mcp-vector-search 0.12.6__py3-none-any.whl → 1.1.22__py3-none-any.whl

mcp_vector_search/cli/commands/visualize/templates/scripts.py

@@ -0,0 +1,4542 @@
+"""Simple D3.js tree visualization for code graph.
+
+Clean, minimal implementation focusing on core functionality:
+- Hierarchical tree layout (linear and circular)
+- Expandable/collapsible directories and files
+- File expansion shows code chunks as child nodes
+- Chunk selection to view content in side panel
+
+Design Decision: Complete rewrite from scratch
+Rationale: Previous implementation was 4085 lines (5x over 800-line limit)
+with excessive complexity. This minimal version provides core functionality
+in <450 lines while maintaining clarity and maintainability.
+
+Node Types and Colors:
+- Orange (collapsed directory) / Blue (expanded directory)
+- Gray (collapsed file) / White (expanded file)
+- Purple (chunk nodes) - smaller circles with purple text
+
+Trade-offs:
+- Simplicity vs Features: Removed advanced features (force-directed, filters)
+- Performance vs Clarity: Straightforward DOM updates over optimized rendering
+- Flexibility vs Simplicity: Fixed layouts instead of customizable options
+
+Extension Points: Add features incrementally based on user feedback rather
+than preemptive feature bloat.
+"""
+
+
+def get_all_scripts() -> str:
+    """Generate all JavaScript for the visualization.
+
+    Returns:
+        Complete JavaScript code as a single string
+    """
+    return """
+// ============================================================================
+// GLOBAL STATE
+// ============================================================================
+
+let allNodes = [];
+let allLinks = [];
+let currentLayout = 'linear';  // 'linear' or 'circular'
+let treeData = null;
+let isViewerOpen = false;
+
+// Navigation history for back/forward
+let navigationHistory = [];
+let navigationIndex = -1;
+
+// Call lines visibility
+let showCallLines = true;
+
+// File filter: 'all', 'code', 'docs'
+let currentFileFilter = 'all';
+
+// Chunk types for code nodes (function, class, method, text, imports, module)
+const chunkTypes = ['function', 'class', 'method', 'text', 'imports', 'module'];
+
+// Size scaling configuration
+const sizeConfig = {
+    minRadius: 12,      // Minimum node radius (50% larger for readability)
+    maxRadius: 24,      // Maximum node radius
+    chunkMinRadius: 5,  // Minimum for small chunks (more visible size contrast)
+    chunkMaxRadius: 28  // Maximum for large chunks (more visible size contrast)
+};
+
+// Dynamic dimensions that update when viewer opens/closes
+function getViewportDimensions() {
+    const container = document.getElementById('main-container');
+    return {
+        width: container.clientWidth,
+        height: container.clientHeight
+    };
+}
+
+const margin = {top: 40, right: 120, bottom: 20, left: 120};
+
+// ============================================================================
+// DATA LOADING
+// ============================================================================
+
+let graphStatusCheckInterval = null;
+
+async function checkGraphStatus() {
+    try {
+        const response = await fetch('/api/graph-status');
+        const status = await response.json();
+        return status;
+    } catch (error) {
+        console.error('Failed to check graph status:', error);
+        return { ready: false, size: 0 };
+    }
+}
+
+function showLoadingIndicator(message) {
+    const loadingDiv = document.getElementById('graph-loading-indicator') || createLoadingDiv();
+    loadingDiv.querySelector('.loading-message').textContent = message;
+    loadingDiv.style.display = 'flex';
+}
+
+function hideLoadingIndicator() {
+    const loadingDiv = document.getElementById('graph-loading-indicator');
+    if (loadingDiv) {
+        loadingDiv.style.display = 'none';
+    }
+}
+
+function createLoadingDiv() {
+    const div = document.createElement('div');
+    div.id = 'graph-loading-indicator';
+    div.style.cssText = `
+        position: fixed;
+        top: 50%;
+        left: 50%;
+        transform: translate(-50%, -50%);
+        background: rgba(255, 255, 255, 0.95);
+        padding: 30px 50px;
+        border-radius: 8px;
+        box-shadow: 0 4px 6px rgba(0, 0, 0, 0.1);
+        display: flex;
+        flex-direction: column;
+        align-items: center;
+        gap: 15px;
+        z-index: 10000;
+    `;
+
+    const spinner = document.createElement('div');
+    spinner.style.cssText = `
+        border: 4px solid #f3f3f3;
+        border-top: 4px solid #3498db;
+        border-radius: 50%;
+        width: 40px;
+        height: 40px;
+        animation: spin 1s linear infinite;
+    `;
+
+    const message = document.createElement('div');
+    message.className = 'loading-message';
+    message.style.cssText = 'color: #333; font-size: 16px; font-family: Arial, sans-serif;';
+    message.textContent = 'Loading graph data...';
+
+    div.appendChild(spinner);
+    div.appendChild(message);
+    document.body.appendChild(div);
+
+    // Add spinner animation
+    const style = document.createElement('style');
+    style.textContent = '@keyframes spin { 0% { transform: rotate(0deg); } 100% { transform: rotate(360deg); } }';
+    document.head.appendChild(style);
+
+    return div;
+}
+
+async function loadGraphData() {
+    try {
+        // Check if graph is ready
+        const status = await checkGraphStatus();
+
+        if (!status.ready) {
+            console.log('Graph data not ready yet, will poll every 5 seconds...');
+            showLoadingIndicator('Generating graph data... This may take a few minutes.');
+
+            // Start polling for graph readiness
+            graphStatusCheckInterval = setInterval(async () => {
+                const checkStatus = await checkGraphStatus();
+                if (checkStatus.ready) {
+                    clearInterval(graphStatusCheckInterval);
+                    console.log('Graph data is now ready, loading...');
+                    showLoadingIndicator('Graph data ready! Loading visualization...');
+                    await loadGraphDataActual();
+                    hideLoadingIndicator();
+                }
+            }, 5000); // Poll every 5 seconds
+
+            return;
+        }
+
+        // Graph is already ready, load it
+        await loadGraphDataActual();
+    } catch (error) {
+        console.error('Failed to load graph data:', error);
+        hideLoadingIndicator();
+        document.body.innerHTML =
+            '<div style="color: red; padding: 20px; font-family: Arial;">Error loading visualization data. Check console for details.</div>';
+    }
+}
+
+async function loadGraphDataActual() {
+    try {
+        const response = await fetch('/api/graph');
+        const data = await response.json();
+
+        // Check if we got an error response
+        if (data.error) {
+            console.warn('Graph data not available yet:', data.error);
+            showLoadingIndicator('Waiting for graph data...');
+            return;
+        }
+
+        allNodes = data.nodes || [];
+        allLinks = data.links || [];
+
+        // Store trend data globally for visualization
+        window.graphTrendData = data.trends || null;
+        if (window.graphTrendData) {
+            console.log(`Loaded trend data: ${window.graphTrendData.entries_count} entries`);
+        }
+
+        console.log(`Loaded ${allNodes.length} nodes and ${allLinks.length} links`);
+
+        // DEBUG: Log first few nodes to see actual structure
+        console.log('=== SAMPLE NODE STRUCTURE ===');
+        if (allNodes.length > 0) {
+            console.log('First node:', JSON.stringify(allNodes[0], null, 2));
+            if (allNodes.length > 1) {
+                console.log('Second node:', JSON.stringify(allNodes[1], null, 2));
+            }
+        }
+
+        // Count node types
+        const typeCounts = {};
+        allNodes.forEach(node => {
+            const type = node.type || 'undefined';
+            typeCounts[type] = (typeCounts[type] || 0) + 1;
+        });
+        console.log('Node type counts:', typeCounts);
+        console.log('=== END SAMPLE NODE STRUCTURE ===');
+
+        buildTreeStructure();
+        renderVisualization();
+    } catch (error) {
+        console.error('Failed to load graph data:', error);
+        document.body.innerHTML =
+            '<div style="color: red; padding: 20px; font-family: Arial;">Error loading visualization data. Check console for details.</div>';
+    }
+}
+
+// ============================================================================
+// TREE STRUCTURE BUILDING
+// ============================================================================
+
+function buildTreeStructure() {
+    // Include directories, files, AND chunks (function, class, method, text, imports, module)
+    const treeNodes = allNodes.filter(node => {
+        const type = node.type;
+        return type === 'directory' || type === 'file' || chunkTypes.includes(type);
+    });
+
+    console.log(`Filtered to ${treeNodes.length} tree nodes (directories, files, and chunks)`);
+
+    // Count node types for debugging
+    const dirCount = treeNodes.filter(n => n.type === 'directory').length;
+    const fileCount = treeNodes.filter(n => n.type === 'file').length;
+    const chunkCount = treeNodes.filter(n => chunkTypes.includes(n.type)).length;
+    console.log(`Node breakdown: ${dirCount} directories, ${fileCount} files, ${chunkCount} chunks`);
