From 5fa273583fa8ce3f3e8a57bb572a791578ef5910 Mon Sep 17 00:00:00 2001
From: Gamosoft <gamosoft@users.noreply.github.com>
Date: Mon, 24 Nov 2025 10:04:20 +0100
Subject: [PATCH 1/4] performance improvements

---
 frontend/app.js     | 232 ++++++++++++++++++++++++++++----------------
 frontend/index.html |  41 ++++----
 2 files changed, 165 insertions(+), 108 deletions(-)

diff --git a/frontend/app.js b/frontend/app.js
index 7041c09..c4685eb 100644
--- a/frontend/app.js
+++ b/frontend/app.js
@@ -94,89 +94,112 @@ function noteApp() {
         // Dropdown state
         showNewDropdown: false,
         
-        // Homepage folder navigation
+        // Homepage state
         selectedHomepageFolder: '',
+        _homepageCache: {
+            folderPath: null,
+            notes: null,
+            folders: null,
+            breadcrumb: null
+        },
         
-        // Computed-like helpers for homepage (use methods for safer evaluation)
+        // Homepage constants
+        HOMEPAGE_MAX_NOTES: 50,
+        
+        // Computed-like helpers for homepage (cached for performance)
         homepageNotes() {
+            // Return cached result if folder hasn't changed
+            if (this._homepageCache.folderPath === this.selectedHomepageFolder && this._homepageCache.notes) {
+                return this._homepageCache.notes;
+            }
+            
             if (!this.folderTree || typeof this.folderTree !== 'object') {
                 return [];
             }
             
             const folderNode = this.getFolderNode(this.selectedHomepageFolder || '');
-            if (!folderNode || !Array.isArray(folderNode.notes)) {
-                return [];
-            }
+            const result = (folderNode && Array.isArray(folderNode.notes)) ? folderNode.notes : [];
             
-            return folderNode.notes;
-        },
-
-        // Helper: Format file size nicely
-        formatSize(bytes) {
-            if (bytes === 0 || !bytes) return '0 B';
-
-            const k = 1024;
-            const sizes = ['B', 'KB', 'MB', 'GB'];
-
-            const i = Math.floor(Math.log(bytes) / Math.log(k));
-
-            return parseFloat((bytes / Math.pow(k, i)).toFixed(1)) + ' ' + sizes[i];
+            // Cache the result
+            this._homepageCache.notes = result;
+            this._homepageCache.folderPath = this.selectedHomepageFolder;
+            
+            return result;
         },
         
         homepageFolders() {
+            // Return cached result if folder hasn't changed
+            if (this._homepageCache.folderPath === this.selectedHomepageFolder && this._homepageCache.folders) {
+                return this._homepageCache.folders;
+            }
+            
             if (!this.folderTree || typeof this.folderTree !== 'object') {
                 return [];
             }
             
+            // Get child folders
             let childFolders = [];
             if (!this.selectedHomepageFolder) {
+                // Root level: all top-level folders
                 childFolders = Object.entries(this.folderTree)
                     .filter(([key]) => key !== '__root__')
                     .map(([, folder]) => folder);
             } else {
+                // Inside a folder: get its children
                 const parentFolder = this.getFolderNode(this.selectedHomepageFolder);
-                if (!parentFolder || !parentFolder.children) {
-                    return [];
+                if (parentFolder && parentFolder.children) {
+                    childFolders = Object.values(parentFolder.children);
                 }
-                childFolders = Object.values(parentFolder.children);
             }
             
