Book-style numbering: format, label, section-tagged TOC, auto-prefix by mmcky · Pull Request #22 · QuantEcon/mystmd

mmcky · 2026-05-14T02:49:44Z

Summary

Adds opt-in book-style numbering so MyST can render long-form books — chapters, appendices, prefixed figures/equations, and the "Chapter N" / "Appendix A" cross-ref conventions readers expect. Strict superset of today's behaviour; gated by numbering.book: true. Originating discussion: #12.

Authors enable book mode with:

project:
  numbering:
    book: true
  toc:
    - file: index
    - title: Chapters
      section: chapters       # heading_1 → arabic + "Chapter %s" label
      children:
        - file: ch1
        - file: ch2
    - title: Appendices
      section: appendices     # heading_1 → Alph + "Appendix %s" label
      children:
        - file: app-a
        - file: app-b

Then [](#ch1) renders "Chapter 1", figures in ch2.md render 2.1, 2.2, an appendix H1 renders "A", and [](#preface) on a section: frontmatter page falls back to the heading text — fixing the literal-template bug from jupyter-book#12.

What's in this PR (7 commits)

#	Commit	Plan §3.5
1	`fbed3d44` Add schema for book-style numbering	(1)
2	`d39288c5` Add `formatCounter` for arabic/alph/Alph/roman/Roman	(2)
3	`1c3251a6` Render heading cross-refs via label / fall back to title	(5)
4	`88ffc86a` Apply label rendering to file-target cross-refs	(5)
5	`61f74f4b` Inject per-section numbering defaults for tagged TOC subtrees	(3)
6	`ccff61a1` Auto-prefix figures/equations/tables/proofs with chapter enumerator	(4)
7	`8409c8cb` Test `proof:*` / `exercise` auto-prefix and render-only format override	(6,7)

NumberingItem extensions — format (arabic/alph/Alph/roman/Roman), label (cross-ref template distinct from template), reset_on_part, new well-known kinds parts/chapters/appendices, and the book opt-in flag.
formatCounter helper in myst-transforms — pure function plus wiring into formatHeadingEnumerator (per-depth formats) and ReferenceState.incrementCount (per-kind format).
Cross-ref label rendering — label > template > heading-text fallback for heading-type targets, including the file-target path ([](#ch1) where ch1 is a page slug).
section: field on ParentEntry in myst-toc — frontmatter | chapters | appendices | backmatter propagates to descendants; section-tagged subtrees are logical (no folder entry, no level bump). Per-section defaults injected in transformMdast.
Auto-prefix — figures/equations/tables, exercise, and the whole proof:* family get the page's chapter/appendix enumerator prepended in book mode. Per-kind opt-out via continue: true.

Backwards compatibility

All gated by numbering.book: true. Projects without the flag see zero behaviour change.
The section: field on TOC entries is optional and inert outside book mode.
Existing numbering.yml golden suite passes unchanged; existing enumerate.spec.ts cases pass unchanged.

Test plan

myst-frontmatter tests pass (499/499, +7 new golden cases for format / label / reset_on_part / book)
myst-transforms tests pass (345/345, +28 formatCounter cases, +4 heading-formats, +5 heading cross-ref, +9 book-mode auto-prefix, +2 proof/render-only-format)
myst-toc tests pass (34/34, +6 section field cases)
myst-cli tests pass (273/273, +9 injectBookSectionDefaults cases)
Fixture project renders chapters / appendices / preface end-to-end with no per-page numbering frontmatter (see quantecon/PLAN.md and quantecon/demo-book-numbering/ on main)

Open scope (deferred)

Honest scope notes are in quantecon/PLAN.md §3.1 on main. The biggest miss vs the plan: parts are not implemented in PR #1. Schema accepts reset_on_part and a parts kind, but no consumer reads them. Books without parts (just chapters + appendices) work fully today.

Also deferred: polymorphic {cref} / {Cref} / {eqref} (a future PR), generic reset_on: / shares_counter: primitives, i18n on label.