+
+    // Create lookup maps
+    const nodeMap = new Map();
+    treeNodes.forEach(node => {
+        nodeMap.set(node.id, {
+            ...node,
+            children: []
+        });
+    });
+
+    // Build parent-child relationships
+    const parentMap = new Map();
+
+    // DEBUG: Analyze link structure
+    console.log('=== LINK STRUCTURE DEBUG ===');
+    console.log(`Total links: ${allLinks.length}`);
+
+    // Get unique link types (handle undefined)
+    const linkTypes = [...new Set(allLinks.map(l => l.type || 'undefined'))];
+    console.log('Link types found:', linkTypes);
+
+    // Count links by type
+    const linkTypeCounts = {};
+    allLinks.forEach(link => {
+        const type = link.type || 'undefined';
+        linkTypeCounts[type] = (linkTypeCounts[type] || 0) + 1;
+    });
+    console.log('Link type counts:', linkTypeCounts);
+
+    // Sample first few links
+    console.log('Sample links (first 5):');
+    allLinks.slice(0, 5).forEach((link, i) => {
+        console.log(`  Link ${i}:`, JSON.stringify(link, null, 2));
+    });
+
+    // Check if links have properties we expect
+    if (allLinks.length > 0) {
+        const firstLink = allLinks[0];
+        console.log('Link properties:', Object.keys(firstLink));
+    }
+    console.log('=== END LINK STRUCTURE DEBUG ===');
+
+    // Build parent-child relationships from links
+    // Process all containment and hierarchy links to establish the tree structure
+    console.log('=== BUILDING TREE RELATIONSHIPS ===');
+
+    let relationshipsProcessed = {
+        dir_hierarchy: 0,
+        dir_containment: 0,
+        file_containment: 0,
+        chunk_hierarchy: 0  // chunk_hierarchy links = class -> method
+    };
+
+    let relationshipsMatched = {
+        dir_hierarchy: 0,
+        dir_containment: 0,
+        file_containment: 0,
+        chunk_hierarchy: 0
+    };
+
+    // Process all relationship links
+    allLinks.forEach(link => {
+        const linkType = link.type;
+
+        // Determine relationship category
+        let category = null;
+        if (linkType === 'dir_hierarchy') {
+            category = 'dir_hierarchy';
+        } else if (linkType === 'dir_containment') {
+            category = 'dir_containment';
+        } else if (linkType === 'file_containment') {
+            category = 'file_containment';
+        } else if (linkType === 'chunk_hierarchy') {
+            // chunk_hierarchy links are chunk-to-chunk (e.g., class -> method)
+            category = 'chunk_hierarchy';
+        } else {
+            // Skip semantic, caller, undefined, and other non-hierarchical links
+            // This includes links without a 'type' field (e.g., subproject links)
+            return;
+        }
+
+        relationshipsProcessed[category]++;
+
+        // Get parent and child nodes from the map
+        const parentNode = nodeMap.get(link.source);
+        const childNode = nodeMap.get(link.target);
+
+        // Both nodes must exist in our tree node set
+        if (!parentNode || !childNode) {
+            if (relationshipsProcessed[category] <= 3) {  // Log first few misses
+                console.log(`${category} link skipped - parent: ${link.source} (exists: ${!!parentNode}), child: ${link.target} (exists: ${!!childNode})`);
+            }
+            return;
+        }
+
+        // Establish parent-child relationship
+        // Add child to parent's children array
+        parentNode.children.push(childNode);
+
+        // Record the parent in parentMap (used to identify root nodes)
+        parentMap.set(link.target, link.source);
+
+        relationshipsMatched[category]++;
+    });
+
+    console.log('Relationship processing summary:');
+    console.log(`  dir_hierarchy: ${relationshipsMatched.dir_hierarchy}/${relationshipsProcessed.dir_hierarchy} matched`);
+    console.log(`  dir_containment: ${relationshipsMatched.dir_containment}/${relationshipsProcessed.dir_containment} matched`);
+    console.log(`  file_containment: ${relationshipsMatched.file_containment}/${relationshipsProcessed.file_containment} matched`);
+    console.log(`  chunk_hierarchy (class→method): ${relationshipsMatched.chunk_hierarchy}/${relationshipsProcessed.chunk_hierarchy} matched`);
+    console.log(`  Total parent-child links: ${parentMap.size}`);
+    console.log('=== END TREE RELATIONSHIPS ===');
+
+    // Find root nodes (nodes with no parents)
+    // IMPORTANT: Exclude chunk types from roots - they should only appear as children of files
+    // Orphaned chunks (without file_containment links) are excluded from the tree
+    const rootNodes = treeNodes
+        .filter(node => !parentMap.has(node.id))
+        .filter(node => !chunkTypes.includes(node.type))  // Exclude orphaned chunks
+        .map(node => nodeMap.get(node.id))
+        .filter(node => node !== undefined);
+
+    console.log('=== ROOT NODE ANALYSIS ===');
+    console.log(`Found ${rootNodes.length} root nodes (directories and files only)`);
+
+    // DEBUG: Count root node types
+    const rootTypeCounts = {};
+    rootNodes.forEach(node => {
+        const type = node.type || 'undefined';
+        rootTypeCounts[type] = (rootTypeCounts[type] || 0) + 1;
+    });
+    console.log('Root node type breakdown:', rootTypeCounts);
+
+    // If we have chunk nodes as roots, something went wrong
+    const chunkRoots = rootNodes.filter(n => chunkTypes.includes(n.type)).length;
+    if (chunkRoots > 0) {
+        console.warn(`WARNING: ${chunkRoots} chunk nodes are roots - they should be children of files!`);
+    }
+
+    // If we have file nodes as roots (except for top-level files), might be missing dir_containment
+    const fileRoots = rootNodes.filter(n => n.type === 'file').length;
+    if (fileRoots > 0) {
+        console.log(`INFO: ${fileRoots} file nodes are roots (this is normal for files not in subdirectories)`);
+    }
+
+    console.log('=== END ROOT NODE ANALYSIS ===');
+
+    // Create virtual root if multiple roots
+    if (rootNodes.length === 0) {
+        console.error('No root nodes found!');
+        treeData = {name: 'Empty', id: 'root', type: 'directory', children: []};
+    } else if (rootNodes.length === 1) {
+        treeData = rootNodes[0];
+    } else {
+        treeData = {
+            name: 'Project Root',
+            id: 'virtual-root',
+            type: 'directory',
+            children: rootNodes
+        };
+    }
+
+    // Collapse single-child chains to make the tree more compact
+    // - Directory with single directory child: src -> mcp_vector_search becomes "src/mcp_vector_search"
+    // - File with single chunk child: promote the chunk's children to the file level
+    function collapseSingleChildChains(node) {
+        if (!node || !node.children) return;
+
+        // First, recursively process all children
+        node.children.forEach(child => collapseSingleChildChains(child));
+
+        // Case 1: Directory with single directory child - combine names
+        if (node.type === 'directory' && node.children.length === 1) {
+            const onlyChild = node.children[0];
+            if (onlyChild.type === 'directory') {
+                // Merge: combine names with "/"
+                console.log(`Collapsing dir chain: ${node.name} + ${onlyChild.name}`);
+                node.name = `${node.name}/${onlyChild.name}`;
+                // Take the child's children as our own
+                node.children = onlyChild.children || [];
+                node._children = onlyChild._children || null;
+                // Preserve the deepest node's id for any link references
+                node.collapsed_ids = node.collapsed_ids || [node.id];
+                node.collapsed_ids.push(onlyChild.id);
+
+                // Recursively check again in case there's another single child
+                collapseSingleChildChains(node);
+            }
+        }
+
+        // Case 2: File with single chunk child - promote chunk's children to file
+        // This handles files where there's just one L1 (e.g., imports or a single class)
+        if (node.type === 'file' && node.children && node.children.length === 1) {
+            const onlyChild = node.children[0];
+            if (chunkTypes.includes(onlyChild.type)) {
+                // If the chunk has children, promote them to the file level
+                const chunkChildren = onlyChild.children || onlyChild._children || [];
+                if (chunkChildren.length > 0) {
+                    console.log(`Promoting ${chunkChildren.length} children from ${onlyChild.type} to file ${node.name}`);
+                    // Replace the single chunk with its children
+                    node.children = chunkChildren;
+                    // Store info about the collapsed chunk (include ALL relevant properties)
+                    node.collapsed_chunk = {
+                        type: onlyChild.type,
+                        name: onlyChild.name,
+                        id: onlyChild.id,
+                        content: onlyChild.content,
+                        docstring: onlyChild.docstring,
+                        start_line: onlyChild.start_line,
+                        end_line: onlyChild.end_line,
+                        file_path: onlyChild.file_path,
+                        language: onlyChild.language,
+                        complexity: onlyChild.complexity
+                    };
+                } else {
