chore: upgrade to next.js 16 + new findable-ui major (phase 2 from findable-ui#952) (#3087)

[frano-m]

Closes #3087
Parent epic: DataBiosphere/findable-ui#952 (Phase 2 — Next 16 rollout across consumers)
Grandparent: DataBiosphere/findable-ui#884 (Next 16 upgrade plan)

Follow-ups (this repo):

• SearchView: encode pagination index in URL query string #3088 — encode pagination index in URL query string (removes the react-hooks/set-state-in-effect suppression in useSearch.ts)
• Sanitize Crossref-fetched publication titles in complete-biccn-publications script #3089 — sanitize Crossref-fetched publication titles in complete-biccn-publications script

Reference PRs for the same upgrade on prior consumers:

• ucscBrainExplorer/data-explorer#108
• human-pangenomics/hprc-data-explorer#282
• clevercanary/hca-atlas-tracker#1388

Summary

• Bumps next ^16 family, next-mdx-remote ^6, @databiosphere/findable-ui ^54.1.
• Wires MUI Emotion cache for SSR via AppCacheProvider (_app.tsx) + DocumentHeadTags / documentGetInitialProps (_document.tsx).
• Pins next dev / next build to webpack — tracks vercel/next.js#82607.
• Migrates .eslintrc.json + .eslintignore → eslint.config.mjs (flat config, ESLint v9). Swaps eslint-plugin-eslint-comments → @eslint-community/eslint-plugin-eslint-comments, eslint-plugin-typescript-sort-keys → eslint-plugin-perfectionist ^4. Bumps react-hooks ^7, jsdoc ^63, sort-destructure-keys ^3.
• Bumps engines.node to 22.13.0; adds .nvmrc; updates CI workflow.
• Drops the redundant glob ^11.0.4 override.

Data-portal-specific surfaces fixed in this PR

• pages/_app.tsx — ErrorBoundary import path → errorBoundary/errorBoundary (v54 dropped the directory barrel).
• utils/docPages.ts — pass blockJS: false to next-mdx-remote/serialize options (v6 default silently strips JSX expression attributes).
• components/.../Publication/publication.tsx — findable-ui v54 removed the Markdown component. Verified the data: of 24 publication titles in constants/biccn-publications.json, 23 are plain strings; one had embedded <sup>+</sup> HTML with stray whitespace from a Crossref scrape. Cleaned that title to use Unicode ⁺, and switched the renderer to plain text — <CardTitle>{publication.title}</CardTitle> etc. Sanitization of future Crossref fetches tracked in Sanitize Crossref-fetched publication titles in complete-biccn-publications script #3089.
• views/SearchView/hooks/useSearch.ts — react-hooks v7 flags the useEffect → setRequestURL sync as set-state-in-effect. The deeper fix (move searchIndex into the URL) is out of scope for the upgrade; suppressed inline with // eslint-disable-next-line ... -- track via #3088.
• theme/typography/constants.ts — @media (...) keys kept after letter keys via inline // eslint-disable-next-line sort-keys -- disabling key order for readability (mirrors findable-ui's own convention).
• Several JSDoc additions, sort-keys reorderings, return-type annotations, and one sonarjs/no-nested-template-literals fix to satisfy the new rule set.
• viewModelBuilders/dataDictionaryMapper/accessorFn.ts — return type of buildTierNSource widened from inferred to ReactNode (matches actual LinkProps['children'] type; no behavior change).
• Uninstalled isomorphic-dompurify (no longer needed once the local Markdown component / MarkdownRenderer path was dropped).

npm audit fix

Ran npm audit fix (no --force); 6 moderate vulns remain, all transitive postcss via next. No fix available until Next ships an update. To be handled separately.

Test plan

• npm run build-dev:data-portal succeeds (verified locally)
• npm run lint — 0 errors, 8 pre-existing TODO warnings (verified locally)
• tsc --noEmit clean (verified locally)
• CI green on this branch
• Deploy to staging and smoke test
• Confirm no React hydration warnings on MUI-styled pages (validates Emotion cache wiring)
• Spot-check /hca-bio-networks/<network>/publications — publication titles + citations render as plain text, including the cleaned Na⁺/K⁺ paper
• Spot-check /search?q=... — search results load and pagination works (no mid-browse resets)
• Spot-check MDX-rendered doc pages — confirm blockJS: false preserved any JSX attributes that were previously rendering

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Upgrades the data-portal app to Next.js 16 and the latest major @databiosphere/findable-ui, with associated tooling and SSR plumbing updates (ESLint v9 flat config, MUI Emotion cache integration, and MDX serialization behavior alignment).

Changes:

• Bump core dependencies (Next.js 16, findable-ui v54, next-mdx-remote v6) and Node engine baseline (22.13.0), updating CI accordingly.
• Add MUI Next.js (pages router) SSR Emotion cache wiring via AppCacheProvider (_app.tsx) and DocumentHeadTags/documentGetInitialProps (_document.tsx).
• Migrate ESLint config to flat config (eslint.config.mjs), update lint script, and apply small code/doc tweaks to satisfy updated rule sets and removed APIs.

Reviewed changes

Copilot reviewed 22 out of 24 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
views/SearchView/hooks/useSearch.ts	Suppresses react-hooks/set-state-in-effect for URL→state sync (tracked follow-up).
viewModelBuilders/viewModelBuilders.ts	Adds explicit JSX return types and JSDoc param clarifications.
viewModelBuilders/dataDictionaryMapper/viewModelBuilders.ts	Simplifies string building (avoids nested template literals).
viewModelBuilders/dataDictionaryMapper/columnDefs.ts	Key reordering to satisfy sort rules.
viewModelBuilders/dataDictionaryMapper/accessorFn.ts	Widen accessor return type to ReactNode.
utils/trackerNetwork.ts	Adds JSDoc param/returns annotations.
utils/docPages.ts	Sets blockJS: false for next-mdx-remote v6 serialization to preserve JSX expression attributes.
utils/availableNetworks.ts	Adds @returns documentation for filtering behavior.
tsconfig.json	Updates TS settings for Next 16 (moduleResolution: bundler, jsx: react-jsx).
theme/typography/constants.ts	Adds scoped sort-keys suppressions to preserve readable key ordering.
site-config/data-portal/dev/config.ts	Reorders dataSource block (no functional change).
pages/_document.tsx	Adds MUI Next.js document helpers for Emotion SSR tags.
pages/_app.tsx	Wraps app in MUI AppCacheProvider; updates findable-ui ErrorBoundary import path.
package.json	Dependency bumps, webpack pin for Next CLI, ESLint v9 tooling, Node engine bump, remove unused override.
eslint.config.mjs	Introduces ESLint v9 flat config replacing legacy .eslintrc.json + .eslintignore.
constants/biccn-publications.json	Cleans a publication title (replaces HTML sup tags with Unicode superscripts).
components/HCABioNetworks/.../publication.tsx	Removes Markdown rendering and renders publication title/citation as plain text.
apis/tracker/api.ts	Adds missing @returns JSDoc lines.
apis/azul/hca-dcp/common/entities.ts	Removes explicit-any suppressions; uses unknown index signatures.
.nvmrc	Pins local Node version to 22.13.0.
.github/workflows/run-checks.yml	Updates CI Node version to 22.13.0.
.eslintrc.json	Removed (replaced by flat config).
.eslintignore	Removed (replaced by flat config ignores).

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