Merge pull request #64 from gamosoft/features/graph

Features/graph

README.md

@@ -43,6 +43,7 @@ NoteDiscovery is a **lightweight, self-hosted note-taking application** that put
 - 📂 **Simple Storage** - Plain markdown files in folders
 - 🧮 **Math Support** - LaTeX/MathJax for beautiful equations
 - 📄 **HTML Export** - Share notes as standalone HTML files
+- 🕸️ **Graph View** - Interactive visualization of connected notes
 
 ## 🚀 Quick Start
 

backend/main.py

@@ -1006,9 +1006,10 @@ async def search(q: str):
 
 @api_router.get("/graph")
 async def get_graph():
-    """Get graph data for note visualization with wikilink detection"""
+    """Get graph data for note visualization with wikilink and markdown link detection"""
     try:
         import re
+        import urllib.parse
         notes = get_all_notes(config['storage']['notes_dir'])
         nodes = []
         edges = []
@@ -1044,8 +1045,9 @@ async def get_graph():
                     # Find wikilinks: [[target]] or [[target|display]]
                     wikilinks = re.findall(r'\[\[([^\]|]+)(?:\|[^\]]+)?\]\]', content)
                     
-                    # Find standard markdown internal links: [text](path.md)
+                    # Find standard markdown internal links: [text](path) - any local path (not http/https)
-                    markdown_links = re.findall(r'\[([^\]]+)\]\(([^\)]+\.md)\)', content)
+                    # Match links that don't start with http://, https://, mailto:, #, etc.
+                    markdown_links = re.findall(r'\[([^\]]+)\]\((?!https?://|mailto:|#|data:)([^\)]+)\)', content)
                     
                     # Process wikilinks
                     for target in wikilinks:
@@ -1079,12 +1081,50 @@ async def get_graph():
                     
                     # Process markdown links
                     for _, link_path in markdown_links:
-                        # Try exact match first, then case-insensitive
+                        # Skip anchor-only links and external protocols
+                        if not link_path or link_path.startswith('#'):
+                            continue
+                            
+                        # Remove anchor part if present (e.g., "note.md#section" -> "note.md")
+                        link_path = link_path.split('#')[0]
+                        if not link_path:
+                            continue
+                        
+                        # Normalize path: remove ./ prefix, handle URL encoding
+                        link_path = urllib.parse.unquote(link_path)
+                        if link_path.startswith('./'):
+                            link_path = link_path[2:]
+                        
+                        # Add .md extension if not present and doesn't have other extension
+                        link_path_with_md = link_path if link_path.endswith('.md') else link_path + '.md'
+                        link_path_lower = link_path.lower()
+                        link_path_with_md_lower = link_path_with_md.lower()
+                        
+                        # Try to match target to an existing note
                         target_path = None
+                        
+                        # 1. Exact path match (with or without .md)
                         if link_path in note_paths:
-                            target_path = link_path
+                            target_path = link_path if link_path.endswith('.md') else link_path + '.md'
-                        elif link_path.lower() in note_paths_lower:
+                        elif link_path_with_md in note_paths:
-                            target_path = note_paths_lower[link_path.lower()]
+                            target_path = link_path_with_md
+                        # 2. Case-insensitive path match
+                        elif link_path_lower in note_paths_lower:
+                            target_path = note_paths_lower[link_path_lower]
+                        elif link_path_with_md_lower in note_paths_lower:
+                            target_path = note_paths_lower[link_path_with_md_lower]
+                        # 3. Try matching by filename only (for relative links)
+                        else:
+                            # Extract just the filename
+                            filename = link_path.split('/')[-1]
+                            filename_lower = filename.lower()
+                            filename_with_md = filename if filename.endswith('.md') else filename + '.md'
+                            filename_with_md_lower = filename_with_md.lower()
+                            
+                            if filename_lower in note_names:
+                                target_path = note_names[filename_lower]
+                            elif filename_with_md_lower in note_names:
+                                target_path = note_names[filename_with_md_lower]
                         
                         if target_path and target_path != note['path']:
                             edges.append({

backend/utils.py

@@ -273,8 +273,9 @@ def search_notes(notes_dir: str, query: str) -> List[Dict]:
     """
     Full-text search through note contents only.
     Does NOT search in file names, folder names, or paths - only note content.
-    Uses character-based context extraction for better snippet quality.
+    Uses character-based context extraction with highlighted matches.
     """
+    from html import escape
     results = []
     notes_path = Path(notes_dir)
     
@@ -292,16 +293,19 @@ def search_notes(notes_dir: str, query: str) -> List[Dict]:
                 for match in matches[:3]:  # Limit to 3 matches per file
                     start_index = match.start()
                     end_index = match.end()
+                    matched_text = match.group()  # Preserve original case
                     
-                    # Create slice window: ±30 characters around match
+                    # Create slice window: ±15 characters around match
-                    context_start = max(0, start_index - 30)
+                    context_start = max(0, start_index - 15)
-                    context_end = min(len(content), end_index + 30)
+                    context_end = min(len(content), end_index + 15)
                     