-            if (!Array.isArray(childFolders) || childFolders.length === 0) {
-                return [];
-            }
-            
-            return childFolders
+            // Map to simplified structure (note count already cached in folder node)
+            const result = childFolders
                 .map(folder => ({
                     name: folder.name,
                     path: folder.path,
-                    noteCount: this.calculateFolderNoteCount(folder)
+                    noteCount: folder.noteCount || 0  // Use pre-calculated count
                 }))
                 .sort((a, b) => a.name.toLowerCase().localeCompare(b.name.toLowerCase()));
+            
+            // Cache the result
+            this._homepageCache.folders = result;
+            this._homepageCache.folderPath = this.selectedHomepageFolder;
+            
+            return result;
         },
         
         homepageBreadcrumb() {
-            // Always return at least Home breadcrumb
-            // Safety check - ensure we always return an array
-            try {
-                const breadcrumb = [{ name: 'Home', path: '' }];
-                
-                if (!this.selectedHomepageFolder) {
-                    return breadcrumb;
-                }
-                
-                const parts = (this.selectedHomepageFolder || '').split('/').filter(part => part.trim() !== '');
-                
+            // Return cached result if folder hasn't changed
+            if (this._homepageCache.folderPath === this.selectedHomepageFolder && this._homepageCache.breadcrumb) {
+                return this._homepageCache.breadcrumb;
+            }
+            
+            const breadcrumb = [{ name: 'Home', path: '' }];
+            
+            if (this.selectedHomepageFolder) {
+                const parts = this.selectedHomepageFolder.split('/').filter(Boolean);
                 let currentPath = '';
+                
                 parts.forEach(part => {
-                    currentPath = currentPath ? currentPath + '/' + part : part;
+                    currentPath = currentPath ? `${currentPath}/${part}` : part;
                     breadcrumb.push({ name: part, path: currentPath });
                 });
-                
-                return breadcrumb;
-            } catch (error) {
-                // Fallback to just Home if anything goes wrong
-                return [{ name: 'Home', path: '' }];
             }
+            
+            // Cache the result
+            this._homepageCache.breadcrumb = breadcrumb;
+            this._homepageCache.folderPath = this.selectedHomepageFolder;
+            
+            return breadcrumb;
+        },
+        
+        // Helper: Format file size nicely
+        formatSize(bytes) {
+            if (!bytes) return '0 B';
+            const k = 1024;
+            const sizes = ['B', 'KB', 'MB', 'GB'];
+            const i = Math.floor(Math.log(bytes) / Math.log(k));
+            return parseFloat((bytes / Math.pow(k, i)).toFixed(1)) + ' ' + sizes[i];
         },
         
         getFolderNode(folderPath = '') {
@@ -185,10 +208,7 @@ function noteApp() {
             }
             
             if (!folderPath) {
-                if (this.folderTree['__root__']) {
-                    return this.folderTree['__root__'];
-                }
-                return { name: '', path: '', children: {}, notes: [] };
+                return this.folderTree['__root__'] || { name: '', path: '', children: {}, notes: [], noteCount: 0 };
             }
             
             const parts = folderPath.split('/').filter(Boolean);
@@ -206,22 +226,6 @@ function noteApp() {
             return node;
         },
         
-        calculateFolderNoteCount(folderNode) {
-            if (!folderNode || typeof folderNode !== 'object') {
-                return 0;
-            }
-            
-            const directNotes = Array.isArray(folderNode.notes) ? folderNode.notes.length : 0;
-            if (!folderNode.children || Object.keys(folderNode.children).length === 0) {
-                return directNotes;
-            }
-            
-            return Object.values(folderNode.children).reduce(
-                (total, child) => total + this.calculateFolderNoteCount(child),
-                directNotes
-            );
-        },
-        
         // Check if app is empty (no notes and no folders)
         get isAppEmpty() {
             const notesArray = Array.isArray(this.notes) ? this.notes : [];
@@ -291,6 +295,14 @@ function noteApp() {
                         this.selectedHomepageFolder = '';
                     }
                     
+                    // Invalidate cache to force recalculation
+                    this._homepageCache = {
+                        folderPath: null,
+                        notes: null,
+                        folders: null,
+                        breadcrumb: null
+                    };
+                    
                     // Clear search
                     this.searchQuery = '';
                     this.searchResults = [];
@@ -590,8 +602,41 @@ function noteApp() {
                 }
             });
             
