Modernize hugo - #2

- .github/workflows/deploy.yml and pixi.toml: replace separate lint/test/build/linkcheck
  steps with one `pixi run validate` gate (lint+test+check-content+check-outputs+check-links),
  add prek hook caching, drop the qa/gh-action task split and debug feature
- .pre-commit-config.yaml: strip to file hygiene only, move check-content/check-outputs/tests
  into pixi tasks so each gate is defined once
- tools/zotero_common.py, tools/update-site-outputs.py: require Zotero's BetterBibTeX
  citationKey on every item instead of falling back to a generated key
- update docs (AGENTS.md, README.md) and tests to match
- layouts/projects/single.html: factor publications/software/datasets rendering into
  a shared "outsections" template
- layouts/partials/partners.html: inline partner-icon.html emoji lookup, drop the partial
- assets/css/main.css, hugo.toml, layouts/partials/footer.html: drop unused meta-block/
  pill/datasets-page CSS, summaryLength, and Stack Overflow footer link
- pixi.lock: drop unused bibtexparser/pdbpp/debug-feature transitive dependencies

- Replace `pixi run validate && pixi run build && pixi run linkcheck` with
  `pixi run validate` across skills and AGENTS.md
- Remove redundant `linkcheck` alias task from pixi.toml
- Update comments referencing `linkcheck` to `check-links`

…heme

- Add self-hosted Source Serif 4 webfonts and fluid modular typography scale
- Rework header nav as mobile-first disclosure menu with dismiss/escape handling
- Extract shared card.html partial to dedupe card markup across list templates
- Add render-table.html to wrap markdown tables in a scrollable container
- Restyle research outputs, thesis meta, and footer with fluid sizing and touch targets

…nventions

- Add pixi package-manager skill reference
- Add python-design-patterns skill with detailed patterns reference
- Document coding style, docstring, import, and commit conventions in AGENTS.md

- Add favicon.svg (Medical AI group mark) as preferred icon, keep favicon.ico
  and new apple-touch-icon.png as fallbacks
- Update validate_content.py allowlist to include the new static icon files

- delete static/images/profile_128.png binary
- drop it from STATIC_ALLOWED_FILES allowlist

- Flatten favicon.svg by removing boxy-svg metadata and consolidating stroke-based outlines into solid fill paths
- Regenerate apple-touch-icon.png and favicon.ico from the updated SVG

- add color accent tokens and gradient hero field, card/pill/badge styling
- introduce hero, icon, sec-head, out-cards, out-featured partials
- convert content lists to vertical card grids with icon-prefixed headings
- add teaching list layout and markdown heading render hook
- curate featured research outputs and add hero profile params
- rework about page and footer to match new hero-based layout

- Add "The theme" section to AGENTS.md covering width, accent, cards, headings, icons, and home page composition
- Note the 3:2 cover crop and cover_position override in add-project/add-talk/add-thesis skills and AGENTS.md front matter reference
- Add tools/tests/test_contrast.py to enforce WCAG AA contrast for the theme palette

- constrain .card__cover with min-width so narrow images fill the card
- regenerate cropped cover images for affected posts

- .card--vertical now sets align-items: stretch so shrink-wrapped
  narrow images no longer leave dead space beside them
- revert the now-unneeded width/min-width workaround on .card__cover
- update the rppg-manhob-hci-tagging cover image

… and reposition covers

- Expand major-achievements copy across all project pages with specific
  figures, numbers, and outcomes drawn from the underlying work
- Move project cover images below the title so a leading `<small>Cover:
  …</small>` block renders as the image's caption
- Style the cover-credit paragraph in main.css to sit tight under the cover
- Add cover credits to fibromuscular-dysplasia and uveitis pages

- Restructure each thesis writeup to explicitly state whether its
  hypothesis was confirmed, refuted, or partially supported
- Add concrete metrics and findings previously summarized generically
- Tighten closing paragraphs to name the practical consequence of
  each result

- add anjos_credible_2023 and anjos_fairical_2025 research outputs to reproducibility project
- rewrite methodology paragraph to credit the thesis and connect credible/fairical
- link antonio-morais thesis back to the reproducibility project