+                    // Collapse file+chunk into combined name (like directory chains)
+                    console.log(`Collapsing file+chunk: ${node.name}/${onlyChild.name}`);
+                    node.name = `${node.name}/${onlyChild.name}`;
+                    node.children = null;  // Remove chunk child - now a leaf node
+                    node._children = null;
+                    node.collapsed_ids = node.collapsed_ids || [node.id];
+                    node.collapsed_ids.push(onlyChild.id);
+
+                    // Store chunk data for display when clicked
+                    node.collapsed_chunk = {
+                        type: onlyChild.type,
+                        name: onlyChild.name,
+                        id: onlyChild.id,
+                        content: onlyChild.content,
+                        start_line: onlyChild.start_line,
+                        end_line: onlyChild.end_line,
+                        complexity: onlyChild.complexity
+                    };
+                }
+            }
+        }
+    }
+
+    // Apply single-child chain collapsing to all root children
+    console.log('=== COLLAPSING SINGLE-CHILD CHAINS ===');
+    if (treeData.children) {
+        treeData.children.forEach(child => collapseSingleChildChains(child));
+    }
+    console.log('=== END COLLAPSING SINGLE-CHILD CHAINS ===');
+
+    // Collapse all directories and files by default
+    function collapseAll(node) {
+        if (node.children && node.children.length > 0) {
+            // First, recursively process all descendants
+            node.children.forEach(child => collapseAll(child));
+
+            // Then collapse this node (move children to _children)
+            node._children = node.children;
+            node.children = null;
+        }
+    }
+
+    // Collapse ALL nodes except the root itself
+    // This ensures only the root node is visible initially, all children are collapsed
+    if (treeData.children) {
+        treeData.children.forEach(child => collapseAll(child));
+    }
+
+    console.log('Tree structure built with all directories and files collapsed');
+
+    // Calculate line counts for all nodes (for proportional node rendering)
+    allLineCounts = [];  // Reset for fresh calculation
+    calculateNodeSizes(treeData);
+    calculatePercentiles();  // Calculate 20th/80th percentile thresholds
+    console.log('Node sizes calculated with percentile-based sizing');
+
+    // DEBUG: Check a few file nodes to see if they have chunks in _children
+    console.log('=== POST-COLLAPSE FILE CHECK ===');
+    let filesChecked = 0;
+    let filesWithChunks = 0;
+
+    function checkFilesRecursive(node) {
+        if (node.type === 'file') {
+            filesChecked++;
+            const chunkCount = (node._children || []).length;
+            if (chunkCount > 0) {
+                filesWithChunks++;
+                console.log(`File ${node.name} has ${chunkCount} chunks in _children`);
+            }
+        }
+
+        // Check both visible and hidden children
+        const childrenToCheck = node.children || node._children || [];
+        childrenToCheck.forEach(child => checkFilesRecursive(child));
+    }
+
+    checkFilesRecursive(treeData);
+    console.log(`Checked ${filesChecked} files, ${filesWithChunks} have chunks`);
+    console.log('=== END POST-COLLAPSE FILE CHECK ===');
+}
+
+// ============================================================================
+// NODE SIZE CALCULATION
+// ============================================================================
+
+// Global variables for size scaling - now tracking line counts
+let globalMinLines = Infinity;
+let globalMaxLines = 0;
+let allLineCounts = [];  // Collect all line counts for percentile calculation
+
+function calculateNodeSizes(node) {
+    if (!node) return 0;
+
+    // For chunks: use actual line count (primary metric)
+    // Falls back to content-based estimate only if line numbers unavailable
+    if (chunkTypes.includes(node.type)) {
+        // Primary: use actual line span from start_line/end_line
+        // This ensures visual correlation with displayed line ranges
+        const contentLength = node.content ? node.content.length : 0;
+        const lineCount = (node.start_line && node.end_line)
+            ? node.end_line - node.start_line + 1
+            : Math.max(1, Math.floor(contentLength / 40));  // Fallback: estimate ~40 chars per line
+
+        // Use actual line count for sizing (NOT content length)
+        // This prevents inversion where sparse 101-line files appear smaller than dense 3-line files
+        node._lineCount = lineCount;
+        allLineCounts.push(lineCount);
+
+        if (lineCount > 0) {
+            globalMinLines = Math.min(globalMinLines, lineCount);
+            globalMaxLines = Math.max(globalMaxLines, lineCount);
+        }
+        return lineCount;
+    }
+
+    // For files and directories: sum of children line counts
+    const children = node.children || node._children || [];
+    let totalLines = 0;
+
+    children.forEach(child => {
+        totalLines += calculateNodeSizes(child);
+    });
+
+    // Handle collapsed file+chunk: use the collapsed chunk's line count
+    if (node.type === 'file' && node.collapsed_chunk) {
+        const cc = node.collapsed_chunk;
+        if (cc.start_line && cc.end_line) {
+            totalLines = cc.end_line - cc.start_line + 1;
+        } else if (cc.content) {
+            totalLines = Math.max(1, Math.floor(cc.content.length / 40));
+        }
+    }
+
+    node._lineCount = totalLines || 1;  // Minimum 1 for empty dirs/files
+
+    // DON'T add files/directories to allLineCounts - they skew percentiles
+    // Only chunks should affect percentile calculation since only chunks use percentile sizing
+    // (Files and directories use separate minRadius/maxRadius, not chunkMinRadius/chunkMaxRadius)
+
+    if (node._lineCount > 0) {
+        globalMinLines = Math.min(globalMinLines, node._lineCount);
+        globalMaxLines = Math.max(globalMaxLines, node._lineCount);
+    }
+
+    return node._lineCount;
+}
+
+// Calculate percentile thresholds after all nodes are processed
+let percentile20 = 0;
+let percentile80 = 0;
+
+function calculatePercentiles() {
+    if (allLineCounts.length === 0) return;
+
+    const sorted = [...allLineCounts].sort((a, b) => a - b);
+    const p20Index = Math.floor(sorted.length * 0.20);
+    const p80Index = Math.floor(sorted.length * 0.80);
+
+    percentile20 = sorted[p20Index] || 1;
+    percentile80 = sorted[p80Index] || sorted[sorted.length - 1] || 1;
+
+    console.log(`Line count percentiles (chunks only): 20th=${percentile20}, 80th=${percentile80}, range=${percentile80 - percentile20}`);
+    console.log(`Total chunks: ${allLineCounts.length}, min=${globalMinLines}, max=${globalMaxLines}`);
+}
+
+// Count external calls for a node
+function getExternalCallCounts(nodeData) {
+    if (!nodeData.id) return { inbound: 0, outbound: 0, inboundNodes: [], outboundNodes: [] };
+
+    const nodeFilePath = nodeData.file_path;
+    const inboundNodes = [];  // Array of {id, name, file_path}
+    const outboundNodes = []; // Array of {id, name, file_path}
+
+    // Use a Set to deduplicate by source/target node
+    const inboundSeen = new Set();
+    const outboundSeen = new Set();
+
+    allLinks.forEach(link => {
+        if (link.type === 'caller') {
+            if (link.target === nodeData.id) {
+                // Something calls this node
+                const callerNode = allNodes.find(n => n.id === link.source);
+                if (callerNode && callerNode.file_path !== nodeFilePath && !inboundSeen.has(callerNode.id)) {
+                    inboundSeen.add(callerNode.id);
+                    inboundNodes.push({ id: callerNode.id, name: callerNode.name, file_path: callerNode.file_path });
+                }
+            }
+            if (link.source === nodeData.id) {
+                // This node calls something
+                const calleeNode = allNodes.find(n => n.id === link.target);
+                if (calleeNode && calleeNode.file_path !== nodeFilePath && !outboundSeen.has(calleeNode.id)) {
+                    outboundSeen.add(calleeNode.id);
+                    outboundNodes.push({ id: calleeNode.id, name: calleeNode.name, file_path: calleeNode.file_path });
+                }
+            }
+        }
+    });
+
+    return {
+        inbound: inboundNodes.length,
+        outbound: outboundNodes.length,
+        inboundNodes,
+        outboundNodes
+    };
+}
+
+// Store external call data for line drawing
+let externalCallData = [];
+
+function collectExternalCallData() {
+    externalCallData = [];
+
+    allNodes.forEach(nodeData => {
+        if (!chunkTypes.includes(nodeData.type)) return;
+
+        const counts = getExternalCallCounts(nodeData);
+        if (counts.inbound > 0 || counts.outbound > 0) {
+            externalCallData.push({
+                nodeId: nodeData.id,
+                inboundNodes: counts.inboundNodes,
+                outboundNodes: counts.outboundNodes
+            });
+        }
+    });
+}
+
+function drawExternalCallLines(svg, root) {
+    // Remove existing external call lines
+    svg.selectAll('.external-call-line').remove();
+
+    // Build a map of node positions from the tree (visible nodes only)
+    const nodePositions = new Map();
+    root.descendants().forEach(d => {
+        nodePositions.set(d.data.id, { x: d.x, y: d.y, node: d });