-            // Force Alpine reactivity by creating a new object reference
-            this.folderTree = { ...tree };
+            // Calculate and cache note counts recursively (for performance)
+            const calculateNoteCounts = (folderNode) => {
+                const directNotes = folderNode.notes ? folderNode.notes.length : 0;
+                
+                if (!folderNode.children || Object.keys(folderNode.children).length === 0) {
+                    folderNode.noteCount = directNotes;
+                    return directNotes;
+                }
+                
+                const childNotesCount = Object.values(folderNode.children).reduce(
+                    (total, child) => total + calculateNoteCounts(child),
+                    0
+                );
+                
+                folderNode.noteCount = directNotes + childNotesCount;
+                return folderNode.noteCount;
+            };
+            
+            // Calculate note counts for all folders
+            Object.values(tree).forEach(folder => {
+                if (folder.path !== undefined || folder === tree['__root__']) {
+                    calculateNoteCounts(folder);
+                }
+            });
+            
+            // Invalidate homepage cache when tree is rebuilt
+            this._homepageCache = {
+                folderPath: null,
+                notes: null,
+                folders: null,
+                breadcrumb: null
+            };
+            
+            // Assign new tree (Alpine will detect the change)
+            this.folderTree = tree;
         },
         
         // Render folder recursively (helper for deep nesting)
@@ -756,8 +801,6 @@ function noteApp() {
             }
             // Force Alpine reactivity by creating new Set reference
             this.expandedFolders = new Set(this.expandedFolders);
-            // Also trigger folderTree reactivity to re-render x-html
-            this.folderTree = { ...this.folderTree };
         },
         
         // Check if folder is expanded
@@ -767,25 +810,22 @@ function noteApp() {
         
         // Expand all folders
         expandAllFolders() {
-            // Add all folder paths to expandedFolders
             this.allFolders.forEach(folder => {
                 this.expandedFolders.add(folder);
             });
-            // Force Alpine reactivity by creating new object reference (no rebuild needed)
-            this.folderTree = { ...this.folderTree };
+            // Force Alpine reactivity
+            this.expandedFolders = new Set(this.expandedFolders);
         },
         
         // Collapse all folders
         collapseAllFolders() {
             this.expandedFolders.clear();
-            // Force Alpine reactivity by creating new object reference (no rebuild needed)
-            this.folderTree = { ...this.folderTree };
+            // Force Alpine reactivity
+            this.expandedFolders = new Set(this.expandedFolders);
         },
         
         // Expand folder tree to show a specific note
         expandFolderForNote(notePath) {
-            // Extract folder path from note path
-            // e.g., "folder1/folder2/note.md" -> ["folder1", "folder1/folder2"]
             const parts = notePath.split('/');
             
             // If note is in root, no folders to expand
@@ -801,13 +841,8 @@ function noteApp() {
                 this.expandedFolders.add(currentPath);
             });
             
-            // Force Alpine reactivity by creating new object reference
-            // This ensures the UI updates to show the expanded folders
-            this.folderTree = { ...this.folderTree };
-            
-            // Also force a re-evaluation by modifying the Set (create new Set)
-            const oldFolders = this.expandedFolders;
-            this.expandedFolders = new Set(oldFolders);
+            // Force Alpine reactivity
+            this.expandedFolders = new Set(this.expandedFolders);
         },
         
         // Scroll note into view in the sidebar navigation
@@ -2955,12 +2990,37 @@ function noteApp() {
         
         // Homepage folder navigation methods
         goToHomepageFolder(folderPath) {
-            // Navigate to folder (empty string = root)
             this.selectedHomepageFolder = folderPath || '';
             
