diff --git a/backend/utils.py b/backend/utils.py
index 93e9e38..9020cbd 100644
--- a/backend/utils.py
+++ b/backend/utils.py
@@ -225,11 +225,7 @@ def delete_note(notes_dir: str, note_path: str) -> bool:
     
     full_path.unlink()
     
-    # Remove empty parent directories
-    try:
-        full_path.parent.rmdir()
-    except OSError:
-        pass  # Directory not empty, that's fine
+    # Note: We don't automatically delete empty folders to preserve user's folder structure
     
     return True
 
diff --git a/docs/index.html b/docs/index.html
index 31fb37d..2527a08 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -7,8 +7,8 @@
     <!-- Primary Meta Tags -->
     <title>NoteDiscovery - Your Self-Hosted Knowledge Base</title>
     <meta name="title" content="NoteDiscovery - Your Self-Hosted Knowledge Base">
-    <meta name="description" content="A lightweight, privacy-focused note-taking application. Self-hosted, free, and open source. Write, organize, and discover your notes with markdown support.">
-    <meta name="keywords" content="note taking, markdown editor, self-hosted, knowledge base, open source, privacy, notes app, docker, second brain, obsidian alternative">
+    <meta name="description" content="A lightweight, privacy-focused Markdown note-taking application with LaTeX math, Mermaid diagrams, and code highlighting. Self-hosted, free, and open source.">
+    <meta name="keywords" content="note taking, markdown editor, self-hosted, knowledge base, open source, privacy, notes app, docker, second brain, obsidian alternative, notion, evernote, onenote, latex, mermaid, diagrams, math equations">
     <meta name="author" content="Gamosoft">
     <meta name="robots" content="index, follow">
     <link rel="canonical" href="https://www.notediscovery.com">
@@ -17,7 +17,7 @@
     <meta property="og:type" content="website">
     <meta property="og:url" content="https://www.notediscovery.com">
     <meta property="og:title" content="NoteDiscovery - Your Self-Hosted Knowledge Base">
-    <meta property="og:description" content="A lightweight, privacy-focused note-taking application. Self-hosted, free, and open source.">
+    <meta property="og:description" content="A lightweight, privacy-focused Markdown note-taking application with LaTeX math, Mermaid diagrams, and code highlighting. Self-hosted, free, and open source.">
     <meta property="og:image" content="https://www.notediscovery.com/og-image.png">
     <meta property="og:image:width" content="1200">
     <meta property="og:image:height" content="630">
@@ -28,7 +28,7 @@
     <meta name="twitter:site" content="@gamosoft">
     <meta name="twitter:creator" content="@gamosoft">
     <meta name="twitter:title" content="NoteDiscovery - Your Self-Hosted Knowledge Base">
-    <meta name="twitter:description" content="A lightweight, privacy-focused note-taking application. Self-hosted, free, and open source.">
+    <meta name="twitter:description" content="A lightweight, privacy-focused note-taking application with LaTeX math, Mermaid diagrams, and code highlighting. Self-hosted, free, and open source.">
     <meta name="twitter:image" content="https://www.notediscovery.com/og-image.png">
     <meta name="twitter:image:alt" content="NoteDiscovery - Self-hosted note-taking application interface">
     
@@ -509,7 +509,7 @@ <h1>NoteDiscovery</h1>
         <div class="hero">
             <div class="hero-content">
                 <h2>Take Control of Your Notes</h2>
-                <p>A lightweight, privacy-focused note-taking application that puts you in complete control of your knowledge base. Write, organize, and discover your notes with a beautiful, modern interface—all running on your own server.</p>
+                <p>A lightweight, privacy-focused note-taking application with powerful features: LaTeX math equations, Mermaid diagrams, code highlighting, and more. Write, organize, and discover your notes with a beautiful, modern interface—all running on your own server.</p>
                 <a href="https://github.com/gamosoft/NoteDiscovery" class="cta-button">Get Started on GitHub →</a>
             </div>
         </div>
@@ -550,6 +550,24 @@ <h3>Lightning Fast</h3>
                 <p>Instant search and navigation. Works offline, always responsive.</p>
             </div>
 