+    });
+
+    // Build a map from node ID to tree node (for parent traversal)
+    const treeNodeMap = new Map();
+    root.descendants().forEach(d => {
+        treeNodeMap.set(d.data.id, d);
+    });
+
+    // Helper: Find position for a node, falling back to visible ancestors
+    // If the target node is not visible (collapsed), find its closest visible ancestor
+    function getPositionWithFallback(nodeId) {
+        // First check if node is directly visible
+        if (nodePositions.has(nodeId)) {
+            return nodePositions.get(nodeId);
+        }
+
+        // Node not visible - try to find via tree traversal
+        // Strategy 1: Find by file_path matching in visible nodes
+        const targetNode = allNodes.find(n => n.id === nodeId);
+        if (!targetNode) {
+            return null;
+        }
+
+        // Strategy 2: Look for the file that contains this chunk
+        if (targetNode.file_path) {
+            // Look for visible file nodes that match this path
+            for (const [id, pos] of nodePositions) {
+                const visibleNode = allNodes.find(n => n.id === id);
+                if (visibleNode) {
+                    // Check if this is the file containing our chunk
+                    if (visibleNode.type === 'file' &&
+                        (visibleNode.path === targetNode.file_path ||
+                         visibleNode.file_path === targetNode.file_path ||
+                         visibleNode.name === targetNode.file_path.split('/').pop())) {
+                        return pos;
+                    }
+                }
+            }
+
+            // Strategy 3: Look for directory containing the file
+            const pathParts = targetNode.file_path.split('/');
+            // Go from most specific (file's directory) to least specific (root)
+            for (let i = pathParts.length - 1; i >= 0; i--) {
+                const dirName = pathParts[i];
+                if (!dirName) continue;
+
+                // Find a visible directory with this name
+                for (const [id, pos] of nodePositions) {
+                    const visibleNode = allNodes.find(n => n.id === id);
+                    if (visibleNode && visibleNode.type === 'directory' && visibleNode.name === dirName) {
+                        return pos;
+                    }
+                }
+            }
+        }
+
+        return null;
+    }
+
+    // Create a group for external call lines (behind nodes)
+    let lineGroup = svg.select('.external-lines-group');
+    if (lineGroup.empty()) {
+        lineGroup = svg.insert('g', ':first-child')
+            .attr('class', 'external-lines-group');
+    }
+
+    // Respect the toggle state
+    lineGroup.style('display', showCallLines ? 'block' : 'none');
+
+    console.log(`[CallLines] Drawing lines for ${externalCallData.length} nodes with external calls`);
+
+    let linesDrawn = 0;
+    externalCallData.forEach(data => {
+        const sourcePos = getPositionWithFallback(data.nodeId);
+        if (!sourcePos) {
+            console.log(`[CallLines] No source position for ${data.nodeId}`);
+            return;
+        }
+
+        // Draw lines to inbound nodes (callers) - dashed blue (fainter)
+        data.inboundNodes.forEach(caller => {
+            const targetPos = getPositionWithFallback(caller.id);
+            if (targetPos) {
+                lineGroup.append('path')
+                    .attr('class', 'external-call-line inbound-line')
+                    .attr('d', `M${targetPos.y},${targetPos.x} C${(targetPos.y + sourcePos.y)/2},${targetPos.x} ${(targetPos.y + sourcePos.y)/2},${sourcePos.x} ${sourcePos.y},${sourcePos.x}`)
+                    .attr('fill', 'none')
+                    .attr('stroke', '#58a6ff')
+                    .attr('stroke-width', 1)
+                    .attr('stroke-dasharray', '4,2')
+                    .attr('opacity', 0.35)
+                    .attr('pointer-events', 'none');
+                linesDrawn++;
+            }
+        });
+
+        // Draw lines to outbound nodes (callees) - dashed orange (fainter)
+        data.outboundNodes.forEach(callee => {
+            const targetPos = getPositionWithFallback(callee.id);
+            if (targetPos) {
+                lineGroup.append('path')
+                    .attr('class', 'external-call-line outbound-line')
+                    .attr('d', `M${sourcePos.y},${sourcePos.x} C${(sourcePos.y + targetPos.y)/2},${sourcePos.x} ${(sourcePos.y + targetPos.y)/2},${targetPos.x} ${targetPos.y},${targetPos.x}`)
+                    .attr('fill', 'none')
+                    .attr('stroke', '#f0883e')
+                    .attr('stroke-width', 1)
+                    .attr('stroke-dasharray', '4,2')
+                    .attr('opacity', 0.35)
+                    .attr('pointer-events', 'none');
+                linesDrawn++;
+            }
+        });
+    });
+
+    console.log(`[CallLines] Drew ${linesDrawn} call lines`);
+}
+
+// Draw external call lines for CIRCULAR layout
+// Converts polar coordinates (angle, radius) to Cartesian (x, y)
+function drawExternalCallLinesCircular(svg, root) {
+    // Remove existing external call lines
+    svg.selectAll('.external-call-line').remove();
+
+    // Helper: Convert polar to Cartesian coordinates
+    // In D3 radial layout: d.x = angle (radians), d.y = radius
+    function polarToCartesian(angle, radius) {
+        return {
+            x: radius * Math.cos(angle - Math.PI / 2),
+            y: radius * Math.sin(angle - Math.PI / 2)
+        };
+    }
+
+    // Build a map of node positions from the tree (visible nodes only)
+    const nodePositions = new Map();
+    root.descendants().forEach(d => {
+        const cartesian = polarToCartesian(d.x, d.y);
+        nodePositions.set(d.data.id, { x: cartesian.x, y: cartesian.y, angle: d.x, radius: d.y, node: d });
+    });
+
+    // Helper: Find position for a node, falling back to visible ancestors
+    function getPositionWithFallback(nodeId) {
+        // First check if node is directly visible
+        if (nodePositions.has(nodeId)) {
+            return nodePositions.get(nodeId);
+        }
+
+        // Node not visible - try to find via tree traversal
+        const targetNode = allNodes.find(n => n.id === nodeId);
+        if (!targetNode) {
+            return null;
+        }
+
+        // Look for the file that contains this chunk
+        if (targetNode.file_path) {
+            // Look for visible file nodes that match this path
+            for (const [id, pos] of nodePositions) {
+                const visibleNode = allNodes.find(n => n.id === id);
+                if (visibleNode) {
+                    if (visibleNode.type === 'file' &&
+                        (visibleNode.path === targetNode.file_path ||
+                         visibleNode.file_path === targetNode.file_path ||
+                         visibleNode.name === targetNode.file_path.split('/').pop())) {
+                        return pos;
+                    }
+                }
+            }
+
+            // Look for directory containing the file
+            const pathParts = targetNode.file_path.split('/');
+            for (let i = pathParts.length - 1; i >= 0; i--) {
+                const dirName = pathParts[i];
+                if (!dirName) continue;
+
+                for (const [id, pos] of nodePositions) {
+                    const visibleNode = allNodes.find(n => n.id === id);
+                    if (visibleNode && visibleNode.type === 'directory' && visibleNode.name === dirName) {
+                        return pos;
+                    }
+                }
+            }
+        }
+
+        return null;
+    }
+
+    // Create a group for external call lines (behind nodes)
+    let lineGroup = svg.select('.external-lines-group');
+    if (lineGroup.empty()) {
+        lineGroup = svg.insert('g', ':first-child')
+            .attr('class', 'external-lines-group');
+    }
+
+    // Respect the toggle state
+    lineGroup.style('display', showCallLines ? 'block' : 'none');
+
+    console.log(`[CallLines Circular] Drawing lines for ${externalCallData.length} nodes with external calls`);
+
+    let linesDrawn = 0;
+    externalCallData.forEach(data => {
+        const sourcePos = getPositionWithFallback(data.nodeId);
+        if (!sourcePos) {
+            return;
+        }
+
+        // Draw lines to inbound nodes (callers) - dashed blue (fainter)
+        data.inboundNodes.forEach(caller => {
+            const targetPos = getPositionWithFallback(caller.id);
+            if (targetPos) {
+                // Use quadratic bezier curves that go through the center for circular layout
+                const midX = (sourcePos.x + targetPos.x) / 2 * 0.3;
+                const midY = (sourcePos.y + targetPos.y) / 2 * 0.3;
+
+                lineGroup.append('path')
+                    .attr('class', 'external-call-line inbound-line')
+                    .attr('d', `M${targetPos.x},${targetPos.y} Q${midX},${midY} ${sourcePos.x},${sourcePos.y}`)
+                    .attr('fill', 'none')
+                    .attr('stroke', '#58a6ff')
+                    .attr('stroke-width', 1)
+                    .attr('stroke-dasharray', '4,2')
+                    .attr('opacity', 0.35)
+                    .attr('pointer-events', 'none');
+                linesDrawn++;
+            }
+        });
+
+        // Draw lines to outbound nodes (callees) - dashed orange (fainter)