-            // Update browser history
-            const state = { homepageFolder: folderPath || '' };
-            window.history.pushState(state, '', '/');
+            // Invalidate cache to force recalculation
+            this._homepageCache = {
+                folderPath: null,
+                notes: null,
+                folders: null,
+                breadcrumb: null
+            };
+            
+            window.history.pushState({ homepageFolder: folderPath || '' }, '', '/');
+        },
+        
+        // Navigate to homepage root and clear all editor state
+        goHome() {
+            this.selectedHomepageFolder = '';
+            this.currentNote = '';
+            this.currentNoteName = '';
+            this.noteContent = '';
+            this.currentImage = '';
+            this.mobileSidebarOpen = false;
+            
+            // Invalidate cache to force recalculation
+            this._homepageCache = {
+                folderPath: null,
+                notes: null,
+                folders: null,
+                breadcrumb: null
+            };
+            
+            window.history.pushState({ homepageFolder: '' }, '', '/');
         }
     }
 }
diff --git a/frontend/index.html b/frontend/index.html
index 224c607..e923670 100644
--- a/frontend/index.html
+++ b/frontend/index.html
@@ -730,7 +730,7 @@
             <div class="p-4 border-b" style="border-color: var(--border-primary);">
                 <button 
                     class="flex items-center gap-2 mb-3 hover:opacity-80 transition"
-                    @click="goToHomepageFolder(''); currentNote = ''; currentImage = ''; currentNoteName = ''; noteContent = ''; mobileSidebarOpen = false"
+                    @click="goHome()"
                     aria-label="Go to homepage"
                     style="background: none; border: none; outline: none; cursor: pointer;"
                 >
@@ -858,7 +858,7 @@
                     style="background-color: var(--bg-secondary); border: 1px solid var(--border-primary);"
                 >
                     <div class="py-1">
-                        <button 
+                <button 
                             @click="createNote()"
                             class="w-full px-4 py-2.5 text-sm text-left flex items-center gap-3 transition-colors"
                             style="color: var(--text-primary);"
@@ -877,7 +877,7 @@
                         >
                             <span class="text-lg">📁</span>
                             <span>New Folder</span>
-                        </button>
+                </button>
                     </div>
                 </div>
             </div>
@@ -1019,21 +1019,21 @@
                     <!-- Welcome Hero - Show when app is empty -->
                     <template x-if="isAppEmpty">
                         <div class="flex flex-col items-center justify-center h-full py-16 text-center">
-                            <svg class="mx-auto h-16 w-16 mb-4" style="color: var(--text-tertiary);" fill="none" stroke="currentColor" viewBox="0 0 24 24">
-                                <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M9 12h6m-6 4h6m2 5H7a2 2 0 01-2-2V5a2 2 0 012-2h5.586a1 1 0 01.707.293l5.414 5.414a1 1 0 01.293.707V19a2 2 0 01-2 2z"></path>
-                            </svg>
+                        <svg class="mx-auto h-16 w-16 mb-4" style="color: var(--text-tertiary);" fill="none" stroke="currentColor" viewBox="0 0 24 24">
+                            <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M9 12h6m-6 4h6m2 5H7a2 2 0 01-2-2V5a2 2 0 012-2h5.586a1 1 0 01.707.293l5.414 5.414a1 1 0 01.293.707V19a2 2 0 01-2 2z"></path>
+                        </svg>
                             <h1 class="text-4xl font-bold mb-4" style="color: var(--text-primary);" x-text="appName"></h1>
                             <p class="text-xl mb-8" style="color: var(--text-secondary);" x-text="appTagline"></p>
-                            <button 
+                        <button 
                                 @click="createNote()"
                                 class="px-8 py-4 text-base font-medium text-white rounded-lg transition-colors"
-                                style="background-color: var(--accent-primary);"
-                                onmouseover="this.style.backgroundColor='var(--accent-hover)'"
-                                onmouseout="this.style.backgroundColor='var(--accent-primary)'"
-                            >
-                                Create Your First Note
-                            </button>
-                        </div>
+                            style="background-color: var(--accent-primary);"
+                            onmouseover="this.style.backgroundColor='var(--accent-hover)'"
+                            onmouseout="this.style.backgroundColor='var(--accent-primary)'"
+                        >
+                            Create Your First Note
+                        </button>
+                    </div>
                     </template>
                     
