]

Mirror of linkml#3993, same head. Review there; this PR tracks the fork stack.

2026-10-23, second push (review): the example of a graph that is not standard RDF was the metamodel's relative IRI bibo:status <testing>, which no generator emits on current main (gen-owl, gen-rdf and gen-shacl canonicalize the metamodel without the fallback). It now names gen-shacl --include-annotations with a non-CURIE annotation tag, which does take the fallback. The section also points to the how-to for the optional dependency --diff-stable needs. Sphinx build of the docs: clean apart from four warnings that main has too (sphinx-click duplicate options, a Jupyter kernel notice).

2026-10-23: rebased onto main (a1593d16c). linkml#3985 is merged, so this is now a single documentation commit against main; no content change.

Summary

Adds a "Deterministic output" section to the gen-owl documentation:

• RDFC-1.0 canonicalization gives byte-identical Turtle across runs for standard RDF.
• --diff-stable (from feat(rdf): add opt-in diff-stable blank-node labels linkml/linkml#3985) reduces blank-node renumbering without guaranteeing minimal diffs. The section links to the how-to that feat(rdf): add opt-in diff-stable blank-node labels linkml/linkml#3985 adds.
• Graphs that are not standard RDF (a relative IRI, or a literal as a predicate, as gen-shacl --include-annotations writes for an annotation tag that is not a CURIE) are serialized by rdflib with a warning. --diff-stable has no effect on them.

Changes since the first version

• Based on feat(rdf): add opt-in diff-stable blank-node labels linkml/linkml#3985 only. Statements that hold only with fix(rdf): delegate canonicalization to the diffable-rdf library linkml/linkml#3987 are removed: that diffable-rdf performs canonicalization, and that the fallback output is reproducible across processes. Every sentence now holds with feat(rdf): add opt-in diff-stable blank-node labels linkml/linkml#3985 alone and stays true after fix(rdf): delegate canonicalization to the diffable-rdf library linkml/linkml#3987.
• Two overstatements are corrected. --diff-stable reduces label churn but does not guarantee minimal diffs, and gen-shex supports it only with --format rdf.
• The section is shorter and links to the how-to instead of repeating it.

Validation

The strict Sphinx build (-W --keep-going) passes, and the cross-reference resolves to howtos/collaborative-development.html#rdf-in-version-control.