+        data.outboundNodes.forEach(callee => {
+            const targetPos = getPositionWithFallback(callee.id);
+            if (targetPos) {
+                // Use quadratic bezier curves that go through the center for circular layout
+                const midX = (sourcePos.x + targetPos.x) / 2 * 0.3;
+                const midY = (sourcePos.y + targetPos.y) / 2 * 0.3;
+
+                lineGroup.append('path')
+                    .attr('class', 'external-call-line outbound-line')
+                    .attr('d', `M${sourcePos.x},${sourcePos.y} Q${midX},${midY} ${targetPos.x},${targetPos.y}`)
+                    .attr('fill', 'none')
+                    .attr('stroke', '#f0883e')
+                    .attr('stroke-width', 1)
+                    .attr('stroke-dasharray', '4,2')
+                    .attr('opacity', 0.35)
+                    .attr('pointer-events', 'none');
+                linesDrawn++;
+            }
+        });
+    });
+
+    console.log(`[CallLines Circular] Drew ${linesDrawn} call lines`);
+}
+
+// Get color based on complexity (darker = more complex)
+// Uses HSL color model for smooth gradients
+function getComplexityColor(d, baseHue) {
+    const nodeData = d.data;
+    const complexity = nodeData.complexity;
+
+    // If no complexity data, return a default based on type
+    if (complexity === undefined || complexity === null) {
+        // Default colors for non-complex nodes
+        if (nodeData.type === 'directory') {
+            return nodeData._children ? '#f39c12' : '#3498db';  // Orange/Blue
+        } else if (nodeData.type === 'file') {
+            return nodeData._children ? '#95a5a6' : '#ecf0f1';  // Gray/White
+        } else if (chunkTypes.includes(nodeData.type)) {
+            return '#9b59b6';  // Default purple
+        }
+        return '#95a5a6';
+    }
+
+    // Complexity ranges: 0-5 (low), 5-10 (medium), 10-20 (high), 20+ (very high)
+    // Map to lightness: 70% (light) to 30% (dark)
+    const maxComplexity = 25;  // Cap for scaling
+    const normalizedComplexity = Math.min(complexity, maxComplexity) / maxComplexity;
+
+    // Lightness goes from 65% (low complexity) to 35% (high complexity)
+    const lightness = 65 - (normalizedComplexity * 30);
+
+    // Saturation increases slightly with complexity (60% to 80%)
+    const saturation = 60 + (normalizedComplexity * 20);
+
+    return `hsl(${baseHue}, ${saturation}%, ${lightness}%)`;
+}
+
+// Get node fill color with complexity shading
+function getNodeFillColor(d) {
+    const nodeData = d.data;
+
+    if (nodeData.type === 'directory') {
+        // Orange (30°) if collapsed, Blue (210°) if expanded
+        const hue = nodeData._children ? 30 : 210;
+        // Directories aggregate complexity from children
+        const avgComplexity = calculateAverageComplexity(nodeData);
+        if (avgComplexity > 0) {
+            const lightness = 55 - (Math.min(avgComplexity, 15) / 15) * 20;
+            return `hsl(${hue}, 70%, ${lightness}%)`;
+        }
+        return nodeData._children ? '#f39c12' : '#3498db';
+    } else if (nodeData.type === 'file') {
+        // Gray files, but show complexity if available
+        const avgComplexity = calculateAverageComplexity(nodeData);
+        if (avgComplexity > 0) {
+            // Gray hue (0° with 0 saturation) to slight red tint for complexity
+            const saturation = Math.min(avgComplexity, 15) * 2;  // 0-30%
+            const lightness = 70 - (Math.min(avgComplexity, 15) / 15) * 25;
+            return `hsl(0, ${saturation}%, ${lightness}%)`;
+        }
+        return nodeData._children ? '#95a5a6' : '#ecf0f1';
+    } else if (chunkTypes.includes(nodeData.type)) {
+        // Purple (280°) for chunks, darker with higher complexity
+        return getComplexityColor(d, 280);
+    }
+
+    return '#95a5a6';
+}
+
+// Calculate average complexity for a node (recursively for dirs/files)
+function calculateAverageComplexity(node) {
+    if (chunkTypes.includes(node.type)) {
+        return node.complexity || 0;
+    }
+
+    const children = node.children || node._children || [];
+    if (children.length === 0) return 0;
+
+    let totalComplexity = 0;
+    let count = 0;
+
+    children.forEach(child => {
+        if (chunkTypes.includes(child.type) && child.complexity) {
+            totalComplexity += child.complexity;
+            count++;
+        } else {
+            const childAvg = calculateAverageComplexity(child);
+            if (childAvg > 0) {
+                totalComplexity += childAvg;
+                count++;
+            }
+        }
+    });
+
+    return count > 0 ? totalComplexity / count : 0;
+}
+
+// Get stroke color based on complexity - red outline for high complexity
+function getNodeStrokeColor(d) {
+    const nodeData = d.data;
+
+    // Only chunks have direct complexity
+    if (chunkTypes.includes(nodeData.type)) {
+        const complexity = nodeData.complexity || 0;
+        // Complexity thresholds:
+        // 0-5: white (simple)
+        // 5-10: orange (moderate)
+        // 10+: red (complex)
+        if (complexity >= 10) {
+            return '#e74c3c';  // Red for high complexity
+        } else if (complexity >= 5) {
+            return '#f39c12';  // Orange for moderate
+        }
+        return '#fff';  // White for low complexity
+    }
+
+    // Files and directories: check average complexity of children
+    if (nodeData.type === 'file' || nodeData.type === 'directory') {
+        const avgComplexity = calculateAverageComplexity(nodeData);
+        if (avgComplexity >= 10) {
+            return '#e74c3c';  // Red
+        } else if (avgComplexity >= 5) {
+            return '#f39c12';  // Orange
+        }
+    }
+
+    return '#fff';  // Default white
+}
+
+// Get stroke width based on complexity - thicker for high complexity
+function getNodeStrokeWidth(d) {
+    const nodeData = d.data;
+    const complexity = chunkTypes.includes(nodeData.type)
+        ? (nodeData.complexity || 0)
+        : calculateAverageComplexity(nodeData);
+
+    if (complexity >= 10) return 3;  // Thick red outline
+    if (complexity >= 5) return 2.5;  // Medium orange outline
+    return 2;  // Default
+}
+
+function getNodeRadius(d) {
+    const nodeData = d.data;
+
+    // Size configuration based on node type
+    const dirMinRadius = 8;   // Min for directories
+    const dirMaxRadius = 40;  // Max for directories
+    const fileMinRadius = 6;  // Min for files
+    const fileMaxRadius = 30; // Max for files
+    const chunkMinRadius = sizeConfig.chunkMinRadius;  // From config
+    const chunkMaxRadius = sizeConfig.chunkMaxRadius;  // From config
+
+    // Directory nodes: size by file_count (logarithmic scale)
+    if (nodeData.type === 'directory') {
+        const fileCount = nodeData.file_count || 0;
+        if (fileCount === 0) return dirMinRadius;
+
+        // Logarithmic scale: log2(fileCount + 1) for smooth scaling
+        // +1 to avoid log(0), gives range [1, log2(max_files+1)]
+        const logCount = Math.log2(fileCount + 1);
+        const maxLogCount = Math.log2(100 + 1);  // Assume max ~100 files per dir
+        const normalized = Math.min(logCount / maxLogCount, 1.0);
+
+        return dirMinRadius + (normalized * (dirMaxRadius - dirMinRadius));
+    }
+
+    // File nodes: size by total lines of code (sum of all chunks)
+    if (nodeData.type === 'file') {
+        const lineCount = nodeData._lineCount || 1;
+
+        // Collapsed file+chunk: use chunk sizing (since it's really a chunk)
+        if (nodeData.collapsed_chunk) {
+            const minLines = 5;
+            const maxLines = 150;
+
+            let normalized;
+            if (lineCount <= minLines) {
+                normalized = 0;
+            } else if (lineCount >= maxLines) {
+                normalized = 1;
+            } else {
+                const logMin = Math.log(minLines);
+                const logMax = Math.log(maxLines);
+                const logCount = Math.log(lineCount);
+                normalized = (logCount - logMin) / (logMax - logMin);
+            }
+            return chunkMinRadius + (normalized * (chunkMaxRadius - chunkMinRadius));
+        }
+
+        // Regular files: linear scaling based on total lines
+        const minFileLines = 5;
+        const maxFileLines = 300;
+
+        let normalized;
+        if (lineCount <= minFileLines) {
+            normalized = 0;
+        } else if (lineCount >= maxFileLines) {
+            normalized = 1;
+        } else {
+            normalized = (lineCount - minFileLines) / (maxFileLines - minFileLines);
+        }
+
+        return fileMinRadius + (normalized * (fileMaxRadius - fileMinRadius));
+    }
+
+    // Chunk nodes: size by lines of code (absolute thresholds, not percentiles)
+    // This ensures 330-line functions are ALWAYS big, regardless of codebase distribution
+    if (chunkTypes.includes(nodeData.type)) {
+        const lineCount = nodeData._lineCount || 1;
+
+        // Absolute thresholds for intuitive sizing:
+        // - 1-10 lines: small (imports, constants, simple functions)
+        // - 10-50 lines: medium (typical functions)
+        // - 50-150 lines: large (complex functions)
+        // - 150+ lines: maximum (very large functions/classes)
+        const minLines = 5;
+        const maxLines = 150;  // Anything over 150 lines gets max size
+
+        let normalized;
+        if (lineCount <= minLines) {