                     <!-- Grid View - Show when app has content -->
@@ -1061,8 +1061,8 @@
                                                 :style="crumb.path === selectedHomepageFolder ? 'color: var(--accent-primary); font-weight: 600;' : 'color: var(--text-secondary);'"
                                                 x-text="crumb.name"
                                             ></span>
-                                        </div>
-                                    </template>
+                </div>
+            </template>
                                 </template>
                             </div>
                             
@@ -1142,7 +1142,7 @@
                                     </template>
                                     
                                     <!-- Notes -->
-                                    <template x-for="note in homepageNotes().slice(0, 50)" :key="note.path">
+                                    <template x-for="note in homepageNotes().slice(0, HOMEPAGE_MAX_NOTES)" :key="note.path">
                                         <div 
                                             @click="note.path.match(/\.(png|jpg|jpeg|gif|webp)$/i) ? (currentImage = note.path, currentNote = '') : loadNote(note.path)"
                                             class="p-4 rounded-lg border-2 cursor-pointer transition-all hover:shadow-lg"
@@ -1164,12 +1164,9 @@
                             </template>
                             
                             <!-- Show More Indicator -->
-                            <div x-show="homepageNotes().length > 50" class="mt-6 text-center">
+                            <div x-show="homepageNotes().length > HOMEPAGE_MAX_NOTES" class="mt-6 text-center">
                                 <p class="text-sm" style="color: var(--text-secondary);">
-                                    Showing 50 of <span x-text="homepageNotes().length"></span> notes. 
-                                    <span class="cursor-pointer underline" style="color: var(--accent-primary);" @click="goToHomepageFolder('')">
-                                        View all in sidebar
-                                    </span>
+                                    Showing <span x-text="HOMEPAGE_MAX_NOTES"></span> of <span x-text="homepageNotes().length"></span> notes in this folder.
                                 </p>
                             </div>
                         </div>

From 5c192862041dd0558fce5b5dcc5de1d0b3cf15d5 Mon Sep 17 00:00:00 2001
From: Gamosoft <gamosoft@users.noreply.github.com>
Date: Mon, 24 Nov 2025 10:17:21 +0100
Subject: [PATCH 2/4] added basic formatting keyboard shortcuts

---
 documentation/FEATURES.md | 10 +++++
 frontend/app.js           | 84 +++++++++++++++++++++++++++++++++++++++
 frontend/index.html       |  1 +
 3 files changed, 95 insertions(+)

diff --git a/documentation/FEATURES.md b/documentation/FEATURES.md
index 994fe06..36d35f6 100644
--- a/documentation/FEATURES.md
+++ b/documentation/FEATURES.md
@@ -139,6 +139,8 @@ graph TD
 
 ## ⚡ Keyboard Shortcuts
 
+### General
+
 | Windows/Linux | Mac | Action |
 |---------------|-----|--------|
 | `Ctrl+S` | `Cmd+S` | Save note |
@@ -149,6 +151,14 @@ graph TD
 | `F3` | `F3` | Next search match |
 | `Shift+F3` | `Shift+F3` | Previous search match |
 
+### Markdown Formatting
+
+| Windows/Linux | Mac | Action | Result |
+|---------------|-----|--------|--------|
+| `Ctrl+B` | `Cmd+B` | Bold | `**text**` |
+| `Ctrl+I` | `Cmd+I` | Italic | `*text*` |
+| `Ctrl+K` | `Cmd+K` | Insert link | `[text](url)` |
+
 ## 🚀 Performance
 
 - **Instant loading** - No lag, no loading spinners
diff --git a/frontend/app.js b/frontend/app.js
index c4685eb..a8bfbcf 100644
--- a/frontend/app.js
+++ b/frontend/app.js
@@ -385,6 +385,28 @@ function noteApp() {
                         e.preventDefault();
                         this.previousMatch();
                     }
+                    
+                    // Only apply markdown shortcuts when editor is focused and a note is open
+                    const isEditorFocused = document.activeElement?.id === 'note-editor';
+                    if (isEditorFocused && this.currentNote) {
+                        // Ctrl/Cmd + B for bold
+                        if ((e.ctrlKey || e.metaKey) && e.key === 'b') {
+                            e.preventDefault();
+                            this.wrapSelection('**', '**', 'bold text');
+                        }
+                        
+                        // Ctrl/Cmd + I for italic
+                        if ((e.ctrlKey || e.metaKey) && e.key === 'i') {
+                            e.preventDefault();
+                            this.wrapSelection('*', '*', 'italic text');
+                        }
+                        
+                        // Ctrl/Cmd + K for link
+                        if ((e.ctrlKey || e.metaKey) && e.key === 'k') {
+                            e.preventDefault();
+                            this.insertLink();
+                        }
+                    }
                 });
             }
             
