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>

assets/js/documentation.js

@@ -0,0 +1,145 @@
+/**
+ * Documentation Page — Table of Contents & Scroll Spy
+ * Peptide Starter Theme
+ *
+ * Handles:
+ * - Auto-generates ToC from h2 headings in the documentation body
+ * - Scroll spy highlights the active section in the sidebar
+ * - Smooth scrolling on ToC link click
+ * - Collapses sidebar to dropdown on mobile
+ *
+ * @see page-documentation.php — renders the two-column layout
+ * @see style.css — .ps-docs-* classes
+ *
+ * Conditionally enqueued only on pages using the Documentation template.
+ */
+
+(function() {
+	'use strict';
+
+	const docsBody   = document.getElementById('ps-docs-body');
+	const tocList    = document.getElementById('ps-docs-toc-list');
+	const sidebar    = document.querySelector('.ps-docs-sidebar');
+
+	if (!docsBody || !tocList) {
+		return;
+	}
+
+	const headings = docsBody.querySelectorAll('h2');
+
+	if (headings.length === 0) {
+		// Hide the sidebar if there are no headings to navigate.
+		if (sidebar) {
+			sidebar.style.display = 'none';
+		}
+		return;
+	}
+
+	/**
+	 * Build the Table of Contents from h2 headings.
+	 * Assigns IDs to headings that lack one for anchor linking.
+	 */
+	function buildToc() {
+		headings.forEach(function(heading, index) {
+			// Ensure every heading has an ID for anchor links.
+			if (!heading.id) {
+				heading.id = 'section-' + (index + 1);
+			}
+
+			var li   = document.createElement('li');
+			var link = document.createElement('a');
+
+			link.href        = '#' + heading.id;
+			link.textContent = heading.textContent;
+			link.className   = 'ps-docs-toc-link';
+
+			link.addEventListener('click', function(e) {
+				e.preventDefault();
+				smoothScrollTo(heading);
+			});
+
+			li.appendChild(link);
+			tocList.appendChild(li);
+		});
+	}
+
+	/**
+	 * Smooth scroll to a target element, accounting for the sticky header.
+	 * @param {HTMLElement} target The element to scroll to.
+	 */
+	function smoothScrollTo(target) {
+		var headerHeight = document.querySelector('.site-header')
+			? document.querySelector('.site-header').offsetHeight
+			: 0;
+		var offset = 24; // Extra breathing room below header.
+		var top    = target.getBoundingClientRect().top + window.pageYOffset - headerHeight - offset;
+
+		window.scrollTo({
+			top: top,
+			behavior: 'smooth'
+		});
+
+		// Update URL hash without jumping.
+		history.replaceState(null, '', '#' + target.id);
+	}
+
+	/**
+	 * Scroll spy — highlights the ToC link corresponding to the
+	 * currently visible section. Uses IntersectionObserver for performance.
+	 */
+	function initScrollSpy() {
+		var tocLinks = tocList.querySelectorAll('.ps-docs-toc-link');
+
+		if (tocLinks.length === 0) {
+			return;
+		}
+
+		var headerHeight = document.querySelector('.site-header')
+			? document.querySelector('.site-header').offsetHeight
+			: 0;
+
+		var observer = new IntersectionObserver(function(entries) {
+			entries.forEach(function(entry) {
+				if (entry.isIntersecting) {
+					var id = entry.target.id;
+					tocLinks.forEach(function(link) {
+						link.classList.remove('ps-docs-toc-link--active');
+						if (link.getAttribute('href') === '#' + id) {
+							link.classList.add('ps-docs-toc-link--active');
+						}
+					});
+				}
+			});
+		}, {
+			rootMargin: '-' + (headerHeight + 32) + 'px 0px -60% 0px',
+			threshold: 0
+		});
+
+		headings.forEach(function(heading) {
+			observer.observe(heading);
+		});
+	}
+
+	/**
+	 * Mobile dropdown toggle for the sidebar ToC.
+	 */
+	function initMobileToggle() {
+		var tocTitle = document.querySelector('.ps-docs-toc-title');
+
+		if (!tocTitle) {
+			return;
+		}
+
+		tocTitle.addEventListener('click', function() {
+			// Only toggle on mobile (sidebar is not sticky).
+			if (window.innerWidth < 1024) {
+				sidebar.classList.toggle('ps-docs-sidebar--open');
+			}
+		});
+	}
+
+	// Initialize.
+	buildToc();
+	initScrollSpy();
+	initMobileToggle();
+})();