From d2560461c7402a1eb9c27ba21c912b371f7e1dfe Mon Sep 17 00:00:00 2001
From: Jiahao Cheng <chengjiahao1234@live.com>
Date: Fri, 6 Feb 2026 23:03:46 -0500
Subject: [PATCH 1/3] fix: allow Projects dropdown to overlap content and
 collapse navbar height on moblie

---
 DEVELOPMENT.md        |  4 ++--
 _includes/header.html |  8 ++++----
 css/main.scss         | 30 +++++++++++++++++++++++++++---
 js/theme-toggle.js    | 14 ++++----------
 4 files changed, 37 insertions(+), 19 deletions(-)

diff --git a/DEVELOPMENT.md b/DEVELOPMENT.md
index 0f387ca..de65925 100644
--- a/DEVELOPMENT.md
+++ b/DEVELOPMENT.md
@@ -564,9 +564,9 @@ front matter...
    - **Impact:** Site-wide - all generated URLs depend on this
    - **Priority:** 🔴 CRITICAL
 
-2. **`robots.txt`** (line 76)
+2. **`robots.txt`** (line 1)
    ```
-   Sitemap: https://atlasanalyticslab.github.io/sitemap.xml
+   Sitemap: {{ site.url }}{{ site.baseurl }}/sitemap.xml
    ```
    - **Purpose:** Tells search engines where to find the sitemap
    - **Impact:** SEO - affects how search engines crawl the site
diff --git a/_includes/header.html b/_includes/header.html
index b0d7b11..ce85150 100644
--- a/_includes/header.html
+++ b/_includes/header.html
@@ -39,13 +39,13 @@
         <li class="nav-item"><a class="nav-link" href="{{ site.url }}{{ site.baseurl }}/openings">Openings</a></li>
         <li class="nav-item"><a class="nav-link" href="{{ site.url }}{{ site.baseurl }}/publications/">Publications</a></li>
         <li class="nav-item dropdown">
-          <a class="nav-link dropdown-toggle dropdown-toggle-no-caret" href="#" id="projectsDropdown" role="button"
-             data-bs-toggle="dropdown" aria-expanded="false">
+          <button class="nav-link projects-dropdown-toggle" id="projectsDropdown" type="button"
+                  data-bs-toggle="dropdown" aria-expanded="false">
             Projects
-          </a>
+          </button>
           <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="projectsDropdown">
             <li>
-              <a class="dropdown-item" href="https://atlasanalyticslab.github.io/AtlasPatch/" target="_blank"
+              <a class="dropdown-item project-link-atlaspatch" href="https://atlasanalyticslab.github.io/AtlasPatch/" target="_blank"
                  rel="noopener noreferrer">
                 AtlasPatch
               </a>
diff --git a/css/main.scss b/css/main.scss
index f0baa5b..d3e9ae6 100644
--- a/css/main.scss
+++ b/css/main.scss
@@ -100,7 +100,6 @@ p.byline {
   background-color: var(--atlas-navbar-bg);
   backdrop-filter: blur(12px);
   border-bottom: 1px solid var(--atlas-border-color);
-  min-height: var(--atlas-nav-height);
   transition: background-color 0.3s ease, border-color 0.3s ease;
 }
 
@@ -125,8 +124,33 @@ p.byline {
   color: var(--atlas-link-color);
 }
 
-.navbar .dropdown-toggle-no-caret::after {
-  display: none;
+.navbar,
+.navbar .container-fluid,
+.navbar .navbar-collapse,
+.navbar .navbar-nav,
+.navbar .dropdown {
+  overflow: visible;
+}
+
+.navbar .projects-dropdown-toggle {
+  background: transparent;
+  border: 0;
+  padding: var(--bs-nav-link-padding-y) var(--bs-nav-link-padding-x);
+}
+
+.navbar .dropdown-menu {
+  z-index: 2000;
+}
+
+.navbar .dropdown-item.project-link-atlaspatch {
+  font-family: system-ui, -apple-system, BlinkMacSystemFont, sans-serif;
+  font-weight: 700;
+  color: #5b5bff;
+}
+
+.navbar .dropdown-item.project-link-atlaspatch:hover,
+.navbar .dropdown-item.project-link-atlaspatch:focus {
+  color: #5b5bff;
 }
 