+            <div class="feature">
+                <div class="feature-icon">🧮</div>
+                <h3>LaTeX Math</h3>
+                <p>Beautiful equation rendering with MathJax. Perfect for scientific notes.</p>
+            </div>
+
+            <div class="feature">
+                <div class="feature-icon">📊</div>
+                <h3>Diagrams</h3>
+                <p>Create flowcharts, mind maps, and diagrams with Mermaid syntax.</p>
+            </div>
+
+            <div class="feature">
+                <div class="feature-icon">💻</div>
+                <h3>Code Highlighting</h3>
+                <p>Syntax highlighting for popular coding languages. Developer-friendly notes.</p>
+            </div>
+
             <div class="feature">
                 <div class="feature-icon">📂</div>
                 <h3>Simple Storage</h3>
@@ -559,7 +577,7 @@ <h3>Simple Storage</h3>
             <div class="feature">
                 <div class="feature-icon">🎨</div>
                 <h3>Beautiful Themes</h3>
-                <p>Multiple built-in themes with full customization support.</p>
+                <p>8 built-in themes with dark/light modes and full customization.</p>
             </div>
 
             <div class="feature">
@@ -619,6 +637,38 @@ <h2>Why Choose NoteDiscovery?</h2>
                         You own your data
                     </div>
                 </div>
+
+                <div class="benefit-item">
+                    <span class="emoji">🔗</span>
+                    <div class="text">
+                        <strong>Wiki Links</strong>
+                        Connect notes with internal links
+                    </div>
+                </div>
+
+                <div class="benefit-item">
+                    <span class="emoji">📄</span>
+                    <div class="text">
+                        <strong>HTML Export</strong>
+                        Share standalone HTML files
+                    </div>
+                </div>
+
+                <div class="benefit-item">
+                    <span class="emoji">⌨️</span>
+                    <div class="text">
+                        <strong>Keyboard Shortcuts</strong>
+                        Navigate and create with speed
+                    </div>
+                </div>
+
+                <div class="benefit-item">
+                    <span class="emoji">🔐</span>
+                    <div class="text">
+                        <strong>Optional Auth</strong>
+                        Password protection when needed
+                    </div>
+                </div>
             </div>
         </div>
 
@@ -671,10 +721,11 @@ <h2>Ready to Get Started?</h2>
       "@context": "https://schema.org",
       "@type": "SoftwareApplication",
       "name": "NoteDiscovery",
-      "description": "A lightweight, privacy-focused note-taking application. Self-hosted, free, and open source.",
+      "description": "A lightweight, Obsidian and Evernote alternative, privacy-focused Markdown note-taking application with LaTeX math, Mermaid diagrams, and code highlighting. Self-hosted, free, and open source.",
       "url": "https://www.notediscovery.com",
       "applicationCategory": "ProductivityApplication",
       "operatingSystem": "Linux, Windows, macOS",
+      "featureList": "Markdown editor, LaTeX math equations, Mermaid diagrams, Code syntax highlighting, Dark mode, Plugin system, Internal wiki links, HTML export, Full-text search, Self-hosted, Obsidian, Evernote, Notion, Onenote, Second brain",
       "offers": {
         "@type": "Offer",
         "price": "0",
diff --git a/frontend/app.js b/frontend/app.js
index 0e6bb7a..849b33f 100644
--- a/frontend/app.js
+++ b/frontend/app.js
@@ -734,8 +734,9 @@ function noteApp() {
             const notePath = this.draggedNoteForLink;
             const noteName = notePath.split('/').pop().replace('.md', '');
             
-            // Create markdown link
-            const link = `[${noteName}](${notePath})`;
+            // Create markdown link (URL-encode the path to handle spaces and special characters)
+            const encodedPath = notePath.split('/').map(segment => encodeURIComponent(segment)).join('/');
+            const link = `[${noteName}](${encodedPath})`;
             
             // Insert at cursor position
             const textarea = event.target;
@@ -775,7 +776,8 @@ function noteApp() {
             event.preventDefault();
             
