v1.5.0: extend theme with navigation dropdowns, 9 page templates, auth UI, newsletter, contact panel

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>

CLAUDE.md

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+# Peptide Starter Theme
+
+WordPress theme for peptiderepo.com — a scientific peptide reference database.
+
+## Repository
+
+- **GitHub**: `peptiderepo/peptide-starter-theme` (private)
+- **Branch**: `main` is the production branch
+- **Live site**: https://peptiderepo.com
+- **Hosting**: Hostinger shared hosting
+
+## Deploy
+
+Push to `main` triggers GitHub Actions → rsync via SSH to Hostinger.
+No CI lint step — the deploy workflow (`deploy.yml`) runs rsync directly.
+LiteSpeed cache is purged automatically after deploy.
+
+Theme path on server: `~/domains/peptiderepo.com/public_html/wp-content/themes/peptide-starter/`
+
+## Architecture
+
+This is a classic WordPress theme (no block/FSE). All styling is in `style.css` (no build step, no preprocessor). JavaScript is vanilla — no bundler.
+
+### Key files
+
+| File | Purpose |
+|------|---------|
+| `style.css` | All theme CSS (~44KB). Organized: reset → tokens → typography → globals → components → regions → pages → animations → a11y → dark mode → responsive |
+| `functions.php` | Theme setup, script enqueueing, Customizer registration, nav walker, helper functions |
+| `front-page.php` | Home page: hero section → PRAutoBlogger widget → Peptide News feed |
+| `header.php` | Global header with nav, dark mode toggle, mobile menu |
+| `footer.php` | 4-column widget footer with copyright |
+| `archive-peptide.php` | Peptide CPT archive grid |
+| `single-peptide.php` | Single peptide detail page |
+| `assets/js/navigation.js` | Mobile menu and nav functionality |
+| `assets/js/theme.js` | Dark mode toggle, theme utilities |
+
+### Template parts
+
+- `template-parts/content.php` — Post/page content loop
+- `template-parts/content-peptide.php` — Peptide card in archive
+- `template-parts/content-none.php` — Empty state
+
+## Coding Conventions
+
+- **PHP**: WordPress coding standards — tabs for indentation, Yoda conditions, braces on same line
+- **CSS**: No preprocessor. Use CSS custom properties (defined in `:root`). All theme classes prefixed `.ps-`
+- **JS**: Vanilla ES6+, no build step. Files in `assets/js/` must pass `node --check`
+- **No `!important`** on global elements — prevents plugin conflicts
+- Plugin CSS namespaces are untouched (`.pn-*` for Peptide News, `.psa-*` for Peptide Search AI, `.prab-*` for PRAutoBlogger)
+
+## Design System
+
+- **Font**: Inter (Google Fonts) with system fallback
+- **Scale**: 1.125x modular, 8px grid base
+- **Primary color**: `#0066CC` (light) / `#3B82F6` (dark)
+- **Breakpoints**: 480px, 768px, 1024px, 1440px (mobile-first)
+- **Dark mode**: CSS custom properties swap via `html[data-theme="dark"]` or `prefers-color-scheme: dark`
+
+## Plugin Integration
+
+The theme integrates with three companion plugins via shortcodes, all wrapped in `shortcode_exists()` for graceful degradation:
+
+1. **Peptide Search AI** (`[peptide_search]`) — AI search in hero section
+2. **Peptide News** (`[peptide_news]`) — News feed on front page
+3. **PRAutoBlogger** (`[prautoblogger_posts]`) — Auto-generated research articles on front page
+
+## Customizer Options
+
+Editable via Appearance → Customize:
+- Hero title, subtitle, search placeholder
+- Footer copyright text
+- Dark mode default on/off
+
+## Version
+
+Current: **v1.3.1** (defined in `style.css` header and `PEPTIDE_STARTER_VERSION` constant in `functions.php`)
+
+When bumping version, update both locations.