Status

We're keeping this PR open and unmerged in QuantEcon/mystmd so the work is available via feature/book-numbering + the combined quantecon build for dogfooding (book-dp1, book-dp2). A future submission upstream to jupyter-book/mystmd will reuse this branch.

🤖 Generated with Claude Code

Extends `NumberingItem` with `format`, `label`, and `reset_on_part`, and adds `parts`, `chapters`, `appendices` as well-known kinds on `Numbering`. Introduces the `book` opt-in flag (typed as a `NumberingItem` for index-signature compatibility; consumers check `numbering.book?.enabled === true`). The new fields are purely additive at this commit — no consumer wires them up yet. Validators normalize and golden-test all the new shapes.

Pure helper that renders an integer counter under any of the five formats from §3.2(b). Wired into: - formatHeadingEnumerator: new optional per-depth `formats` array, so the chapter/appendix prefix of a sub-heading (e.g. "A.1", "III.2.1") renders correctly. Omitted formats default to arabic so today's behaviour is preserved. - ReferenceState.incrementCount: per-kind `format` on figure / equation / table / etc. is applied when stringifying the main counter (and the subcontainer parent enumerator). Render-only — `format` does not touch counter state (§3.4(9)).

…(5)) Implements §3.2(h)'s heading cross-ref policy: when [](#target) resolves to a heading-type target and link text is omitted, prefer `numbering.heading_N.label` over `template`, with the heading text as the unnumbered fallback. - §3.2(h) label precedence: `label` wins over `template` for heading cross-refs, so `[](#ch1)` renders "Chapter 1" rather than "Section 1" once a project sets `numbering.heading_1.label: "Chapter %s"`. `template` continues to drive cross-refs when no label is set, so existing projects see no change. - #12 fix: a heading whose numbering is nominally enabled but which never received an enumerator (e.g. on a page with page-level `numbering: false`, or anything that would land in front/back matter once book mode is wired) now falls through to the heading text instead of substituting `%s` against UNKNOWN_REFERENCE_ENUMERATOR and rendering "Chapter ??". Scope-limited to heading-type targets. Figures, equations, tables, and other kinds keep today's labelling — extending the policy to non-heading kinds is PR #2 (§6).

The cross-ref to a page's H1 (e.g. \`[](#ch1)\` where \`ch1\` is the file slug) resolves through the file-target path, not the heading-target path. Without this change, that path always rendered the page title — so a book with \`numbering.heading_1.label: 'Chapter %s'\` still showed "Introduction" instead of "Chapter 1" for \`[](#ch1)\`. Authors had to invent extra anchors to get label rendering. Extend \`ReferenceState.resolveReferenceContent\` so the file-target branch applies the same \`label > template > title\` policy as inline headings, keyed off the page's \`heading_1\` numbering item and the page-level \`enumerator\` that the constructor already computes. Title remains the fallback when no label/template is set or the page is unnumbered (#12 case).

… §3.5(3)) When a ParentEntry in the TOC carries `section: chapters | appendices | frontmatter | backmatter` (new field on myst-toc CommonEntry), each descendant page inherits that section. With project `numbering.book: true`, the section drives sensible heading_1 defaults: arabic + "Chapter %s" for chapters, Alph + "Appendix %s" for appendices, and `enabled: false` (skip-semantic) for front/back matter. The first page of each section gets `start: 1` so the first appendix renders "A" rather than continuing the chapter sequence. This is a deviation from PLAN.md §3.2(a)'s literal YAML, which puts named sections as top-level keys under `toc: { format: jb-book }`. That form is the legacy Sphinx `_toc.yml` surface (used only by `myst upgrade`); MyST's `myst.yml toc:` is `MySTEntry[]`. Adding the named keys at the myst.yml level needs a format-discriminated union on the toc validator, which is invasive enough that PR #1 ships the section-tagged primitive instead. A later PR can layer the named-key form on top. Authors now write: numbering: book: true toc: - file: index - title: Appendices section: appendices children: - file: app-a The section subtree is logical, not structural — no folder is emitted, no level bump — so app-a's H1 stays at heading_1 instead of becoming heading_2.

