feat: upgrade to next.js 16 and findable-ui v54 (#1391)

[frano-m]

Summary

Phase 2 of the Next 16 rollout (DataBiosphere/findable-ui#952): upgrades brc-analytics to Next.js 16 + the new findable-ui v54 major, with the associated React/MUI/ESLint/Node bumps.

Closes #1391

Dependencies

• @databiosphere/findable-ui ^51 → ^54, next ^15 → ^16, react/react-dom → ^19.2.3, next-mdx-remote ^5 → ^6, @next/mdx ^16.
• Added @mui/material-nextjs, @emotion/server (Next 16 Emotion SSR).
• Lint stack → ESLint 9 flat config: eslint ^9, eslint-config-next ^16, @next/eslint-plugin-next ^16, eslint-plugin-react-hooks ^7, eslint-plugin-perfectionist, @eslint/js, @eslint/eslintrc, @eslint-community/eslint-plugin-eslint-comments.
• Removed: eslint-plugin-eslint-comments, eslint-plugin-typescript-sort-keys (→ perfectionist), isomorphic-dompurify (unused), and the glob override.
• Shared peers aligned to findable-ui's versions.

Next 16 wiring

• _app.tsx wrapped in AppCacheProvider; _document.tsx adds DocumentHeadTags + documentGetInitialProps (@mui/material-nextjs/v16-pagesRouter).
• dev/build scripts pinned to --webpack; lint → eslint ..
• Migrated .eslintrc.json/.eslintignore → eslint.config.mjs (mirrors findable-ui).

Node 22.13.0

engines, new .nvmrc, CI workflows (×4), Dockerfile.

Findable v54 + bundler-resolution fallout

• Module-path updates: Index/indexView.styles, ErrorBoundary/errorBoundary.
• Next 16 set tsconfig moduleResolution: "bundler" (matches hprc-data-explorer). This surfaced two pre-existing issues that were silently any under node resolution:
  • vega-embed's malformed exports map can't expose VisualizationSpec under bundler; reconstructed it from its sources (vega-lite TopLevelSpec | vega Spec) and added a proper "datasets" in spec narrow.
  • workflows.json direct imports cast to WorkflowCategory[] at the boundary (catalog JSON is schema-validated in CI).

Lint fallout

react-hooks v7 flagged pre-existing effects. Our team's 6 set-state-in-effect sites carry a documented disable and are tracked for refactor in #1393; 6 other-team (account/auth/assistant) sites carry a neutral disable. react-hooks/preserve-manual-memoization is turned off (Compiler-readiness rule; we don't run the Compiler — same as findable's incompatible-library).

Verification

• tsc clean, eslint . clean, prettier clean.
• Unit tests: 568 passing.
• Both sites build under Next 16 (next build --webpack, static export): BRC (122,671 pages) + GA2.
• npm audit (no --force): 45 → 32; remainder require breaking changes / are transitive via the next-auth peer findable declares (brc doesn't use it).

Follow-ups

• Lint cleanup: react-hooks v7 set-state-in-effect refactors (follow-up to #1391) #1393 — refactor our team's set-state-in-effect effects.

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Upgrades the application’s frontend stack to Next.js 16 and findable-ui v54, aligning React/MUI/ESLint/Node versions and wiring up Next 16 + MUI Emotion SSR integration across the Pages Router.

Changes:

• Bumped core deps (Next 16, findable-ui v54, React 19.2.3, MUI + Emotion) and updated scripts to use next * --webpack.
• Migrated linting to ESLint 9 flat config (eslint.config.mjs) and switched lint to eslint ..
• Updated TS/Next wiring and type-safety fixes (bundler module resolution, JSON typing boundary, vega-embed type reconstruction), plus Node 22.13.0 pinning in CI/Docker.