-                    # Extract snippet
+                    # Extract and clean parts (newlines → spaces)
-                    snippet = content[context_start:context_end]
+                    before = escape(content[context_start:start_index].replace('\n', ' '))
+                    after = escape(content[end_index:context_end].replace('\n', ' '))
+                    matched_clean = escape(matched_text.replace('\n', ' '))
                     
-                    # Replace all newlines with spaces to ensure UI doesn't break
+                    # Build snippet with <mark> highlight (styled via CSS)
-                    snippet = snippet.replace('\n', ' ')
+                    snippet = f'{before}<mark class="search-highlight">{matched_clean}</mark>{after}'
                     
                     # Add ellipsis if truncated at start
                     if context_start > 0:

docs/index.html

@@ -7,7 +7,7 @@
     <!-- 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 Markdown note-taking application with wikilinks, LaTeX math, Mermaid diagrams, tags, templates, and code highlighting. Self-hosted, free, and open source.">
+    <meta name="description" content="A lightweight, privacy-focused Markdown note-taking application with wikilinks, graph view, LaTeX math, Mermaid diagrams, tags, templates, 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, templates, tags, yaml frontmatter">
     <meta name="author" content="Gamosoft">
     <meta name="robots" content="index, follow">
@@ -586,6 +586,12 @@
                 <p>Link notes with [[double brackets]] Obsidian-style. Broken links shown dimmed.</p>
             </div>
 
+            <div class="feature">
+                <div class="feature-icon">🕸️</div>
+                <h3>Graph View</h3>
+                <p>Interactive visualization of connected notes. Drag to explore relationships.</p>
+            </div>
+
             <div class="feature">
                 <div class="feature-icon">📂</div>
                 <h3>Simple Storage</h3>
@@ -664,6 +670,14 @@
                     </div>
                 </div>
 
+                <div class="benefit-item">
+                    <span class="emoji">🕸️</span>
+                    <div class="text">
+                        <strong>Graph View</strong>
+                        Visualize note connections
+                    </div>
+                </div>
+
                 <div class="benefit-item">
                     <span class="emoji">🖼️</span>
                     <div class="text">
@@ -759,7 +773,7 @@
       "url": "https://www.notediscovery.com",
       "applicationCategory": "ProductivityApplication",
       "operatingSystem": "Linux, Windows, macOS",
-      "featureList": "Markdown editor, Wikilinks, LaTeX math equations, Mermaid diagrams, Code syntax highlighting, Dark mode, Plugin system, Internal links, Properties panel, HTML export, Full-text search, Self-hosted, Obsidian, Evernote, Notion, Onenote, Second brain",
+      "featureList": "Markdown editor, Wikilinks, Graph view, LaTeX math equations, Mermaid diagrams, Code syntax highlighting, Dark mode, Plugin system, Internal links, Properties panel, HTML export, Full-text search, Self-hosted, Obsidian, Evernote, Notion, Onenote, Second brain",
       "offers": {
         "@type": "Offer",
         "price": "0",

documentation/FEATURES.md

@@ -28,6 +28,12 @@
 
 ## 🔗 Linking & Discovery
 
+### Graph View
+- **Interactive graph** - Visualize all your notes and their connections
+- **Navigate with mouse** - Drag to pan, scroll to zoom, double-click nodes to open notes
+- **Multiple link types** - See wikilinks and markdown links distinguished by color
+- **Theme-aware** - Graph colors adapt to your current theme
+
 ### Internal Links
 - **Wikilinks** - `[[Note Name]]` Obsidian-style syntax for quick linking
 - **Wikilinks with display text** - `[[Note Name|Click here]]` to customize link text

frontend/app.js

@@ -42,6 +42,12 @@ function noteApp() {
         noteContent: '',
         viewMode: 'split', // 'edit', 'split', 'preview'
         searchQuery: '',
+        
+        // Graph state (separate overlay, doesn't affect viewMode)
+        showGraph: false,
+        graphInstance: null,
+        graphLoaded: false,
+        graphData: null,
         searchResults: [],
         currentSearchHighlight: '', // Track current highlighted search term
         currentMatchIndex: 0, // Current match being viewed
@@ -549,6 +555,11 @@ function noteApp() {
                         this.renderMermaid();
                     }, 100);
                 }
+                
+                // Refresh graph if visible (longer delay to ensure CSS is applied)
+                if (this.showGraph) {
+                    setTimeout(() => this.initGraph(), 300);
+                }
             } catch (error) {
                 console.error('Failed to load theme:', error);
             }
@@ -971,7 +982,7 @@ function noteApp() {
                         @dragenter.prevent="dragOverFolder = '${folder.path.replace(/'/g, "\\'")}'"
                         @dragleave="dragOverFolder = null"
                         @drop.stop="onFolderDrop('${folder.path.replace(/'/g, "\\'")}' )"
-                        class="folder-item px-3 py-3 mb-1 text-sm rounded transition-all relative"
+                        class="folder-item px-2 py-1 text-sm relative"
                         style="color: var(--text-primary); cursor: pointer;"
                         :class="{
                             'border-2 border-dashed bg-accent-light': (draggedNote || draggedFolder) && dragOverFolder === '${folder.path.replace(/'/g, "\\'")}',
@@ -1029,7 +1040,7 @@ function noteApp() {
             