#1, §3.5(4)) When `numbering.book.enabled` is true and the page itself is numbered (heading_1 ticks, so `state.enumerator` is set), every auto-prefixed kind picks up that enumerator as a leading prefix: ch1.md (heading_1 → "1"): Figure 1.1, 1.2; (1.1), (1.2); Table 1.1 app-a.md (heading_1 → "A"): Figure A.1, A.2; Theorem A.1; Exercise A.2 Each kind keeps its own per-page counter (today's reset-per-page behaviour), so figures/equations restart at the chapter/appendix boundary naturally. Pages without an enumerator (front-/backmatter, explicit `numbering: false`) get the flat global counter — no prefix. Authors opt out per-kind via the existing `continue: true` field (§3.4(6)): `numbering.figure.continue: true` keeps the figure counter flat across the whole book and drops the prefix. Auto-prefix kinds: figure, subfigure, equation, subequation, table, exercise, plus all `proof:*` / `prf:*` (theorem, lemma, proposition, …). The matcher uses a prefix test on `proof:` so new proof-family kinds added upstream are picked up automatically.

Closes the remaining test gaps in PR #1: - **§3.5(6) integration**: confirm a `proof` node with `kind: theorem` (which renders as kind "proof:theorem") and an `exercise` both pick up the chapter prefix in book mode. Asserts each proof-family kind keeps its own counter and only the chapter enumerator is shared — what the matcher claims, now exercised. - **§3.4(9) regression**: a chapter page sets `heading_1.format: Roman` in its frontmatter. The page renders "II" but the underlying counter stays 2, so the next chapter (without the override) continues at "3" rather than restarting or re-formatting. Uses the `previousCounts` chain across three ReferenceState instances to model the multi-page flow.

Copilot

Pull request overview

Adds opt-in book-style numbering across frontmatter schema, TOC parsing, project processing, and reference enumeration so book projects can render chapter/appendix labels and prefixed counters.

Changes:

Extends numbering schema/types with book mode, counter formats, labels, and section-related keys.
Adds formatted counters, heading label rendering, file-target label rendering, and book-mode auto-prefixing in reference enumeration.
Adds TOC section propagation and CLI-side injection of per-section numbering defaults.

Reviewed changes

Copilot reviewed 14 out of 14 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
`packages/myst-transforms/src/index.ts`	Exports new counter formatting helpers.
`packages/myst-transforms/src/enumerate.ts`	Implements formatted counters, heading labels, file-target labels, and book-mode auto-prefixing.
`packages/myst-transforms/src/enumerate.spec.ts`	Adds coverage for counter formats, labels, and auto-prefix behavior.
`packages/myst-toc/src/types.ts`	Adds `BookSection` and section metadata to TOC entries.
`packages/myst-toc/src/toc.ts`	Validates the new TOC `section` field.
`packages/myst-toc/tests/examples.spec.ts`	Adds TOC validation tests for book sections.
`packages/myst-frontmatter/src/numbering/types.ts`	Extends numbering item and numbering map types.
`packages/myst-frontmatter/src/numbering/validators.ts`	Validates new numbering keys and item options.
`packages/myst-frontmatter/src/numbering/numbering.yml`	Adds golden cases for new numbering options.
`packages/myst-cli/src/project/types.ts`	Carries inherited book section metadata on local project entries.
`packages/myst-cli/src/project/fromTOC.ts`	Propagates TOC section metadata into project pages.
`packages/myst-cli/src/process/site.ts`	Computes section metadata and passes it into mdast transforms.
`packages/myst-cli/src/process/mdast.ts`	Injects book-section numbering defaults before document transforms.
`packages/myst-cli/src/process/bookSection.spec.ts`	Adds tests for injected book-section defaults.

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CI `lint:format` job flagged these two files. Pure prettier --write output, no semantic change. Tests stay green (345/345).