+            normalized = 0;
+        } else if (lineCount >= maxLines) {
+            normalized = 1;
+        } else {
+            // Logarithmic scaling for better visual distribution
+            const logMin = Math.log(minLines);
+            const logMax = Math.log(maxLines);
+            const logCount = Math.log(lineCount);
+            normalized = (logCount - logMin) / (logMax - logMin);
+        }
+
+        return chunkMinRadius + (normalized * (chunkMaxRadius - chunkMinRadius));
+    }
+
+    // Default fallback for other node types
+    return sizeConfig.minRadius;
+}
+
+// ============================================================================
+// VISUALIZATION RENDERING
+// ============================================================================
+
+function renderVisualization() {
+    console.log('=== RENDER VISUALIZATION ===');
+    console.log(`Current layout: ${currentLayout}`);
+    console.log(`Tree data exists: ${treeData !== null}`);
+    if (treeData) {
+        console.log(`Root node: ${treeData.name}, children: ${(treeData.children || []).length}, _children: ${(treeData._children || []).length}`);
+    }
+
+    // Clear existing content
+    const graphElement = d3.select('#graph');
+    console.log(`Graph element found: ${!graphElement.empty()}`);
+    graphElement.selectAll('*').remove();
+
+    if (currentLayout === 'linear') {
+        console.log('Calling renderLinearTree()...');
+        renderLinearTree();
+    } else {
+        console.log('Calling renderCircularTree()...');
+        renderCircularTree();
+    }
+    console.log('=== END RENDER VISUALIZATION ===');
+}
+
+// ============================================================================
+// LINEAR TREE LAYOUT
+// ============================================================================
+
+function renderLinearTree() {
+    console.log('=== RENDER LINEAR TREE ===');
+    const { width, height } = getViewportDimensions();
+    console.log(`Viewport dimensions: ${width}x${height}`);
+
+    const svg = d3.select('#graph')
+        .attr('width', width)
+        .attr('height', height);
+
+    const g = svg.append('g')
+        .attr('transform', `translate(${margin.left},${margin.top})`);
+
+    // Create tree layout
+    // For horizontal tree: size is [height, width] where height controls vertical spread
+    const treeLayout = d3.tree()
+        .size([height - margin.top - margin.bottom, width - margin.left - margin.right]);
+
+    console.log(`Tree layout size: ${height - margin.top - margin.bottom} x ${width - margin.left - margin.right}`);
+
+    // Create hierarchy from tree data
+    // D3 hierarchy automatically respects children vs _children
+    console.log('Creating D3 hierarchy...');
+
+    // DEBUG: Check if treeData children have content property BEFORE D3 processes them
+    console.log('=== PRE-D3 HIERARCHY DEBUG ===');
+    if (treeData.children && treeData.children.length > 0) {
+        const firstChild = treeData.children[0];
+        console.log('First root child:', firstChild.name, 'type:', firstChild.type);
+        console.log('First child keys:', Object.keys(firstChild));
+        console.log('First child has content:', 'content' in firstChild);
+
+        // Find a chunk node in the tree
+        function findFirstChunk(node) {
+            if (chunkTypes.includes(node.type)) {
+                return node;
+            }
+            if (node.children) {
+                for (const child of node.children) {
+                    const found = findFirstChunk(child);
+                    if (found) return found;
+                }
+            }
+            if (node._children) {
+                for (const child of node._children) {
+                    const found = findFirstChunk(child);
+                    if (found) return found;
+                }
+            }
+            return null;
+        }
+
+        const sampleChunk = findFirstChunk(treeData);
+        if (sampleChunk) {
+            console.log('Sample chunk node BEFORE D3:', sampleChunk.name, 'type:', sampleChunk.type);
+            console.log('Sample chunk keys:', Object.keys(sampleChunk));
+            console.log('Sample chunk has content:', 'content' in sampleChunk);
+            console.log('Sample chunk content length:', sampleChunk.content ? sampleChunk.content.length : 0);
+        }
+    }
+    console.log('=== END PRE-D3 HIERARCHY DEBUG ===');
+
+    const root = d3.hierarchy(treeData, d => d.children);
+    console.log(`Hierarchy created: ${root.descendants().length} nodes`);
+
+    // DEBUG: Check if content is preserved AFTER D3 processes them
+    console.log('=== POST-D3 HIERARCHY DEBUG ===');
+    const debugDescendants = root.descendants();
+    const chunkDescendants = debugDescendants.filter(d => chunkTypes.includes(d.data.type));
+    console.log(`Found ${chunkDescendants.length} chunk nodes in D3 hierarchy`);
+    if (chunkDescendants.length > 0) {
+        const firstChunkD3 = chunkDescendants[0];
+        console.log('First chunk in D3 hierarchy:', firstChunkD3.data.name, 'type:', firstChunkD3.data.type);
+        console.log('First chunk d.data keys:', Object.keys(firstChunkD3.data));
+        console.log('First chunk has content in d.data:', 'content' in firstChunkD3.data);
+        console.log('First chunk content length:', firstChunkD3.data.content ? firstChunkD3.data.content.length : 0);
+    }
+    console.log('=== END POST-D3 HIERARCHY DEBUG ===');
+
+    // Apply tree layout
+    console.log('Applying tree layout...');
+    treeLayout(root);
+    console.log('Tree layout applied');
+
+    // Add zoom behavior
+    const zoom = d3.zoom()
+        .scaleExtent([0.1, 3])
+        .on('zoom', (event) => {
+            g.attr('transform', `translate(${margin.left},${margin.top}) ${event.transform}`);
+        });
+
+    svg.call(zoom);
+
+    // Draw links
+    const links = root.links();
+    console.log(`Drawing ${links.length} links`);
+    g.selectAll('.link')
+        .data(links)
+        .enter()
+        .append('path')
+        .attr('class', 'link')
+        .attr('d', d3.linkHorizontal()
+            .x(d => d.y)
+            .y(d => d.x))
+        .attr('fill', 'none')
+        .attr('stroke', '#ccc')
+        .attr('stroke-width', 1.5);
+
+    // Draw nodes
+    const descendants = root.descendants();
+    console.log(`Drawing ${descendants.length} nodes`);
+    const nodes = g.selectAll('.node')
+        .data(descendants)
+        .enter()
+        .append('g')
+        .attr('class', 'node')
+        .attr('transform', d => `translate(${d.y},${d.x})`)
+        .on('click', handleNodeClick)
+        .style('cursor', 'pointer');
+
+    console.log(`Created ${nodes.size()} node elements`);
+
+    // Node circles - sized proportionally to content, colored by complexity
+    nodes.append('circle')
+        .attr('r', d => getNodeRadius(d))  // Dynamic size based on content
+        .attr('fill', d => getNodeFillColor(d))  // Complexity-based coloring
+        .attr('stroke', d => getNodeStrokeColor(d))  // Red/orange for high complexity
+        .attr('stroke-width', d => getNodeStrokeWidth(d))
+        .attr('class', d => {
+            // Add complexity grade class if available
+            const grade = d.data.complexity_grade || '';
+            const hasSmells = (d.data.smell_count && d.data.smell_count > 0) || (d.data.smells && d.data.smells.length > 0);
+            const classes = [];
+            if (grade) classes.push(`grade-${grade}`);
+            if (hasSmells) classes.push('has-smells');
+            return classes.join(' ');
+        });
+
+    // Add external call arrow indicators (only for chunk nodes)
+    nodes.each(function(d) {
+        const node = d3.select(this);
+        const nodeData = d.data;
+
+        // Only add indicators for code chunks (functions, classes, methods)
+        if (!chunkTypes.includes(nodeData.type)) return;
+
+        const counts = getExternalCallCounts(nodeData);
+        const radius = getNodeRadius(d);
+
+        // Inbound arrow: ← before the node (functions from other files call this)
+        if (counts.inbound > 0) {
+            node.append('text')
+                .attr('class', 'call-indicator inbound')
+                .attr('x', -(radius + 8))
+                .attr('y', 5)
+                .attr('text-anchor', 'end')
+                .attr('fill', '#58a6ff')
+                .attr('font-size', '14px')
+                .attr('font-weight', 'bold')
+                .attr('cursor', 'pointer')
+                .text(counts.inbound > 1 ? `${counts.inbound}←` : '←')
+                .append('title')
+                .text(`Called by ${counts.inbound} external function(s):\n${counts.inboundNodes.map(n => n.name).join(', ')}`);
+        }
+
+        // Outbound arrow: → after the label (this calls functions in other files)
+        if (counts.outbound > 0) {
+            // Get approximate label width
+            const labelText = nodeData.name || '';
+            const labelWidth = labelText.length * 7;
+
+            node.append('text')
+                .attr('class', 'call-indicator outbound')
+                .attr('x', radius + labelWidth + 16)
+                .attr('y', 5)
+                .attr('text-anchor', 'start')
+                .attr('fill', '#f0883e')
+                .attr('font-size', '14px')
+                .attr('font-weight', 'bold')
+                .attr('cursor', 'pointer')