             // If expanded, render folder contents (child folders + notes)
             if (isExpanded) {
-                html += `<div class="folder-contents" style="padding-left: 12px;">`;
+                html += `<div class="folder-contents" style="padding-left: 10px;">`;
                 
                 // First, render child folders (if any)
                 if (folder.children && Object.keys(folder.children).length > 0) {
@@ -1055,9 +1066,7 @@ function noteApp() {
                         const icon = isImage ? '🖼️' : '';
                         
                         // Click handler
-                        const clickHandler = isImage 
+                        const clickHandler = `openItem('${note.path.replace(/'/g, "\\'")}', '${note.type}')`; 
-                            ? `viewImage('${note.path.replace(/'/g, "\\'")}')`
-                            : `loadNote('${note.path.replace(/'/g, "\\'")}')`; 
                         
                         // Delete handler
                         const deleteHandler = isImage
@@ -1071,7 +1080,7 @@ function noteApp() {
                                 @dragstart="onNoteDragStart('${note.path.replace(/'/g, "\\'")}', $event)"
                                 @dragend="onNoteDragEnd()"
                                 @click="${clickHandler}"
-                                class="note-item px-3 py-2 mb-1 text-sm rounded relative border-2 border-transparent"
+                                class="note-item px-2 py-1 text-sm relative border-2 border-transparent"
                                 style="${isCurrent ? 'background-color: var(--accent-light); color: var(--accent-primary);' : 'color: var(--text-primary);'} ${isImage ? 'opacity: 0.85;' : ''} cursor: pointer;"
                                 @mouseover="if('${note.path}' !== currentNote && '${note.path}' !== currentImage) $el.style.backgroundColor='var(--bg-hover)'"
                                 @mouseout="if('${note.path}' !== currentNote && '${note.path}' !== currentImage) $el.style.backgroundColor='transparent'"
@@ -1160,7 +1169,7 @@ function noteApp() {
                 const sidebar = document.querySelector('.flex-1.overflow-y-auto.custom-scrollbar');
                 if (!sidebar) return;
                 
-                const noteElements = sidebar.querySelectorAll('[class*="px-3 py-2 mb-1"]');
+                const noteElements = sidebar.querySelectorAll('.note-item');
                 let targetElement = null;
                 const noteName = notePath.split('/').pop().replace('.md', '');
                 
@@ -1431,8 +1440,19 @@ function noteApp() {
             }
         },
         
+        // Open a note or image (unified handler for sidebar/homepage clicks)
+        openItem(path, type = 'note', searchHighlight = '') {
+            this.showGraph = false;
+            if (type === 'image' || path.match(/\.(png|jpg|jpeg|gif|webp)$/i)) {
+                this.viewImage(path);
+            } else {
+                this.loadNote(path, true, searchHighlight);
+            }
+        },
+        
         // View an image in the main pane
         viewImage(imagePath, updateHistory = true) {
+            this.showGraph = false; // Ensure graph is closed
             this.currentNote = '';
             this.currentNoteName = '';
             this.noteContent = '';
@@ -1526,8 +1546,8 @@ function noteApp() {
                     );
                     if (noteByPathCI) {
                         this.loadNote(noteByPathCI.path);
-                    } else {
+                } else {
-                        alert(`Note not found: ${notePath}`);
+                    alert(`Note not found: ${notePath}`);
                     }
                 }
             }
@@ -1895,18 +1915,10 @@ function noteApp() {
                         mark.className = 'search-highlight';
                         mark.setAttribute('data-match-index', matchIndex);
                         mark.textContent = text.substring(index, index + searchTerm.length);
-                        mark.style.padding = '2px 4px';
-                        mark.style.borderRadius = '3px';
-                        mark.style.transition = 'all 0.2s';
                         
-                        // Style first match as active, others as inactive
+                        // First match is active (styled via CSS)
                         if (matchIndex === 0) {
-                            mark.style.backgroundColor = 'var(--accent-primary)';
-                            mark.style.color = 'white';
                             mark.classList.add('active-match');
-                        } else {
-                            mark.style.backgroundColor = 'rgba(255, 193, 7, 0.4)';
-                            mark.style.color = 'var(--text-primary)';
                         }
                         
                         fragment.appendChild(mark);
@@ -1961,17 +1973,9 @@ function noteApp() {
             const allMatches = preview.querySelectorAll('mark.search-highlight');
             if (index < 0 || index >= allMatches.length) return;
             
-            // Update styling - make current match prominent
+            // Update styling - make current match prominent (via CSS class)
             allMatches.forEach((mark, i) => {
-                if (i === index) {
+                mark.classList.toggle('active-match', i === index);
-                    mark.style.backgroundColor = 'var(--accent-primary)';
-                    mark.style.color = 'white';
-                    mark.classList.add('active-match');
-                } else {
-                    mark.style.backgroundColor = 'rgba(255, 193, 7, 0.4)';
-                    mark.style.color = 'var(--text-primary)';
-                    mark.classList.remove('active-match');
-                }
             });
             