Reviewed changes

Copilot reviewed 28 out of 31 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tsconfig.json	Switches to moduleResolution: bundler, jsx: react-jsx, and expands Next dev types include paths for Next 16.
package.json	Upgrades Next/findable-ui/React/MUI/ESLint toolchain, updates scripts (--webpack), and pins Node engine to 22.13.0.
eslint.config.mjs	Adds ESLint 9 flat configuration aligned to the new lint stack and project conventions.
.eslintrc.json	Removes legacy ESLint config (replaced by flat config).
.eslintignore	Removes legacy ignore file (replaced by ignores in flat config).
next-env.d.ts	Updates Next-generated types inclusion for routes typing.
pages/_app.tsx	Wires in MUI Next 16 Pages Router cache provider and updates findable-ui import paths.
pages/_document.tsx	Adds MUI Next 16 Pages Router document head tags + documentGetInitialProps integration for Emotion SSR.
Dockerfile	Pins builder image to node:22.13.0-alpine.
.github/workflows/run-checks.yml	Pins CI Node version to 22.13.0.
.github/workflows/publish-release.yml	Pins CI Node version to 22.13.0.
.github/workflows/check-pr-title.yml	Pins CI Node version to 22.13.0.
tests/configureWorkflow/sampleSheetStep/useFilePicker.hook.test.ts	Removes now-unnecessary local lint disables under the new flat-config overrides for tests.
pages/data/[entityListType]/[entityId]/analyze/workflows/[trsId]/index.tsx	Casts schema-validated workflow catalog JSON at the boundary to restore typing under bundler resolution.
app/views/AnalyzeWorkflowsView/components/Main/main.tsx	Applies typed cast for workflow categories JSON passed into workflow-building utilities.
app/views/PriorityPathogensView/priorityPathogensView.styles.ts	Updates findable-ui import path for Index view styles after v54 changes.
app/components/common/VegaEmbed/vegaEmbed.tsx	Reconstructs VisualizationSpec typing using vega/vega-lite due to vega-embed export-map issues under bundler resolution.
app/providers/workflowHandoff/actions/clearHandoff/action.ts	Adjusts eslint-disable to match updated lint rules/config behavior.
pages/assistant/saved.tsx	Adds targeted lint disable for react-hooks/set-state-in-effect per v7 rule enforcement.
pages/account/workflow-runs.tsx	Adds targeted lint disable for react-hooks/set-state-in-effect per v7 rule enforcement.
pages/account/preferences.tsx	Adds targeted lint disable for react-hooks/set-state-in-effect per v7 rule enforcement.
app/providers/authentication.tsx	Adds targeted lint disable for react-hooks/set-state-in-effect per v7 rule enforcement.
app/hooks/useAssistantChat.ts	Adds targeted lint disable for react-hooks/set-state-in-effect per v7 rule enforcement.
app/hooks/useAssemblyFavorites.ts	Adds targeted lint disable for react-hooks/set-state-in-effect per v7 rule enforcement.
app/hooks/useSwipeInteraction/useSwipeInteraction.tsx	Adds targeted lint disable and references planned refactor tracking for the v7 rule.
app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/DESeq2FormulaStep/hooks/UseFormulaSelection/hook.ts	Adds targeted lint disable with refactor tracking for the v7 rule.
app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SampleSheetClassificationStep/hooks/UseColumnClassification/hook.ts	Adds targeted lint disable with refactor tracking for the v7 rule.
app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/PrimaryContrastsStep/hooks/UseExplicitContrasts/hook.ts	Adds targeted lint disable with refactor tracking for the v7 rule.
app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/PrimaryContrastsStep/hooks/UseBaselineContrasts/hook.ts	Adds targeted lint disable with refactor tracking for the v7 rule.
app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/components/DataSelector/components/Alert/hooks/UseTaxonomyMatches/hook.ts	Adds targeted lint disable with refactor tracking for the v7 rule.

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[Copilot]

Pull request overview

Copilot reviewed 28 out of 31 changed files in this pull request and generated 1 comment.