feat: move to mystmd

[henryiii]

Experimenting with a MystMD version.

Used CopilotCLI:claude-sonnet-4.6.

Moved prettier -> rumdl, works nicely with myst. Fewer ignores.

Some remaining issues:

• Coverage could use tab sync (mystmd feature) to keep tabs in sync (also documentation page for mkdocs / sphinx)
• Some {% commands still show up in output.

And I'm not sure these are solvable:

• No TOML highlighting - we have a lot of TOML. Looks like mystmd uses a really old highlighter
• I'd like a three-way toggle (auto/light/dark), not just (light/dark)
• Very plain and empty, maybe we could theme a bit?
• Repo-review is an iframe, seems you can't easily put in custom html? Probably solvable without an iframe.

Positives:

• Lots of built-in functionality we can just use (tabs, admonitions, etc)
• Can adopt some new functionality later, too (glossary, etc)
• Wide / mid screen layout is good, header stays on top in narrow layout
• Pretty fast, bun serve from docs folder.

[Copilot]

Pull request overview

This PR migrates the documentation site from the previous Jekyll/Ruby setup to a MystMD (MyST) build, updating pages to MyST-native directives (tabs/admonitions/includes), replacing the interactive repo-review embed, and switching Markdown formatting from Prettier to rumdl (MyST flavor).

Changes:

• Replace Jekyll/Ruby docs tooling with MystMD config, Node/Bun scaffolding, and updated RTD build commands.
• Convert docs content to MyST-native constructs (tab-sets, admonitions, includes, internal links) and add a custom {rr} role plugin.
• Adopt rumdl for Markdown formatting/linting and update related ignore/disable markers.