             // Scroll to the match
@@ -3753,6 +3757,7 @@ function noteApp() {
         
         // Homepage folder navigation methods
         goToHomepageFolder(folderPath) {
+            this.showGraph = false; // Close graph when navigating
             this.selectedHomepageFolder = folderPath || '';
             
             // Clear editor state to show landing page
@@ -3774,6 +3779,7 @@ function noteApp() {
         
         // Navigate to homepage root and clear all editor state
         goHome() {
+            this.showGraph = false; // Close graph when going home
             this.selectedHomepageFolder = '';
             this.currentNote = '';
             this.currentNoteName = '';
@@ -3790,6 +3796,291 @@ function noteApp() {
             };
             
             window.history.pushState({ homepageFolder: '' }, '', '/');
+        },
+        
+        // ==================== GRAPH VIEW ====================
+        
+        // Initialize the graph visualization
+        async initGraph() {
+            // Check if vis is loaded
+            if (typeof vis === 'undefined') {
+                console.error('vis-network library not loaded');
+                return;
+            }
+            
+            this.graphLoaded = false;
+            
+            try {
+                // Fetch graph data from API
+                const response = await fetch('/api/graph');
+                if (!response.ok) throw new Error('Failed to fetch graph data');
+                const data = await response.json();
+                this.graphData = data;
+                
+                // Get container
+                const container = document.getElementById('graph-overlay');
+                if (!container) return;
+                
+                // Get theme colors (force reflow to ensure CSS is applied)
+                document.body.offsetHeight; // Force reflow
+                const style = getComputedStyle(document.documentElement);
+                
+                // Helper to get CSS variable with fallback
+                const getCssVar = (name, fallback) => {
+                    const value = style.getPropertyValue(name).trim();
+                    return value || fallback;
+                };
+                
+                const accentPrimary = getCssVar('--accent-primary', '#7c3aed');
+                const accentSecondary = getCssVar('--accent-secondary', '#a78bfa');
+                const textPrimary = getCssVar('--text-primary', '#111827');
+                const textSecondary = getCssVar('--text-secondary', '#6b7280');
+                const bgPrimary = getCssVar('--bg-primary', '#ffffff');
+                const bgSecondary = getCssVar('--bg-secondary', '#f3f4f6');
+                const borderColor = getCssVar('--border-primary', '#e5e7eb');
+                
+                // Prepare nodes with styling - all nodes same base color
+                const nodes = new vis.DataSet(data.nodes.map(n => ({
+                    id: n.id,
+                    label: n.label,
+                    title: n.id, // Tooltip shows full path
+                    color: {
+                        background: accentPrimary,
+                        border: accentPrimary,
+                        highlight: {
+                            background: accentPrimary,
+                            border: textPrimary  // Darker border when selected
+                        },
+                        hover: {
+                            background: accentSecondary,
+                            border: accentPrimary
+                        }
+                    },
+                    font: {
+                        color: textPrimary,
+                        size: 12,
+                        face: 'system-ui, -apple-system, sans-serif'
+                    },
+                    borderWidth: this.currentNote === n.id ? 4 : 2,
+                    chosen: {
+                        node: (values) => {
+                            values.size = 22;
+                            values.borderWidth = 4;
+                            values.borderColor = textPrimary;
+                        }
+                    }
+                })));
+                
+                // Prepare edges with styling based on type
+                const edges = new vis.DataSet(data.edges.map((e, i) => ({
+                    id: i,
+                    from: e.source,
+                    to: e.target,
+                    color: {
+                        color: e.type === 'wikilink' ? accentPrimary : borderColor,
+                        highlight: accentPrimary,
+                        hover: accentSecondary,
+                        opacity: 0.8
+                    },
+                    width: e.type === 'wikilink' ? 2 : 1,
+                    smooth: {
+                        type: 'continuous',
+                        roundness: 0.5
+                    },
+                    chosen: {
+                        edge: (values) => {
+                            values.width = 3;
+                            values.color = accentPrimary;
+                        }
+                    }
+                })));
+                
+                // Network options
+                const options = {
+                    nodes: {
+                        shape: 'dot',
+                        size: 16,
+                        borderWidth: 2,
+                        shadow: {
+                            enabled: true,
+                            color: 'rgba(0,0,0,0.1)',
+                            size: 5,
+                            x: 2,
+                            y: 2
+                        }
+                    },
+                    edges: {
+                        arrows: {
+                            to: {
+                                enabled: true,
+                                scaleFactor: 0.5,
+                                type: 'arrow'
+                            }
+                        }
+                    },
+                    physics: {
+                        enabled: true,
+                        solver: 'forceAtlas2Based',
+                        forceAtlas2Based: {
+                            gravitationalConstant: -50,
+                            centralGravity: 0.01,
+                            springLength: 100,
+                            springConstant: 0.08,
+                            damping: 0.4,
+                            avoidOverlap: 0.5
+                        },
+                        stabilization: {
+                            enabled: true,
+                            iterations: 200,
+                            updateInterval: 25
+                        }
+                    },
+                    interaction: {
+                        hover: true,
+                        tooltipDelay: 200,
+                        navigationButtons: false,  // Using custom buttons instead
+                        keyboard: {
+                            enabled: true,