             // Remove any anchor from the href (e.g., "note.md#section" -> "note.md")
-            const notePath = href.split('#')[0];
+            // Also decode URL encoding (e.g., "note%203.md" -> "note 3.md")
+            const notePath = decodeURIComponent(href.split('#')[0]);
             
             // Skip if it's just an anchor link
             if (!notePath) return;
@@ -2424,11 +2426,11 @@ function noteApp() {
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
     <title>${noteName}</title>
     
-    <!-- Highlight.js for code syntax highlighting -->
+    <!-- Highlight.js for code syntax highlighting (v11.9.0) -->
     ${highlightTheme ? `<link rel="stylesheet" href="${highlightTheme}">` : '<!-- No highlight.js theme detected -->'}
     <script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.9.0/highlight.min.js"></script>
     
-    <!-- MathJax for LaTeX math rendering (same config as preview) -->
+    <!-- MathJax for LaTeX math rendering (v3.2.2) -->
     <script>
         MathJax = {
             tex: {
@@ -2452,11 +2454,11 @@ function noteApp() {
             }
         };
     </script>
-    <script src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
+    <script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js"></script>
     
-    <!-- Mermaid.js for diagrams (if used in note) -->
+    <!-- Mermaid.js for diagrams (v10.9.0) -->
     <script type="module">
-        import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@10/dist/mermaid.esm.min.mjs';
+        import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@10.9.0/dist/mermaid.esm.min.mjs';
         const isDark = ${this.getThemeType() === 'dark'};
         mermaid.initialize({ 
             startOnLoad: false,
diff --git a/frontend/index.html b/frontend/index.html
index f01b5b9..f52dce6 100644
--- a/frontend/index.html
+++ b/frontend/index.html
@@ -11,14 +11,14 @@
     <link rel="icon" type="image/png" sizes="16x16" href="/static/favicon.svg">
     <link rel="apple-touch-icon" href="/static/logo.svg">
     
-    <!-- Tailwind CSS from CDN -->
-    <script src="https://cdn.tailwindcss.com"></script>
+    <!-- Tailwind CSS from CDN (v3.4.17) -->
+    <script src="https://cdn.tailwindcss.com/3.4.17"></script>
     
-    <!-- Alpine.js -->
-    <script defer src="https://cdn.jsdelivr.net/npm/alpinejs@3.x.x/dist/cdn.min.js"></script>
+    <!-- Alpine.js (v3.14.1) -->
+    <script defer src="https://cdn.jsdelivr.net/npm/alpinejs@3.14.1/dist/cdn.min.js"></script>
     
-    <!-- Marked.js for Markdown parsing -->
-    <script src="https://cdn.jsdelivr.net/npm/marked/marked.min.js"></script>
+    <!-- Marked.js for Markdown parsing (v12.0.2) -->
+    <script src="https://cdn.jsdelivr.net/npm/marked@12.0.2/marked.min.js"></script>
     
     <!-- MathJax for LaTeX math rendering -->
     <script>
@@ -39,9 +39,9 @@
             }
         };
     </script>
-    <script src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
+    <script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js"></script>
     
-    <!-- Highlight.js for code syntax highlighting -->
+    <!-- Highlight.js for code syntax highlighting (v11.9.0) -->
     <link rel="stylesheet" id="highlight-theme" href="">
     <script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.9.0/highlight.min.js"></script>
     <script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.9.0/languages/csharp.min.js"></script>
@@ -57,9 +57,9 @@
     <script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.9.0/languages/css.min.js"></script>
     <script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.9.0/languages/http.min.js"></script>
     
-    <!-- Mermaid.js for diagram rendering -->
+    <!-- Mermaid.js for diagram rendering (v10.9.0) -->
     <script type="module">
-        import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@10/dist/mermaid.esm.min.mjs';
+        import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@10.9.0/dist/mermaid.esm.min.mjs';
         // Note: Mermaid is initialized dynamically by app.js renderMermaid() based on current theme
         window.mermaid = mermaid;
     </script>