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>

page-protocol-builder.php

@@ -0,0 +1,48 @@
+<?php
+/**
+ * Template Name: Protocol Builder
+ *
+ * Page template for the interactive protocol builder wizard.
+ * Loads the Peptide Tools plugin protocol builder via shortcode.
+ *
+ * @see page-calculator.php — sibling tool template
+ * @see functions.php — enqueue and page auto-creation
+ *
+ * What: Renders the protocol builder page with plugin shortcode integration.
+ * Who calls it: WordPress template hierarchy when a page uses this template.
+ * Dependencies: Peptide Tools plugin (optional — graceful fallback).
+ *
+ * @package peptide-starter
+ */
+
+// Exit if accessed directly.
+if ( ! defined( 'ABSPATH' ) ) {
+	exit;
+}
+
+get_header();
+?>
+
+<main id="main" class="site-main">
+	<section class="ps-tool-page">
+		<div class="ps-container">
+			<?php
+			if ( shortcode_exists( 'peptide_tools_protocol_builder' ) ) {
+				echo do_shortcode( '[peptide_tools_protocol_builder]' );
+			} else {
+				?>
+				<div class="ps-tool-fallback">
+					<h1><?php esc_html_e( 'Protocol Builder', 'peptide-starter' ); ?></h1>
+					<p><?php esc_html_e( 'The protocol builder tool is currently being set up. Please check back soon.', 'peptide-starter' ); ?></p>
+					<a href="<?php echo esc_url( home_url( '/' ) ); ?>" class="ps-btn ps-btn-primary">
+						<?php esc_html_e( 'Return Home', 'peptide-starter' ); ?>
+					</a>
+				</div>
+				<?php
+			}
+			?>
+		</div>
+	</section>
+</main>
+
+<?php get_footer(); ?>