+                            bindToWindow: false
+                        },
+                        zoomView: true,
+                        dragView: true
+                    },
+                    layout: {
+                        improvedLayout: true,
+                        randomSeed: 42
+                    }
+                };
+                
+                // Destroy existing instance if any
+                if (this.graphInstance) {
+                    this.graphInstance.destroy();
+                    this.graphInstance = null;
+                }
+                
+                // Clear container to ensure clean state
+                const graphCanvas = container.querySelector('canvas');
+                if (graphCanvas) graphCanvas.remove();
+                const visElements = container.querySelectorAll('.vis-network, .vis-navigation');
+                visElements.forEach(el => el.remove());
+                
+                // Create the network
+                this.graphInstance = new vis.Network(container, { nodes, edges }, options);
+                
+                // Store reference for callbacks
+                const graphRef = this.graphInstance;
+                const currentNoteRef = this.currentNote;
+                
+                // Wait for stabilization
+                this.graphInstance.once('stabilizationIterationsDone', () => {
+                    graphRef.setOptions({ physics: { enabled: false } });
+                    this.graphLoaded = true;
+                    
+                    // Focus and select current note if one is loaded
+                    if (currentNoteRef) {
+                        setTimeout(() => {
+                            try {
+                                if (graphRef && this.showGraph) {
+                                    const nodeIds = graphRef.body.data.nodes.getIds();
+                                    if (nodeIds.includes(currentNoteRef)) {
+                                        // Focus on the node
+                                        graphRef.focus(currentNoteRef, {
+                                            scale: 1.2,
+                                            animation: {
+                                                duration: 500,
+                                                easingFunction: 'easeInOutQuad'
+                                            }
+                                        });
+                                        // Select the node to highlight it
+                                        graphRef.selectNodes([currentNoteRef]);
+                                    }
+                                }
+                            } catch (e) {
+                                // Ignore - graph may have been destroyed
+                            }
+                        }, 150);
+                    }
+                });
+                
+                // Click event - open note
+                this.graphInstance.on('click', (params) => {
+                    if (params.nodes.length > 0) {
+                        const noteId = params.nodes[0];
+                        this.loadNote(noteId);
+                        // Node is already selected by vis-network on click, no need to call selectNodes
+                    }
+                });
+                
+                // Double-click event - open note and close graph
+                this.graphInstance.on('doubleClick', (params) => {
+                    if (params.nodes.length > 0) {
+                        const noteId = params.nodes[0];
+                        // Close graph and load note
+                        this.showGraph = false;
+                        this.loadNote(noteId);
+                    }
+                });
+                
+                // Hover event - highlight connections
+                this.graphInstance.on('hoverNode', (params) => {
+                    const nodeId = params.node;
+                    const connectedNodes = this.graphInstance.getConnectedNodes(nodeId);
+                    const connectedEdges = this.graphInstance.getConnectedEdges(nodeId);
+                    
+                    // Dim all nodes except hovered and connected
+                    const allNodes = nodes.getIds();
+                    const updates = allNodes.map(id => ({
+                        id,
+                        opacity: (id === nodeId || connectedNodes.includes(id)) ? 1 : 0.2
+                    }));
+                    nodes.update(updates);
+                });
+                
+                this.graphInstance.on('blurNode', () => {
+                    // Reset all nodes to full opacity
+                    const allNodes = nodes.getIds();
+                    const updates = allNodes.map(id => ({ id, opacity: 1 }));
+                    nodes.update(updates);
+                });
+                
+                // Add legend to container
+                this.addGraphLegend(container, accentPrimary, borderColor, textSecondary);
+                
+            } catch (error) {
+                console.error('Failed to initialize graph:', error);
+                this.graphLoaded = true; // Stop loading indicator
+            }
+        },
+        
+        // Add legend to graph container
+        addGraphLegend(container, wikiColor, mdColor, textColor) {
+            // Remove existing legend if any
+            const existingLegend = container.querySelector('.graph-legend');
+            if (existingLegend) existingLegend.remove();
+            
+            const legend = document.createElement('div');
+            legend.className = 'graph-legend';
+            legend.innerHTML = `
+                <div class="graph-legend-item">
+                    <span class="graph-legend-dot" style="background: ${wikiColor};"></span>
+                    <span style="color: ${textColor};">Wikilinks</span>
+                </div>
+                <div class="graph-legend-item">
+                    <span class="graph-legend-dot" style="background: ${mdColor};"></span>
+                    <span style="color: ${textColor};">Markdown links</span>
+                </div>
+                <div style="margin-top: 8px; font-size: 10px; color: ${textColor}; opacity: 0.7;">
+                    Click: select • Double-click: open
+                </div>
+            `;
+            container.appendChild(legend);
+        },
+        
+        // Refresh graph when theme changes
+        refreshGraph() {
+            if (this.viewMode === 'graph' && this.graphInstance) {
+                this.initGraph();
+            }
         }
     }
 }

frontend/index.html

@@ -64,6 +64,9 @@
         window.mermaid = mermaid;
     </script>
     
+    <!-- vis-network for graph visualization (v9.1.9) -->
+    <script src="https://unpkg.com/vis-network@9.1.9/standalone/umd/vis-network.min.js"></script>
+    
     <!-- Theme styles will be loaded dynamically -->
     <link rel="stylesheet" id="theme-stylesheet" href="">
     