@@ -1967,6 +1989,68 @@ function noteApp() {
             });
         },
         
+        // Markdown formatting helpers
+        wrapSelection(before, after, placeholder) {
+            const editor = document.getElementById('note-editor');
+            if (!editor) return;
+            
+            const start = editor.selectionStart;
+            const end = editor.selectionEnd;
+            const selectedText = this.noteContent.substring(start, end);
+            const textToWrap = selectedText || placeholder;
+            
+            // Build the new text
+            const newText = before + textToWrap + after;
+            
+            // Update content
+            this.noteContent = this.noteContent.substring(0, start) + newText + this.noteContent.substring(end);
+            
+            // Set cursor position (select the wrapped text or placeholder)
+            this.$nextTick(() => {
+                if (selectedText) {
+                    // If text was selected, keep it selected (inside the wrapper)
+                    editor.setSelectionRange(start + before.length, start + before.length + selectedText.length);
+                } else {
+                    // If no text selected, select the placeholder
+                    editor.setSelectionRange(start + before.length, start + before.length + placeholder.length);
+                }
+                editor.focus();
+            });
+            
+            // Trigger autosave
+            this.autoSave();
+        },
+        
+        insertLink() {
+            const editor = document.getElementById('note-editor');
+            if (!editor) return;
+            
+            const start = editor.selectionStart;
+            const end = editor.selectionEnd;
+            const selectedText = this.noteContent.substring(start, end);
+            
+            // If text is selected, use it as link text; otherwise use placeholder
+            const linkText = selectedText || 'link text';
+            const linkUrl = 'url';
+            
+            // Build the markdown link
+            const newText = `[${linkText}](${linkUrl})`;
+            
+            // Update content
+            this.noteContent = this.noteContent.substring(0, start) + newText + this.noteContent.substring(end);
+            
+            // Set cursor position to select the URL part for easy editing
+            this.$nextTick(() => {
+                const urlStart = start + linkText.length + 3; // After "[linkText]("
+                const urlEnd = urlStart + linkUrl.length;
+                editor.setSelectionRange(urlStart, urlEnd);
+                editor.focus();
+            });
+            
+            // Trigger autosave
+            this.autoSave();
+        },
+        
         // Save current note
         async saveNote() {
             if (!this.currentNote) return;
diff --git a/frontend/index.html b/frontend/index.html
index e923670..204260a 100644
--- a/frontend/index.html
+++ b/frontend/index.html
@@ -1298,6 +1298,7 @@
                             :style="viewMode === 'split' ? `width: ${editorWidth}%;` : 'width: 100%;'"
                         >
                             <textarea 
+                                id="note-editor"
                                 x-model="noteContent"
                                 @input="autoSave()"
                                 @drop="onEditorDrop($event)"

From d14028e7275e37aa86fe1e74aed0f3d2ea047c57 Mon Sep 17 00:00:00 2001
From: Gamosoft <gamosoft@users.noreply.github.com>
Date: Mon, 24 Nov 2025 11:46:40 +0100
Subject: [PATCH 3/4] added link to website

---
 README.md           |  2 ++
 frontend/index.html | 11 +++++++++++
 2 files changed, 13 insertions(+)

diff --git a/README.md b/README.md
index 8c33fae..b3a3e0e 100644
--- a/README.md
+++ b/README.md
@@ -2,6 +2,8 @@
 
 > Your Self-Hosted Knowledge Base
 
+🌐 **[Visit the official website](https://www.notediscovery.com)**
+
 ## What is NoteDiscovery?
 