Three errors surfaced by the `lint` workflow's `eslint` job (the `lint:format` job, which is prettier-based, went green after db7ddea): - mdast.ts: inline `import('myst-toc').BookSection` annotations violate `@typescript-eslint/consistent-type-imports`. Hoist to a top-level `import type { BookSection } from 'myst-toc'` and use the bare name in the two annotations. - site.ts: `sawAnyInSection` is only `.add()`-ed, never reassigned, so `prefer-const` flags it. Change `let` → `const`. 273/273 myst-cli tests still pass. Local `npm run lint` now reports 0 errors (12 pre-existing warnings unrelated to this PR).

Three substantive findings on the PR, plus one type-import lint fixup discovered along the way. **#1 — File-target labels for nested pages (enumerate.ts:633)** The file-target branch of `resolveReferenceContent` unconditionally read `numbering.heading_1` when applying the chapter/appendix label. A nested TOC page (offset > 0) has its title enumerator generated at `heading_${offset + 1}`, so reading heading_1 produced "Chapter 1.1" where the page is actually a heading_2 subsection. Use the page's offset to pick the right depth. Adds a regression test using `MultiPageReferenceResolver` with an offset=1 file target. **#2 — `numbering.chapters` / `numbering.appendices` were inert** PR #1 accepted these schema keys but `injectBookSectionDefaults` never read them — so setting `numbering.chapters.label: "Module %s"` or `numbering.appendices.format: roman` had no effect. The keys were live config that did nothing. Now the injection merges the section's block into `heading_1` between page frontmatter and the hardcoded defaults. Precedence: page heading_1 > numbering.<section> > hardcoded fallback All via `??=` so explicit author values always win. Adds three spec cases pinning the precedence. **#3 — section-tagged `FileEntry` should still bump children's level** The same-level recursion fired for any entry with `section:`, including a `FileEntry` like `{ file: ch1.md, section: chapters, children: [...] }`. Only section-only `ParentEntry` groups are meant to be logical wrappers; a section-tagged file is still a structural parent and its sub-pages should land at the next level. Narrowed the condition with an `isFile` check. **Drive-by — `Math` type import shadowed the JS global** CI surfaced `consistent-type-imports: Type import "Math" is used by decorator metadata`. The type-only import of `Math` from myst-spec-ext shadowed `Math.floor` (used in `formatCounter`). Renamed to `MathNode` and updated the one type reference. All four touched packages green: myst-frontmatter 499/499, myst-transforms 346/346 (+1 nested-file-target), myst-toc 34/34, myst-cli 276/276 (+3 chapters/appendices precedence cases).

…ker (#24) Records which QuantEcon-specific features are merged into this fork's main, identified by a `qe-vN` tag that also exists as a git tag on the corresponding squash-merge commit. Doubles as a tracker for upstream PR status — each feature has an `upstream` block that fills in as features get upstreamed to jupyter-book/mystmd. Populated with the two features already on main: - qe-v1: feature/myst-to-ipynb (#16) - qe-v2: feature/book-numbering (#22) Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