@@ -290,6 +293,19 @@
             opacity: 1;
         }
 
+        /* Search highlight base style (used in note preview and search results) */
+        .search-highlight {
+            padding: 2px 4px;
+            border-radius: 3px;
+            background-color: rgba(255, 193, 7, 0.4);
+            color: var(--text-primary);
+            transition: all 0.2s;
+        }
+        .search-highlight.active-match {
+            background-color: var(--accent-primary);
+            color: white;
+        }
+        
         /* Note Properties Panel */
         .note-properties {
             font-size: 0.8125rem;
@@ -308,6 +324,42 @@
             border-bottom-style: solid;
         }
         
+        /* Graph View */
+        #graph-overlay {
+            position: absolute;
+            top: 0;
+            left: 0;
+            right: 0;
+            bottom: 0;
+        }
+        #graph-overlay .vis-network {
+            outline: none;
+            width: 100% !important;
+            height: 100% !important;
+        }
+        .graph-legend {
+            position: absolute;
+            top: 10px;
+            right: 10px;
+            padding: 8px 12px;
+            border-radius: 8px;
+            font-size: 12px;
+            background: var(--bg-secondary);
+            border: 1px solid var(--border-primary);
+            z-index: 10;
+        }
+        .graph-legend-item {
+            display: flex;
+            align-items: center;
+            gap: 6px;
+            margin: 4px 0;
+        }
+        .graph-legend-dot {
+            width: 10px;
+            height: 10px;
+            border-radius: 50%;
+        }
+        
         /* Standard internal links (non-wikilink, e.g. [text](path)) */
         .markdown-preview a:not([href^="http"]):not([href^="https"]):not([href^="//"]):not([href^="mailto:"]):not([data-wikilink]) {
             color: var(--accent-primary);
@@ -391,10 +443,10 @@
             cursor: copy !important;
         }
         
-        /* Folder tree styling */
+        /* Folder tree styling - compact Obsidian-like */
         .folder-item {
             user-select: none;
-            transition: all 0.2s ease;
+            border-radius: 4px;
         }
         
         .folder-item:hover {
@@ -406,8 +458,11 @@
         }
         
         .note-item {
-            padding-left: 1.5rem;
+            border-radius: 4px;
-            transition: all 0.2s ease;
+        }
+        
+        .note-item:hover {
+            background-color: var(--bg-hover);
         }
         
         /* Drag and drop improvements */
@@ -424,7 +479,7 @@
         /* Smooth transitions for drag states */
         .folder-item,
         .note-item {
-            transition: opacity 0.2s ease, transform 0.15s ease, background-color 0.15s ease, border-color 0.15s ease;
+            transition: background-color 0.15s ease, border-color 0.15s ease;
         }
         
         /* Better drop zone visibility */
@@ -794,25 +849,25 @@
             </div>
             
             <!-- Search -->
-            <div class="flex-shrink-0 p-3 border-b" style="border-color: var(--border-primary);">
+            <div class="flex-shrink-0 px-2 py-2 border-b" style="border-color: var(--border-primary);">
                 <div class="relative">
                     <input 
                         type="text" 
                         x-model="searchQuery"
                         @input="searchNotes()"
-                        placeholder="Search notes..."
+                        placeholder="Search..."
-                        class="w-full px-3 py-2 pl-8 pr-8 text-sm rounded-lg focus:outline-none focus:ring-2"
+                        class="w-full px-2 py-1.5 pl-7 pr-7 text-xs rounded focus:outline-none focus:ring-1"
                         style="background-color: var(--bg-primary); color: var(--text-primary); border: 1px solid var(--border-primary);"
                     >
                     <!-- Search Icon -->
-                    <svg class="absolute left-2 top-2.5 w-4 h-4" style="color: var(--text-tertiary);" fill="none" stroke="currentColor" viewBox="0 0 24 24">
+                    <svg class="absolute left-2 top-2 w-3.5 h-3.5" 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="M21 21l-6-6m2-5a7 7 0 11-14 0 7 7 0 0114 0z"></path>
                     </svg>
                     <!-- Clear Button -->
                     <button
                         x-show="searchQuery.length > 0"
                         @click="searchQuery = ''; searchResults = []; currentSearchHighlight = ''; clearSearchHighlights();"
-                        class="absolute right-2 top-2.5 w-4 h-4 flex items-center justify-center rounded-full hover:bg-gray-300 dark:hover:bg-gray-600 transition-colors"
+                        class="absolute right-1.5 top-1.5 w-4 h-4 flex items-center justify-center rounded-full hover:bg-gray-300 dark:hover:bg-gray-600 transition-colors"
                         style="color: var(--text-tertiary);"
                         title="Clear search"
                     >
@@ -825,7 +880,7 @@
                 <!-- Match Navigation (shown when there are matches in current note) -->
                 <div 
                     x-show="totalMatches > 0" 
-                    class="flex items-center justify-between mt-2 px-2 py-1 rounded text-xs"
+                    class="flex items-center justify-between mt-1.5 px-2 py-0.5 rounded text-xs"
                     style="background-color: var(--bg-secondary); color: var(--text-secondary);"
                 >
                     <span x-text="`Match ${currentMatchIndex + 1} of ${totalMatches}`"></span>
@@ -923,16 +978,16 @@
             </div>
             