Reviewed changes

Copilot reviewed 60 out of 63 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
src/sp_repo_review/checks/ruff.py	Adjusts fenced-code language tags in check guidance text.
src/sp_repo_review/checks/pyproject.py	Adjusts fenced-code language tags in check guidance text.
src/sp_repo_review/checks/noxfile.py	Adjusts fenced-code language tags in check guidance text.
src/sp_repo_review/checks/mypy.py	Adjusts fenced-code language tags in check guidance text.
README.md	Updates Markdown formatting/ignore markers and minor heading/list formatting.
pyproject.toml	Adds [tool.rumdl] configuration for MyST-flavored Markdown lint/format.
package.json	Adds MystMD dependency and build/serve scripts for docs.
helpers/fetch_repo_review_app.sh	Removes helper used to fetch the legacy repo-review JS bundle.
helpers/cog_helpers.py	Updates code-fence helper to use rumdl markers and TOML→INI highlighting workaround.
Gemfile.lock	Removes Ruby dependency lockfile (Jekyll toolchain removal).
Gemfile	Removes Ruby/Jekyll dependency definitions.
docs/rr-role.mjs	Adds Myst plugin for {rr} inline role used in docs.
docs/pages/tutorials/test.md	Converts Jekyll frontmatter/TOC and links to MyST-native structure.
docs/pages/tutorials/packaging.md	Converts Jekyll frontmatter/TOC and links to MyST-native structure.
docs/pages/tutorials/module.md	Converts Jekyll frontmatter/TOC and links to MyST-native structure.
docs/pages/tutorials/index.md	Converts Jekyll frontmatter and adds MyST table-of-contents directive.
docs/pages/tutorials/docs.md	Converts headings/directives/links to MyST-native forms.
docs/pages/tutorials/dev-environment.md	Replaces Liquid tabs/admonitions and removes tabs.js dependency.
docs/pages/principles/testing.md	Converts headings, anchors, admonitions, and links to MyST-native forms.
docs/pages/principles/process.md	Converts headings/directives to MyST-native forms.
docs/pages/principles/index.md	Converts links and adds MyST table-of-contents directive.
docs/pages/principles/design.md	Converts admonitions and removes legacy prettier ignore markers.
docs/pages/patterns/index.md	Converts links and adds MyST table-of-contents directive.
docs/pages/patterns/exports.md	Converts admonitions/headings to MyST-native forms.
docs/pages/patterns/data_files.md	Converts details blocks to MyST dropdown directives and updates formatting.
docs/pages/patterns/backports.md	Converts headings and fenced-code language tags for highlighting.
docs/pages/index.md	Converts home page content/admonitions/links to MyST-native forms.
docs/pages/guides/tasks.md	Converts tabs/admonitions/rr markers and replaces legacy Jekyll constructs.
docs/pages/guides/style.md	Large MyST conversion: tabs, dropdowns, admonitions, rr markers, and link updates.
docs/pages/guides/repo_review.md	Replaces legacy iframe/include with an {anywidget} embed configuration.
docs/pages/guides/pytest.md	Converts tabs/admonitions/headings and updates fenced-code language tags.
docs/pages/guides/packaging_simple.md	Converts tabs/admonitions and uses MyST {include} for shared partial content.
docs/pages/guides/packaging_compiled.md	Converts tab-sets with :sync: keys and updates code-fence markers.
docs/pages/guides/packaging_classic.md	Converts admonitions/headings and link references to MyST-native forms.
docs/pages/guides/mypy.md	Converts headings/links to MyST-native forms.
docs/pages/guides/index.md	Converts links and adds MyST table-of-contents directive.
docs/pages/guides/gha_wheels.md	Converts tabs/admonitions/headings and updates code fences and raw blocks.
docs/pages/guides/gha_pure.md	Converts tabs/admonitions and updates links/headings for MyST.
docs/pages/guides/gha_basic.md	Converts tabs/admonitions and updates code-fence markers.
docs/pages/guides/docs.md	Converts extensive tabs/admonitions/includes to MyST-native directives.
docs/pages/guides/coverage.md	Converts tabs/headings and updates coverage guidance structure.
docs/myst.yml	Adds MystMD project/site configuration and explicit TOC structure.
docs/config/scientific-python.yml	Adds shared MystMD theme options/config extension.
docs/assets/js/tabs.js	Removes legacy JS used to implement Jekyll-era tabs.
docs/assets/css/site.css	Adds custom CSS overrides for the MystMD theme and {rr} badges.
docs/_sass/custom/custom.scss	Removes Jekyll-era SCSS customizations.
docs/_sass/color_schemes/skhep.scss	Removes Jekyll-era color scheme SCSS.
docs/_plugins/tabs.rb	Removes Jekyll Liquid plugin for tabs.
docs/_plugins/repo_review.rb	Removes Jekyll Liquid plugin for repo-review badges.
docs/_plugins/details.rb	Removes Jekyll Liquid plugin for details/summary blocks.
docs/_partials/pyproject.md	Updates shared partial used via MyST {include} and adjusts formatting.
docs/_includes/toc.html	Removes Jekyll include for TOC.
docs/_includes/interactive_repo_review.html	Removes Jekyll include for interactive repo-review embed.
docs/_includes/head.html	Removes Jekyll custom head include.
docs/_includes/head_custom.html	Removes Jekyll custom head include for repo-review assets.
bun.lock	Adds Bun lockfile for the MystMD dependency.
AGENTS.md	Adds repository agent/contributor guide, including docs tooling notes.
action.yml	Removes legacy prettier-ignore comment in the action steps.
.ruby-version	Removes Ruby version pin (Jekyll toolchain removal).
.readthedocs.yaml	Updates RTD build to MystMD/Node-based commands and output copy.
.pre-commit-config.yaml	Switches Markdown formatting from Prettier to rumdl and updates cog target paths.
.gitignore	Stops ignoring package.json and keeps Node-related ignores relevant to new tooling.
_config.yml	Removes Jekyll site configuration.

Comments suppressed due to low confidence (2)

docs/_partials/pyproject.md:1

• This file is included into other pages via the {include} directive. Starting the partial with an H1 (# ...) can create multiple top-level headings on the rendered page and distort the ToC. Consider using a lower heading level (e.g. ##/###) or removing the heading and letting the parent page introduce the section.
  docs/_partials/pyproject.md:67
• Within this included partial, ## License jumps heading levels relative to nearby subsections (e.g. ### Extras, ### Command line). This can produce a confusing outline when included. Consider making this heading consistent with the rest of the partial (likely ### License).

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