 NoteDiscovery is a **lightweight, self-hosted 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.
diff --git a/frontend/index.html b/frontend/index.html
index 204260a..0db64b9 100644
--- a/frontend/index.html
+++ b/frontend/index.html
@@ -997,6 +997,17 @@
                     <span x-text="notes.length"></span> notes
                     <span class="mx-1">·</span>
                     <span x-text="'v' + appVersion"></span>
+                    <span class="mx-1">·</span>
+                    <a 
+                        href="https://www.notediscovery.com" 
+                        target="_blank" 
+                        rel="noopener noreferrer"
+                        class="hover:underline"
+                        style="color: var(--accent-primary);"
+                        title="Visit NoteDiscovery website"
+                    >
+                        Website
+                    </a>                    
                 </div>
             </div>
         </div>

From 806ccf24cff08989e47436f29bd4e5d0cf6fbf9b Mon Sep 17 00:00:00 2001
From: Gamosoft <gamosoft@users.noreply.github.com>
Date: Mon, 24 Nov 2025 14:12:45 +0100
Subject: [PATCH 4/4] removed wikilinks (for now)

---
 backend/main.py                         | 35 +++++++++----------------
 backend/utils.py                        |  7 -----
 docs/index.html                         |  6 ++---
 documentation/FEATURES.md               |  2 +-
 documentation/PLUGIN_NOTE_STATISTICS.md |  4 +--
 frontend/app.js                         |  7 +----
 6 files changed, 19 insertions(+), 42 deletions(-)

diff --git a/backend/main.py b/backend/main.py
index 4b0e2c1..35a99e4 100644
--- a/backend/main.py
+++ b/backend/main.py
@@ -23,7 +23,6 @@ from .utils import (
     save_note,
     delete_note,
     search_notes,
-    parse_wiki_links,
     create_note_metadata,
     ensure_directories,
     create_folder,
@@ -336,8 +335,8 @@ async def api_documentation():
             {
                 "method": "GET",
                 "path": "/api/graph",
-                "description": "Get graph data for note visualization (wiki links)",
-                "response": "{ nodes: [{ id, label }], edges: [{ from, to }] }"
+                "description": "Get graph data for note visualization",
+                "response": "{ nodes: [{ id, label }], edges: [] }"
             },
             {
                 "method": "GET",
@@ -651,13 +650,9 @@ async def get_note(note_path: str):
         if transformed_content is not None:
             content = transformed_content
         
-        # Parse wiki links
-        links = parse_wiki_links(content)
-        
         return {
             "path": note_path,
             "content": content,
-            "links": links,
             "metadata": create_note_metadata(config['storage']['notes_dir'], note_path)
         }
     except HTTPException:
@@ -745,28 +740,22 @@ async def search(q: str):
 
 @api_router.get("/graph")
 async def get_graph():
-    """Get graph data for visualization"""
+    """Get graph data for note visualization (currently only returns nodes, link detection not implemented)"""
     try:
         notes = get_all_notes(config['storage']['notes_dir'])
         nodes = []
         edges = []
         
-        # Build graph structure
+        # Build graph structure - only nodes for now
         for note in notes:
-            nodes.append({
-                "id": note['path'],
-                "label": note['name']
-            })
-            
-            # Get links from this note
-            content = get_note_content(config['storage']['notes_dir'], note['path'])
-            if content:
-                links = parse_wiki_links(content)
-                for link in links:
-                    edges.append({
-                        "from": note['path'],
-                        "to": link
-                    })
+            if note.get('type') == 'note':  # Only include actual notes
+                nodes.append({
+                    "id": note['path'],
+                    "label": note['name']
+                })
+        
+        # Note: Link detection between notes could be implemented here using markdown link parsing
+        # For now, returning empty edges
         
         return {"nodes": nodes, "edges": edges}
     except Exception as e:
diff --git a/backend/utils.py b/backend/utils.py
index e953e93..365cf53 100644
--- a/backend/utils.py
+++ b/backend/utils.py
@@ -236,13 +236,6 @@ def delete_note(notes_dir: str, note_path: str) -> bool:
     return True
 