             <!-- New Item Dropdown -->
-            <div class="flex-shrink-0 p-3 border-b" style="border-color: var(--border-primary);">
+            <div class="flex-shrink-0 px-2 py-1.5 border-b" style="border-color: var(--border-primary);">
                 <button 
                     @click="dropdownTargetFolder = ''; toggleNewDropdown($event)"
-                    class="w-full px-4 py-2 text-sm font-medium text-white rounded-lg focus:outline-none focus:ring-2 flex items-center justify-center gap-2"
+                    class="w-full px-3 py-1.5 text-xs font-medium text-white rounded focus:outline-none focus:ring-1 flex items-center justify-center gap-1.5"
                     style="background-color: var(--accent-primary);"
                     onmouseover="this.style.backgroundColor='var(--accent-hover)'"
                     onmouseout="this.style.backgroundColor='var(--accent-primary)'"
                 >
                     <span>+ New</span>
-                    <svg class="w-4 h-4" fill="none" stroke="currentColor" viewBox="0 0 24 24">
+                    <svg class="w-3 h-3" fill="none" stroke="currentColor" viewBox="0 0 24 24">
                         <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M19 9l-7 7-7-7"></path>
                     </svg>
                 </button>
@@ -948,15 +1003,15 @@
                         </div>
                         <template x-for="note in searchResults" :key="note.path">
                             <div 
-                                @click="loadNote(note.path, true, searchQuery)"
+                                @click="openItem(note.path, note.type, searchQuery)"
-                                class="px-3 py-2 mb-1 text-sm rounded cursor-pointer"
+                                class="px-2 py-1.5 text-sm cursor-pointer rounded"
                                 :style="currentNote === note.path ? 'background-color: var(--accent-light); color: var(--accent-primary);' : 'color: var(--text-primary);'"
                                 onmouseover="if(this.style.backgroundColor !== 'var(--accent-light)') this.style.backgroundColor='var(--bg-hover)'"
                                 onmouseout="if(this.style.backgroundColor !== 'var(--accent-light)') this.style.backgroundColor='transparent'"
                                 :title="note.path"
                             >
                                 <div class="font-medium truncate" x-text="note.name"></div>
-                                <div class="text-xs truncate" style="color: var(--text-tertiary);" x-text="(note.matches && note.matches.length > 0) ? note.matches[0].context : (note.folder || 'Root')"></div>
+                                <div class="text-xs truncate" style="color: var(--text-tertiary);" x-html="(note.matches && note.matches.length > 0) ? note.matches[0].context : (note.folder || 'Root')"></div>
                             </div>
                         </template>
                     </div>
@@ -1062,8 +1117,8 @@
                                 draggable="true"
                                 @dragstart="onNoteDragStart(note.path, $event)"
                                 @dragend="onNoteDragEnd()"
-                                @click="note.type === 'image' ? viewImage(note.path) : loadNote(note.path)"
+                                @click="openItem(note.path, note.type)"
-                                class="note-item px-3 py-2 mb-1 text-sm rounded relative border-2 border-transparent"
+                                class="note-item px-2 py-1 text-sm relative border-2 border-transparent"
                                 :style="((note.type === 'image' ? currentImage === note.path : currentNote === note.path) ? 'background-color: var(--accent-light); color: var(--accent-primary);' : 'color: var(--text-primary);') + (note.type === 'image' ? ' opacity: 0.85;' : '') + (draggedNote || draggedFolder ? ' cursor: grabbing;' : ' cursor: pointer;')"
                                 @mouseover="if(currentNote !== note.path && currentImage !== note.path) $el.style.backgroundColor='var(--bg-hover)'"
                                 @mouseout="if(currentNote !== note.path && currentImage !== note.path) $el.style.backgroundColor='transparent'"
@@ -1097,18 +1152,28 @@
             
