Major theme extension adding full-featured navigation with dropdown submenus (Tools, My Data, Resources),
9 new page templates (Calculator, Protocol Builder, Tracker, Subject Log, Documentation, Directory,
Science Feed, Profile, Sign In/Register), documentation page with sidebar ToC and scroll spy,
branded AJAX authentication forms, newsletter signup with admin export, slide-out contact/support panel,
Research Modules 6-card grid on front page, and comprehensive footer update.
Split functions.php (554→206 lines) into 6 focused inc/ modules: helpers, customizer, auth-handlers,
contact-handler, page-setup, newsletter-admin. All new components include dark mode support, CSRF
protection, input sanitization, output escaping, and graceful plugin degradation via shortcode_exists().
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Reduce hero padding from 96/80px to 64/48px, shrink subtitle and
search margins, tighten news-feed and archive section padding,
and reduce peptides grid gap for better content density.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Warm off-white light palette, decorative geometric shapes,
category-coded peptide cards with tinted borders and pill badges,
larger hero typography with accent word, header CTA button,
and redesigned single-peptide detail page with meta card grid.
Dark mode stays default per user preference. Light mode gets the
warm treatment when toggled or via prefers-color-scheme.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
The CI was overriding the project PHPCS config by passing
--standard=WordPress-Core directly. Now uses the project
.phpcs.xml.dist which includes exclusions for standard WP
patterns (class in functions.php).
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Convert all PHP files from CRLF to LF line endings
- Reformat multi-line function calls per WPCS standard
(opening paren last on line, closing paren on own line)
- Fix assignment-in-conditional in single-peptide.php
- Change double quotes to single quotes in content-none.php
- Exclude InvalidClassFileName sniff (standard WP functions.php pattern)
- Fix archive-peptide.php opening PHP tag placement
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Wrapped get_search_query() with esc_attr() in 404.php, front-page.php,
and searchform.php. Without this, a crafted search query can inject
arbitrary HTML attributes into the search input value field.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Renders PRAutoBlogger-generated research articles as a card grid
between the hero section and the peptide news feed. Wrapped in
shortcode_exists() so it degrades gracefully if the plugin is
deactivated.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