…ERSION.yml Two tracker files now record orthogonal facts, cross-referenced by squash-commit SHA: - VERSION.yml answers "what's in our main?" — diagnostic identifier for the integration build. Drops its `upstream:` block (was an always-`pending` placeholder). - UPSTREAM-PRS.yml answers "how do we plan to ship those squash commits upstream?" — bundles related squashes into logical upstream PR candidates (so a feature spanning multiple commits, or two features that form one upstream story, can be tracked as a single unit), records dependency order for cherry-pick, tracks status. Seeds UPSTREAM-PRS.yml with three candidates: myst-to-ipynb (#16), book-mode-with-section-scope (#22 + #28, bundled — they form one coherent upstream story since #28 builds on #22's auto-prefix hooks), and book-parts (#26, planned). Adds the missing book-proof-scope entry to VERSION.yml's merged_features. README updated to partition the two files' roles and reference UPSTREAM-PRS.yml from the cherry-pick workflow. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* docs(quantecon): cherry-pick upstream model, batched tags Replace the "preserve feature branch, push as upstream PR" workflow with "delete feature branch after merge; cherry-pick main squash commits onto a fresh branch off upstream/main when upstreaming." Why: - Feature branches that depend on prior QuantEcon-only features were awkward to branch from upstream/main (had to carry the dependency inline or wait for it to upstream first). - Branching from main lets dependencies just work; the squash commit on main is already the upstream-ready artifact. - Cherry-picking at upstream-PR time lets us bundle related squashes into a coherent story ("book mode + section scope") when that's the right unit for upstream review, or split them. Tagging also moves from per-PR to batched: a `qe-vN` tag is cut at a checkpoint covering multiple features, not on each merge. Updates the diagram, branching-model table, "Develop a new feature", "Opening an upstream PR" (now cherry-pick-driven), "When upstream merges", "Resolving merge conflicts between features", and the VERSION.yml comment block. Adds an `upstream/<topic>` branch type to the branching model. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * docs(quantecon): add UPSTREAM-PRS.yml; split upstream tracking from VERSION.yml Two tracker files now record orthogonal facts, cross-referenced by squash-commit SHA: - VERSION.yml answers "what's in our main?" — diagnostic identifier for the integration build. Drops its `upstream:` block (was an always-`pending` placeholder). - UPSTREAM-PRS.yml answers "how do we plan to ship those squash commits upstream?" — bundles related squashes into logical upstream PR candidates (so a feature spanning multiple commits, or two features that form one upstream story, can be tracked as a single unit), records dependency order for cherry-pick, tracks status. Seeds UPSTREAM-PRS.yml with three candidates: myst-to-ipynb (#16), book-mode-with-section-scope (#22 + #28, bundled — they form one coherent upstream story since #28 builds on #22's auto-prefix hooks), and book-parts (#26, planned). Adds the missing book-proof-scope entry to VERSION.yml's merged_features. README updated to partition the two files' roles and reference UPSTREAM-PRS.yml from the cherry-pick workflow. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * docs(quantecon): address Copilot feedback on PR #30 - VERSION.yml header: remove double-accounting in the tag-cut steps. Per-PR landing already appends each feature to merged_features with tag: null; the tag-cut workflow just *sets* the tag field on those pre-existing entries and bumps qe_version. The old wording said "Append each newly-included feature" which contradicted the per-PR-landing description below it. - README "About this folder": the allow-list now contains README.md, VERSION.yml, UPSTREAM-PRS.yml, and .gitignore itself — the original text only mentioned the first two. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