 .navbar .navbar-toggler {
diff --git a/js/theme-toggle.js b/js/theme-toggle.js
index 90de782..7fea265 100644
--- a/js/theme-toggle.js
+++ b/js/theme-toggle.js
@@ -40,20 +40,14 @@
     }
 
     const measuredHeight = Math.round(navbar.getBoundingClientRect().height);
-    const collapseExpanded = navCollapse && navCollapse.classList.contains('show');
-    // Treat the collapse as expanded while Bootstrap is mid-transition to avoid measuring intermediate heights.
-    const isTransitioning = navCollapse && navCollapse.classList.contains('collapsing');
-    const treatAsExpanded = collapseExpanded || isTransitioning;
+    const collapseVisible =
+      navCollapse && (navCollapse.classList.contains('show') || navCollapse.classList.contains('collapsing'));
 
-    if (options.forceBase && !treatAsExpanded && measuredHeight > 0) {
-      baseNavHeight = measuredHeight;
-    } else if (treatAsExpanded && baseNavHeight === null && measuredHeight > 0) {
+    if ((options.forceBase || !collapseVisible) && measuredHeight > 0) {
       baseNavHeight = measuredHeight;
     }
 
-    const targetHeight = treatAsExpanded
-      ? Math.max(measuredHeight, baseNavHeight || measuredHeight)
-      : baseNavHeight || measuredHeight;
+    const targetHeight = baseNavHeight || measuredHeight;
 
     if (targetHeight > 0) {
       html.style.setProperty('--atlas-nav-height', `${targetHeight}px`);

From 2df51a41f6d412fcb7d39ee252574ed30a5ac4f2 Mon Sep 17 00:00:00 2001
From: Jiahao Cheng <chengjiahao1234@live.com>
Date: Fri, 6 Feb 2026 23:04:15 -0500
Subject: [PATCH 2/3] chore: add wdm to avoid Jekyll polling on Windows

---
 Gemfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Gemfile b/Gemfile
index 8765621..345c2d1 100644
--- a/Gemfile
+++ b/Gemfile
@@ -30,3 +30,4 @@ gem "jekyll", "4.4.1"
 
 gem "jekyll-scholar", group: :jekyll_plugins
 gem "webrick", "~> 1.9"
+gem "wdm", ">= 0.1.0" if Gem.win_platform?

From 72f54a909393947e43cc319aa88d07f4f067bea6 Mon Sep 17 00:00:00 2001
From: Jiahao Cheng <chengjiahao1234@live.com>
Date: Fri, 6 Feb 2026 23:05:18 -0500
Subject: [PATCH 3/3] feat: add a real sitemap and brought robots.txt in sync

---
 robots.txt  | 11 ++++++++---
 sitemap.xml | 28 ++++++++++++++++++++++++++++
 2 files changed, 36 insertions(+), 3 deletions(-)
 create mode 100644 sitemap.xml

diff --git a/robots.txt b/robots.txt
index d9a8651..ee3c1e8 100644
--- a/robots.txt
+++ b/robots.txt
@@ -1,3 +1,7 @@
+---
+layout: null
+permalink: /robots.txt
+---
 # robots.txt - Crawler Access Control
 #
 # Purpose:
@@ -60,17 +64,18 @@ Crawl-delay: 10
 Disallow: /images/
 Disallow: /assets/
 Disallow: /_site/
-Disallow: /css/
-Disallow: /js/
 
 # Allow access to main pages
 Allow: /$
+Allow: /allnews
+Allow: /allnews.html
 Allow: /team
 Allow: /publications
 Allow: /contact
 Allow: /funding
 Allow: /gallery
 Allow: /openings
+Allow: /sitemap.xml
 
 # Sitemap location (helps good crawlers index efficiently)
-Sitemap: https://atlasanalyticslab.github.io/sitemap.xml
+Sitemap: {{ site.url }}{{ site.baseurl }}/sitemap.xml
diff --git a/sitemap.xml b/sitemap.xml
new file mode 100644
index 0000000..84a0624
--- /dev/null
+++ b/sitemap.xml
@@ -0,0 +1,28 @@
+---
+layout: null
+permalink: /sitemap.xml
+---
+<?xml version="1.0" encoding="UTF-8"?>
+<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
+  {% for page in site.pages %}
+    {% if page.url == nil %}
+      {% continue %}
+    {% endif %}
+
+    {% if page.exclude_from_sitemap == true %}
+      {% continue %}
+    {% endif %}
+
+    {% if page.url == "/404.html" or page.url == "/sitemap.xml" or page.url == "/robots.txt" %}
+      {% continue %}
+    {% endif %}
+
+    {% if page.url contains ".css" or page.url contains ".js" or page.url contains ".xml" or page.url contains ".txt" %}
+      {% continue %}
+    {% endif %}
+
+    <url>
+      <loc>{{ site.url }}{{ site.baseurl }}{{ page.url | replace: "index.html", "" }}</loc>
+    </url>
+  {% endfor %}
+</urlset>