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>

inc/page-setup.php

@@ -0,0 +1,105 @@
+<?php
+/**
+ * Auto-Create Pages on Theme Activation
+ *
+ * Creates the required WordPress pages (with correct templates assigned)
+ * when the theme is activated, if they don't already exist.
+ *
+ * @see functions.php — includes this file
+ * @see ARCHITECTURE.md — documents the page/template mapping
+ *
+ * What: Theme activation hook that auto-creates pages for all new templates.
+ * Who calls it: WordPress after_switch_theme action.
+ * Dependencies: None — uses WordPress core functions only.
+ *
+ * @package peptide-starter
+ */
+
+// Exit if accessed directly.
+if ( ! defined( 'ABSPATH' ) ) {
+	exit;
+}
+
+/**
+ * Create required pages on theme activation.
+ *
+ * Checks if each page slug exists; creates it if missing with the
+ * correct page template assigned. Skips existing pages to avoid duplicates.
+ *
+ * @return void
+ */
+function peptide_starter_create_pages() {
+	$pages = array(
+		array(
+			'title'    => __( 'Calculator', 'peptide-starter' ),
+			'slug'     => 'calculator',
+			'template' => 'page-calculator.php',
+		),
+		array(
+			'title'    => __( 'Protocol Builder', 'peptide-starter' ),
+			'slug'     => 'protocol-builder',
+			'template' => 'page-protocol-builder.php',
+		),
+		array(
+			'title'    => __( 'Tracker', 'peptide-starter' ),
+			'slug'     => 'tracker',
+			'template' => 'page-tracker.php',
+		),
+		array(
+			'title'    => __( 'Subject Log', 'peptide-starter' ),
+			'slug'     => 'subject-log',
+			'template' => 'page-subject-log.php',
+		),
+		array(
+			'title'    => __( 'Documentation', 'peptide-starter' ),
+			'slug'     => 'documentation',
+			'template' => 'page-documentation.php',
+		),
+		array(
+			'title'    => __( 'Peptide Directory', 'peptide-starter' ),
+			'slug'     => 'peptides',
+			'template' => 'page-directory.php',
+		),
+		array(
+			'title'    => __( 'Science Feed', 'peptide-starter' ),
+			'slug'     => 'news',
+			'template' => 'page-science-feed.php',
+		),
+		array(
+			'title'    => __( 'Profile', 'peptide-starter' ),
+			'slug'     => 'profile',
+			'template' => 'page-profile.php',
+		),
+		array(
+			'title'    => __( 'Sign In', 'peptide-starter' ),
+			'slug'     => 'auth',
+			'template' => 'page-auth.php',
+		),
+	);
+
+	foreach ( $pages as $page_data ) {
+		$existing = get_page_by_path( $page_data['slug'] );
+
+		if ( $existing ) {
+			// Page exists — ensure the template is assigned.
+			update_post_meta( $existing->ID, '_wp_page_template', $page_data['template'] );
+			continue;
+		}
+
+		$page_id = wp_insert_post(
+			array(
+				'post_title'   => $page_data['title'],
+				'post_name'    => $page_data['slug'],
+				'post_status'  => 'publish',
+				'post_type'    => 'page',
+				'post_content' => '',
+				'post_author'  => 1,
+			)
+		);
+
+		if ( $page_id && ! is_wp_error( $page_id ) ) {
+			update_post_meta( $page_id, '_wp_page_template', $page_data['template'] );
+		}
+	}
+}
+add_action( 'after_switch_theme', 'peptide_starter_create_pages' );