* feat(book): full title→heading chain in injectBookSectionDefaults (#25) Wires `title.enabled`, `heading_2.enabled`, and `heading_3.enabled` per `section:` tag in `injectBookSectionDefaults` so the chapter-prefix machinery in enumerate.ts composes without authors needing project-level workarounds. Background: `enumerate.ts`'s book-mode auto-prefix only fires when the page-title heading is itself numbered (it provides `this.enumerator` for figures/theorems/sub-headings to prepend). The page-title heading in turn requires `numbering.title.enabled: true`. PR #22 wired `heading_1.enabled` per section but missed `title`, so chapter pages rendered `Figure 1` / `Section 1` instead of `Figure 1.1` / `Section 1.1` on a default `numbering.book: true` config. Authors hit this on pandoc- generated chapter files (LaTeX `\chapter{}` → MD `# Title`) where they cannot add per-page frontmatter. This patch: - chapters / appendices: seeds `title.enabled ??= true`, `heading_2.enabled ??= true`, `heading_3.enabled ??= true` alongside the existing `heading_1` defaults. - frontmatter / backmatter: seeds those same keys to `??= false` so a project-level `heading_2.enabled: true` (often used so chapters number correctly) doesn't leak through and number the preface's `##` headings. - Changes the legacy hard `h1.enabled = false` on frontmatter/backmatter to `??= false` for symmetry — a page that explicitly wants its title numbered (e.g. "Chapter 0: Preface") can now override the section default. The hard assignment had made this impossible. All assignments use `??=` so the layered precedence (page > project > section default > hardcoded) is preserved. Adds 10 new tests covering the new wiring and the per-page override paths. Closes #25. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * docs(book): align section-defaults claims with §3.5(g) precedence Comment-and-changeset cleanup of injectBookSectionDefaults after a deep review confirmed the documented precedence chain (page > project > section > built-in) matches the code. The previous claim that frontmatter/backmatter section defaults block project-level numbering leakage contradicted that chain — `injectBookSectionDefaults` runs after `processPageFrontmatter` merges project numbering into the page, so `??=` no-ops for any key the project explicitly set. Reframe the comments and changeset around the real story: the new chapter-side wiring (title/heading_2/heading_3 seeded true on chapter pages) means authors no longer need a project-level `heading_2.enabled: true` workaround, so the leak scenario stops happening in the common case. A project that explicitly enables those depths still wins — by design, per §3.5(g). Also replace the `start: 0` page-override test (rejected by the `min: 1` validator at validators.ts:148) with a valid override using `title.enabled: true`. No code logic changes, no signature changes. All 19 bookSection tests pass; full myst-cli suite 293/293 green. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * feat(book): extend section-defaults chain to heading_6 (#36) Extend `injectBookSectionDefaults` to wire heading_4/5/6 alongside the existing title/heading_1/heading_2/heading_3 chain. With the depth-1–3 fix in place, authors who removed the project-level workaround discovered that `####`+ headings on chapter pages rendered unnumbered (verified against book-dp1 — ch_intro had H4s rendering with enum=None instead of `1.1.1.1`). mystmd's numbering schema caps at heading_6 (matches HTML h1–h6, see myst-frontmatter numbering/types.ts), so wiring 1–6 is exhaustive rather than arbitrary — there is no heading_7 to forget. All assignments stay `??=` per §3.5(g) precedence (page > project > section > built-in), so a project or page that explicitly disables a deeper level still wins. Tests updated to assert the full 1–6 chain on chapters/appendices and the matching full disable on frontmatter/backmatter. All 19 bookSection tests pass; full myst-cli suite 293/293 green. Closes #36. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * fix(book): no-op injectBookSectionDefaults for unhandled sections Move all numbering mutations inside the `switch` cases so any `BookSection` value not explicitly handled (currently only `parts`, which is divider-only) is a clean no-op past the gate checks. Previously the function pre-initialized `heading_1` and (after the heading_6 extension in 33ae25c) `title`/`heading_2…heading_6` to empty `{}` objects before the switch, which leaked into the resolved frontmatter for any page tagged `section: parts`. The `firstInSection` branch could also have set `h1.start = 1` on such pages. Both are now contained to the chapters/appendices and frontmatter/backmatter cases that actually need them. Caught by Copilot review on PR #33. Add a regression test pinning the no-op behavior for `section: parts` with `firstInSection: true` — the path that previously leaked the most. 20 bookSection tests pass; full myst-cli suite 294/294 green. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

mmcky added 7 commits May 14, 2026 10:49

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Comment thread packages/myst-cli/src/process/mdast.ts

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mmcky added 3 commits May 14, 2026 12:59

Apply prettier formatting to enumerate.ts and enumerate.spec.ts

db7ddea

CI `lint:format` job flagged these two files. Pure prettier --write output, no semantic change. Tests stay green (345/345).

mmcky mentioned this pull request May 14, 2026

chore(quantecon): switch to merge-to-main development model #23

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Merge branch 'main' into feature/book-numbering

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mmcky merged commit 032957c into main May 14, 2026
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mmcky mentioned this pull request May 14, 2026

chore(quantecon): add VERSION.yml as build identifier + upstream tracker #24

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mmcky mentioned this pull request May 15, 2026

chore(quantecon): cut qe-v4 (book-parts, #26) #32

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Book-style numbering: format, label, section-tagged TOC, auto-prefix#22

Book-style numbering: format, label, section-tagged TOC, auto-prefix#22
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What's in this PR (7 commits)

Backwards compatibility

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Open scope (deferred)

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mmcky commented May 14, 2026 •

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