Respect heading numbering offsets in references

[sapunyangkut]

Summary

• Forward the existing heading numbering offset into the reference enumeration decision.
• Add a regression covering shifted first- and second-level heading templates.
• Add the required myst-transforms patch changeset.

Fixes #2998

Validation

Preserved exact-SHA evidence for the unchanged two-file implementation patch:

• pre-fix focused regression: 1 failed as expected
• focused regression: 1 passed
• adjacent enumeration suites: 36 passed
• full myst-transforms package: 320 passed
• dependency-aware target build: 8/8 tasks passed
• package lint: 0 errors (6 unrelated existing warnings)
• touched-file formatting and git diff --check: passed

The current no-install checkout has no node_modules, so no fresh dependency-backed rerun was claimed. No dependencies or lockfiles were changed.

AI assistance

This Draft PR was prepared with OpenAI Codex. Automated root-cause analysis, patching, and validation evidence were used; no human self-review is claimed. It remains a draft for maintainer and user review.

[changeset-bot]

🦋 Changeset detected

Latest commit: 494f9f6

The changes in this PR will be included in the next version bump.

This PR includes changesets to release 1 package

Name	Type
myst-transforms	Patch

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