+                .text(counts.outbound > 1 ? `→${counts.outbound}` : '→')
+                .append('title')
+                .text(`Calls ${counts.outbound} external function(s):\n${counts.outboundNodes.map(n => n.name).join(', ')}`);
+        }
+    });
+
+    // Collect and draw external call lines
+    collectExternalCallData();
+    drawExternalCallLines(g, root);
+
+    // Node labels - positioned to the right of node, left-aligned
+    // Use transform to position text, as x attribute can have rendering issues
+    const labels = nodes.append('text')
+        .attr('class', 'node-label')
+        .attr('transform', d => `translate(${getNodeRadius(d) + 6}, 0)`)
+        .attr('dominant-baseline', 'middle')
+        .attr('text-anchor', 'start')
+        .text(d => d.data.name)
+        .style('font-size', d => chunkTypes.includes(d.data.type) ? '15px' : '18px')
+        .style('font-family', 'Arial, sans-serif')
+        .style('fill', d => chunkTypes.includes(d.data.type) ? '#bb86fc' : '#adbac7')
+        .style('cursor', 'pointer')
+        .style('pointer-events', 'all')
+        .on('click', handleNodeClick);
+
+    console.log(`Created ${labels.size()} label elements`);
+    console.log('=== END RENDER LINEAR TREE ===');
+}
+
+// ============================================================================
+// CIRCULAR TREE LAYOUT
+// ============================================================================
+
+function renderCircularTree() {
+    const { width, height } = getViewportDimensions();
+    const svg = d3.select('#graph')
+        .attr('width', width)
+        .attr('height', height);
+
+    const radius = Math.min(width, height) / 2 - 100;
+
+    const g = svg.append('g')
+        .attr('transform', `translate(${width/2},${height/2})`);
+
+    // Create radial tree layout
+    const treeLayout = d3.tree()
+        .size([2 * Math.PI, radius])
+        .separation((a, b) => (a.parent === b.parent ? 1 : 2) / a.depth);
+
+    // Create hierarchy
+    // D3 hierarchy automatically respects children vs _children
+    const root = d3.hierarchy(treeData, d => d.children);
+
+    // Apply layout
+    treeLayout(root);
+
+    // Add zoom behavior
+    const zoom = d3.zoom()
+        .scaleExtent([0.1, 3])
+        .on('zoom', (event) => {
+            g.attr('transform', `translate(${width/2},${height/2}) ${event.transform}`);
+        });
+
+    svg.call(zoom);
+
+    // Draw links
+    g.selectAll('.link')
+        .data(root.links())
+        .enter()
+        .append('path')
+        .attr('class', 'link')
+        .attr('d', d3.linkRadial()
+            .angle(d => d.x)
+            .radius(d => d.y))
+        .attr('fill', 'none')
+        .attr('stroke', '#ccc')
+        .attr('stroke-width', 1.5);
+
+    // Draw nodes
+    const nodes = g.selectAll('.node')
+        .data(root.descendants())
+        .enter()
+        .append('g')
+        .attr('class', 'node')
+        .attr('transform', d => `
+            rotate(${d.x * 180 / Math.PI - 90})
+            translate(${d.y},0)
+        `)
+        .on('click', handleNodeClick)
+        .style('cursor', 'pointer');
+
+    // Node circles - sized proportionally to content, colored by complexity
+    nodes.append('circle')
+        .attr('r', d => getNodeRadius(d))  // Dynamic size based on content
+        .attr('fill', d => getNodeFillColor(d))  // Complexity-based coloring
+        .attr('stroke', d => getNodeStrokeColor(d))  // Red/orange for high complexity
+        .attr('stroke-width', d => getNodeStrokeWidth(d))
+        .attr('class', d => {
+            // Add complexity grade class if available
+            const grade = d.data.complexity_grade || '';
+            const hasSmells = (d.data.smell_count && d.data.smell_count > 0) || (d.data.smells && d.data.smells.length > 0);
+            const classes = [];
+            if (grade) classes.push(`grade-${grade}`);
+            if (hasSmells) classes.push('has-smells');
+            return classes.join(' ');
+        });
+
+    // Add external call arrow indicators (only for chunk nodes)
+    nodes.each(function(d) {
+        const node = d3.select(this);
+        const nodeData = d.data;
+
+        if (!chunkTypes.includes(nodeData.type)) return;
+
+        const counts = getExternalCallCounts(nodeData);
+        const radius = getNodeRadius(d);
+
+        // Inbound indicator
+        if (counts.inbound > 0) {
+            node.append('text')
+                .attr('x', 0)
+                .attr('y', -(radius + 8))
+                .attr('text-anchor', 'middle')
+                .attr('fill', '#58a6ff')
+                .attr('font-size', '10px')
+                .attr('font-weight', 'bold')
+                .text(counts.inbound > 1 ? `↓${counts.inbound}` : '↓')
+                .append('title')
+                .text(`Called by ${counts.inbound} external function(s)`);
+        }
+
+        // Outbound indicator
+        if (counts.outbound > 0) {
+            node.append('text')
+                .attr('x', 0)
+                .attr('y', radius + 12)
+                .attr('text-anchor', 'middle')
+                .attr('fill', '#f0883e')
+                .attr('font-size', '10px')
+                .attr('font-weight', 'bold')
+                .text(counts.outbound > 1 ? `↑${counts.outbound}` : '↑')
+                .append('title')
+                .text(`Calls ${counts.outbound} external function(s)`);
+        }
+    });
+
+    // Node labels - positioned to the right of node, left-aligned
+    // Use transform to position text, as x attribute can have rendering issues
+    nodes.append('text')
+        .attr('class', 'node-label')
+        .attr('transform', d => {
+            const offset = getNodeRadius(d) + 6;
+            const rotate = d.x >= Math.PI ? 'rotate(180)' : '';
+            return `translate(${offset}, 0) ${rotate}`;
+        })
+        .attr('dominant-baseline', 'middle')
+        .attr('text-anchor', d => d.x >= Math.PI ? 'end' : 'start')
+        .text(d => d.data.name)
+        .style('font-size', d => chunkTypes.includes(d.data.type) ? '15px' : '18px')
+        .style('font-family', 'Arial, sans-serif')
+        .style('fill', d => chunkTypes.includes(d.data.type) ? '#bb86fc' : '#adbac7')
+        .style('cursor', 'pointer')
+        .style('pointer-events', 'all')
+        .on('click', handleNodeClick);
+
+    // Collect and draw external call lines (circular version)
+    collectExternalCallData();
+    drawExternalCallLinesCircular(g, root);
+}
+
+// ============================================================================
+// INTERACTION HANDLERS
+// ============================================================================
+
+function handleNodeClick(event, d) {
+    event.stopPropagation();
+
+    const nodeData = d.data;
+
+    console.log('=== NODE CLICK DEBUG ===');
+    console.log(`Clicked node: ${nodeData.name} (type: ${nodeData.type}, id: ${nodeData.id})`);
+    console.log(`Has children: ${nodeData.children ? nodeData.children.length : 0}`);
+    console.log(`Has _children: ${nodeData._children ? nodeData._children.length : 0}`);
+
+    if (nodeData.type === 'directory') {
+        // Toggle directory: swap children <-> _children
+        if (nodeData.children) {
+            // Currently expanded - collapse it
+            console.log('Collapsing directory');
+            nodeData._children = nodeData.children;
+            nodeData.children = null;
+        } else if (nodeData._children) {
+            // Currently collapsed - expand it
+            console.log('Expanding directory');
+            nodeData.children = nodeData._children;
+            nodeData._children = null;
+        }
+
+        // Re-render to show/hide children
+        renderVisualization();
+
+        // Don't auto-open viewer panel for directories - just expand/collapse
+    } else if (nodeData.type === 'file') {
+        // Check if this file has a collapsed chunk (single chunk with no children)
+        if (nodeData.collapsed_chunk) {
+            console.log(`Collapsed file+chunk: ${nodeData.name}, showing content directly`);
+            displayChunkContent({
+                ...nodeData.collapsed_chunk,
+                name: nodeData.collapsed_chunk.name,
+                type: nodeData.collapsed_chunk.type
+            });
+            return;
+        }
+
+        // Check if this is a single-chunk file - skip to content directly
+        const childrenArray = nodeData._children || nodeData.children;
+
+        if (childrenArray && childrenArray.length === 1) {
+            const onlyChild = childrenArray[0];
+
+            if (chunkTypes.includes(onlyChild.type)) {
+                console.log(`Single-chunk file: ${nodeData.name}, showing content directly`);
+
+                // Expand the file visually (for tree consistency)
+                if (nodeData._children) {
+                    nodeData.children = nodeData._children;
+                    nodeData._children = null;
+                    renderVisualization();
+                }
+
+                // Auto-display the chunk content
+                displayChunkContent(onlyChild);
+                return; // Skip normal file toggle behavior
+            }
+        }
+
+        // Continue with existing toggle logic for multi-chunk files
+        // Toggle file: swap children <-> _children
+        if (nodeData.children) {
+            // Currently expanded - collapse it
+            console.log('Collapsing file');