 
-def parse_wiki_links(content: str) -> List[str]:
-    """Extract wiki-style links [[link]] from markdown content"""
-    pattern = r'\[\[([^\]]+)\]\]'
-    matches = re.findall(pattern, content)
-    return matches
-
-
 def search_notes(notes_dir: str, query: str) -> List[Dict]:
     """Simple full-text search through all notes"""
     results = []
diff --git a/docs/index.html b/docs/index.html
index 2527a08..e9f3244 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -641,8 +641,8 @@
                 <div class="benefit-item">
                     <span class="emoji">🔗</span>
                     <div class="text">
-                        <strong>Wiki Links</strong>
-                        Connect notes with internal links
+                        <strong>Internal Links</strong>
+                        Connect notes with markdown links
                     </div>
                 </div>
 
@@ -725,7 +725,7 @@
       "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",
+      "featureList": "Markdown editor, LaTeX math equations, Mermaid diagrams, Code syntax highlighting, Dark mode, Plugin system, Internal links, HTML export, Full-text search, Self-hosted, Obsidian, Evernote, Notion, Onenote, Second brain",
       "offers": {
         "@type": "Offer",
         "price": "0",
diff --git a/documentation/FEATURES.md b/documentation/FEATURES.md
index 36d35f6..be629fa 100644
--- a/documentation/FEATURES.md
+++ b/documentation/FEATURES.md
@@ -28,7 +28,7 @@
 ## 🔗 Linking & Discovery
 
 ### Internal Links
-- **Wiki-style links** - `[[Note Name]]` syntax
+- **Markdown links** - `[Note Name](note.md)` syntax
 - **Drag to link** - Drag notes or images into the editor to insert links
 - **Click to navigate** - Jump between notes seamlessly
 - **External links** - Open in new tabs automatically
diff --git a/documentation/PLUGIN_NOTE_STATISTICS.md b/documentation/PLUGIN_NOTE_STATISTICS.md
index 1633012..2494dc5 100644
--- a/documentation/PLUGIN_NOTE_STATISTICS.md
+++ b/documentation/PLUGIN_NOTE_STATISTICS.md
@@ -55,7 +55,7 @@ curl -X POST http://localhost:8000/api/plugins/note_stats/toggle \
 
 ### 🔗 Links & References
 - **Total Links** - All `[text](url)` links
-- **Internal Links** - `[[WikiLinks]]` to other notes
+- **Internal Links** - Links to other notes (`.md` files)
 - **External Links** - HTTP/HTTPS URLs
 - **Images** - `![alt](image.png)` count
 
@@ -191,7 +191,7 @@ Find orphaned notes or track reference density.
 
 **Words:** Split on whitespace, excluding code blocks  
 **Reading Time:** `words / 200 minutes`  
-**Links:** Regex match `[text](url)` and `[[WikiLink]]`  
+**Links:** Regex match `[text](url)` markdown links  
 **Tasks:** Match `- [ ]` and `- [x]`  
 **Code Blocks:** Match ` ```language ` ` fences  
 **Headings:** Match `#`, `##`, `###` at line start  
diff --git a/frontend/app.js b/frontend/app.js
index a8bfbcf..56d0a22 100644
--- a/frontend/app.js
+++ b/frontend/app.js
@@ -2321,13 +2321,8 @@ function noteApp() {
                 }
             });
             
-            // Convert wiki-style links [[link]] to HTML links
-            let content = this.noteContent.replace(/\[\[([^\]]+)\]\]/g, (match, linkText) => {
-                return `<a href="#" style="color: var(--accent-primary);" onclick="return false;">[[${linkText}]]</a>`;
-            });
-            
             // Parse markdown
-            let html = marked.parse(content);
+            let html = marked.parse(this.noteContent);
             
             // Post-process: Add target="_blank" to external links and title attributes to images
             // Parse as DOM to safely manipulate