             <!-- Footer -->
             <div class="flex-shrink-0 p-3 border-t" style="border-color: var(--border-primary);">
-                <!-- Theme Selector (compact) -->
+                <!-- Theme Selector and Graph Button -->
-                <select 
+                <div class="flex gap-2 mb-2">
-                    x-model="currentTheme"
+                    <select 
-                    @change="setTheme(currentTheme)"
+                        x-model="currentTheme"
-                    class="w-full px-2 py-1.5 text-xs rounded mb-2 focus:outline-none focus:ring-2 focus:ring-opacity-50"
+                        @change="setTheme(currentTheme)"
-                    style="background-color: var(--bg-primary); color: var(--text-primary); border: 1px solid var(--border-primary); cursor: pointer;"
+                        class="flex-1 px-2 py-1.5 text-xs rounded focus:outline-none focus:ring-2 focus:ring-opacity-50"
-                    title="Select theme"
+                        style="background-color: var(--bg-primary); color: var(--text-primary); border: 1px solid var(--border-primary); cursor: pointer;"
-                >
+                        title="Select theme"
-                    <template x-for="theme in availableThemes" :key="theme.id">
+                    >
-                        <option :value="theme.id" x-text="theme.name"></option>
+                        <template x-for="theme in availableThemes" :key="theme.id">
-                    </template>
+                            <option :value="theme.id" x-text="theme.name"></option>
-                </select>
+                        </template>
+                    </select>
+                    <button 
+                        @click="showGraph = true; initGraph()"
+                        class="px-2 py-1.5 text-xs rounded transition-colors"
+                        :style="showGraph ? 'background-color: var(--accent-primary); color: white;' : 'background-color: var(--bg-primary); color: var(--text-primary); border: 1px solid var(--border-primary);'"
+                        title="View note connections graph"
+                    >
+                        🔗
+                    </button>
+                </div>
                 
                 <!-- Stats -->
                 <div class="text-xs text-center" style="color: var(--text-tertiary);">
@@ -1140,7 +1205,36 @@
         ></div>
         
         <!-- Main Content Area -->
-        <div class="flex-1 flex flex-col overflow-hidden">
+        <div class="flex-1 flex flex-col overflow-hidden relative">
+            
+            <!-- Graph View Overlay (works from homepage or editor) -->
+            <div 
+                x-show="showGraph"
+                id="graph-overlay"
+                class="absolute inset-0"
+                style="background-color: var(--bg-primary); z-index: 50;"
+            >
+                <!-- Graph renders here via vis-network -->
+                <div x-show="!graphLoaded" class="flex items-center justify-center h-full">
+                    <div class="text-center" style="color: var(--text-secondary);">
+                        <svg class="animate-spin h-8 w-8 mx-auto mb-3" style="color: var(--accent-primary);" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24">
+                            <circle class="opacity-25" cx="12" cy="12" r="10" stroke="currentColor" stroke-width="4"></circle>
+                            <path class="opacity-75" fill="currentColor" d="M4 12a8 8 0 018-8V0C5.373 0 0 5.373 0 12h4zm2 5.291A7.962 7.962 0 014 12H0c0 3.042 1.135 5.824 3 7.938l3-2.647z"></path>
+                        </svg>
+                        <p>Loading graph...</p>
+                    </div>
+                </div>
+                <!-- Close button -->
+                <button 
+                    @click="showGraph = false"
+                    class="absolute top-4 left-4 px-3 py-2 text-sm font-medium rounded-lg transition-colors z-10"
+                    style="background-color: var(--bg-secondary); color: var(--text-primary); border: 1px solid var(--border-primary);"
+                    onmouseover="this.style.backgroundColor='var(--bg-hover)'"
+                    onmouseout="this.style.backgroundColor='var(--bg-secondary)'"
+                >
+                    ← Back
+                </button>
+            </div>
             
             <template x-if="!currentNote && !currentImage">
                 <!-- Notes Homepage -->
@@ -1310,7 +1404,7 @@
                                     <!-- Notes -->
                                     <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)"
+                                            @click="openItem(note.path, note.type)"
                                             class="p-4 rounded-lg border-2 cursor-pointer transition-all hover:shadow-lg"
                                             style="background-color: var(--bg-secondary); border-color: var(--border-primary); min-height: 140px; display: flex; flex-direction: column; position: relative;"
                                             onmouseover="this.style.borderColor='var(--accent-primary)'; this.style.transform='translateY(-2px)'; this.querySelector('.card-delete-btn').style.opacity='1';"
@@ -1476,11 +1570,11 @@
                         </div>
                     </div>
                     
-                    <!-- Editor/Preview -->
+                    <!-- Editor/Preview/Graph -->
                     <div class="flex-1 flex relative" style="min-height: 0;">
                         <!-- Editor -->
                         <div 
-                            x-show="viewMode === 'edit' || viewMode === 'split'"
+                            x-show="!currentImage && (viewMode === 'edit' || viewMode === 'split')"
                             class="flex flex-col"
                             style="min-height: 0;"
                             :style="viewMode === 'split' ? `width: ${editorWidth}%;` : 'width: 100%;'"
@@ -1502,7 +1596,7 @@
                         
                         <!-- Split view resize handle -->
                         <div 
-                            x-show="viewMode === 'split'"
+                            x-show="!currentImage && viewMode === 'split'"
                             @mousedown="startSplitResize($event)"
                             class="split-resize-handle"
                             style="width: 6px; cursor: col-resize; background: linear-gradient(90deg, transparent 0%, var(--border-secondary) 50%, transparent 100%); transition: all 0.2s; position: relative; z-index: 10; opacity: 0.5;"