+            nodeData._children = nodeData.children;
+            nodeData.children = null;
+        } else if (nodeData._children) {
+            // Currently collapsed - expand it
+            console.log('Expanding file');
+            nodeData.children = nodeData._children;
+            nodeData._children = null;
+        } else {
+            console.log('WARNING: File has neither children nor _children!');
+        }
+
+        // Re-render to show/hide children
+        renderVisualization();
+
+        // Don't auto-open viewer panel for files - just expand/collapse
+    } else if (chunkTypes.includes(nodeData.type)) {
+        // Chunks can have children too (e.g., imports -> functions, class -> methods)
+        // If chunk has children, toggle expand/collapse
+        if (nodeData.children || nodeData._children) {
+            if (nodeData.children) {
+                // Currently expanded - collapse it
+                console.log(`Collapsing ${nodeData.type} chunk`);
+                nodeData._children = nodeData.children;
+                nodeData.children = null;
+            } else if (nodeData._children) {
+                // Currently collapsed - expand it
+                console.log(`Expanding ${nodeData.type} chunk to show ${nodeData._children.length} children`);
+                nodeData.children = nodeData._children;
+                nodeData._children = null;
+            }
+            // Re-render to show/hide children
+            renderVisualization();
+        }
+
+        // Also show chunk content in side panel
+        console.log('Displaying chunk content');
+        displayChunkContent(nodeData);
+    }
+
+    console.log('=== END NODE CLICK DEBUG ===');
+}
+
+function displayDirectoryInfo(dirData, addToHistory = true) {
+    openViewerPanel();
+
+    // Add to navigation history
+    if (addToHistory) {
+        addToNavHistory({type: 'directory', data: dirData});
+    }
+
+    const title = document.getElementById('viewer-title');
+    const content = document.getElementById('viewer-content');
+
+    title.textContent = `📁 ${dirData.name}`;
+
+    // Count children
+    const children = dirData.children || dirData._children || [];
+    const dirs = children.filter(c => c.type === 'directory').length;
+    const files = children.filter(c => c.type === 'file').length;
+
+    let html = '';
+
+    // Navigation bar with breadcrumbs and back/forward
+    html += renderNavigationBar(dirData);
+
+    html += '<div class="viewer-section">';
+    html += '<div class="viewer-section-title">Directory Information</div>';
+    html += '<div class="viewer-info-grid">';
+    html += `<div class="viewer-info-row">`;
+    html += `<span class="viewer-info-label">Name:</span>`;
+    html += `<span class="viewer-info-value">${escapeHtml(dirData.name)}</span>`;
+    html += `</div>`;
+    html += `<div class="viewer-info-row">`;
+    html += `<span class="viewer-info-label">Subdirectories:</span>`;
+    html += `<span class="viewer-info-value">${dirs}</span>`;
+    html += `</div>`;
+    html += `<div class="viewer-info-row">`;
+    html += `<span class="viewer-info-label">Files:</span>`;
+    html += `<span class="viewer-info-value">${files}</span>`;
+    html += `</div>`;
+    html += `<div class="viewer-info-row">`;
+    html += `<span class="viewer-info-label">Total Items:</span>`;
+    html += `<span class="viewer-info-value">${children.length}</span>`;
+    html += `</div>`;
+    html += '</div>';
+    html += '</div>';
+
+    if (children.length > 0) {
+        html += '<div class="viewer-section">';
+        html += '<div class="viewer-section-title">Contents</div>';
+        html += '<div class="dir-list">';
+
+        // Sort: directories first, then files
+        const sortedChildren = [...children].sort((a, b) => {
+            if (a.type === 'directory' && b.type !== 'directory') return -1;
+            if (a.type !== 'directory' && b.type === 'directory') return 1;
+            return a.name.localeCompare(b.name);
+        });
+
+        sortedChildren.forEach(child => {
+            const icon = child.type === 'directory' ? '📁' : '📄';
+            const type = child.type === 'directory' ? 'dir' : 'file';
+            const childData = JSON.stringify(child).replace(/"/g, '&quot;');
+            const clickHandler = child.type === 'directory'
+                ? `navigateToDirectory(${childData})`
+                : `navigateToFile(${childData})`;
+            html += `<div class="dir-list-item clickable" onclick="${clickHandler}">`;
+            html += `<span class="dir-icon">${icon}</span>`;
+            html += `<span class="dir-name">${escapeHtml(child.name)}</span>`;
+            html += `<span class="dir-type">${type}</span>`;
+            html += `<span class="dir-arrow">→</span>`;
+            html += `</div>`;
+        });
+
+        html += '</div>';
+        html += '</div>';
+    }
+
+    content.innerHTML = html;
+
+    // Hide section dropdown for directories (no code sections)
+    populateSectionDropdown([]);
+}
+
+function displayFileInfo(fileData, addToHistory = true) {
+    openViewerPanel();
+
+    // Add to navigation history
+    if (addToHistory) {
+        addToNavHistory({type: 'file', data: fileData});
+    }
+
+    const title = document.getElementById('viewer-title');
+    const content = document.getElementById('viewer-content');
+
+    title.textContent = `📄 ${fileData.name}`;
+
+    // Get chunks
+    const chunks = fileData.children || fileData._children || [];
+
+    let html = '';
+
+    // Navigation bar with breadcrumbs and back/forward
+    html += renderNavigationBar(fileData);
+
+    html += '<div class="viewer-section">';
+    html += '<div class="viewer-section-title">File Information</div>';
+    html += '<div class="viewer-info-grid">';
+    html += `<div class="viewer-info-row">`;
+    html += `<span class="viewer-info-label">Name:</span>`;
+    html += `<span class="viewer-info-value">${escapeHtml(fileData.name)}</span>`;
+    html += `</div>`;
+    html += `<div class="viewer-info-row">`;
+    html += `<span class="viewer-info-label">Chunks:</span>`;
+    html += `<span class="viewer-info-value">${chunks.length}</span>`;
+    html += `</div>`;
+    if (fileData.path) {
+        html += `<div class="viewer-info-row">`;
+        html += `<span class="viewer-info-label">Path:</span>`;
+        html += `<span class="viewer-info-value" style="word-break: break-all;">${escapeHtml(fileData.path)}</span>`;
+        html += `</div>`;
+    }
+    html += '</div>';
+    html += '</div>';
+
+    if (chunks.length > 0) {
+        html += '<div class="viewer-section">';
+        html += '<div class="viewer-section-title">Code Chunks</div>';
+        html += '<div class="chunk-list">';
+
+        chunks.forEach(chunk => {
+            const icon = getChunkIcon(chunk.type);
+            const chunkName = chunk.name || chunk.type || 'chunk';
+            const lines = chunk.start_line && chunk.end_line
+                ? `Lines ${chunk.start_line}-${chunk.end_line}`
+                : 'Unknown lines';
+
+            html += `<div class="chunk-list-item" onclick="displayChunkContent(${JSON.stringify(chunk).replace(/"/g, '&quot;')})">`;
+            html += `<span class="chunk-icon">${icon}</span>`;
+            html += `<div class="chunk-info">`;
+            html += `<div class="chunk-name">${escapeHtml(chunkName)}</div>`;
+            html += `<div class="chunk-meta">${lines} • ${chunk.type || 'code'}</div>`;
+            html += `</div>`;
+            html += `</div>`;
+        });
+
+        html += '</div>';
+        html += '</div>';
+    }
+
+    content.innerHTML = html;
+
+    // Hide section dropdown for files (no code sections in file view)
+    populateSectionDropdown([]);
+}
+
+function displayChunkContent(chunkData, addToHistory = true) {
+    openViewerPanel();
+
+    // Expand path to node and highlight it in tree
+    if (chunkData.id) {
+        expandAndHighlightNode(chunkData.id);
+    }
+
+    // Add to navigation history
+    if (addToHistory) {
+        addToNavHistory({type: 'chunk', data: chunkData});
+    }
+
+    const title = document.getElementById('viewer-title');
+    const content = document.getElementById('viewer-content');
+
+    const chunkName = chunkData.name || chunkData.type || 'Chunk';
+    title.textContent = `${getChunkIcon(chunkData.type)} ${chunkName}`;
+
+    let html = '';
+
+    // Navigation bar with breadcrumbs and back/forward
+    html += renderNavigationBar(chunkData);
+
+    // Track sections for dropdown navigation
+    const sections = [];
+
+    // === ORDER: Docstring (comments), Code, Metadata ===
+
+    // === 1. Docstring Section (Comments) ===
+    if (chunkData.docstring) {
+        sections.push({ id: 'docstring', label: '📖 Docstring' });
+        html += '<div class="viewer-section" data-section="docstring">';
+        html += '<div class="viewer-section-title">📖 Docstring</div>';
+        html += `<div style="color: #8b949e; font-style: italic; padding: 8px 12px; background: #161b22; border-radius: 4px; white-space: pre-wrap;">${escapeHtml(chunkData.docstring)}</div>`;
+        html += '</div>';
+    }
+
+    // === 2. Source Code Section ===
+    if (chunkData.content) {
+        sections.push({ id: 'source-code', label: '📝 Source Code' });
+        html += '<div class="viewer-section" data-section="source-code">';
+        html += '<div class="viewer-section-title">📝 Source Code</div>';
+        const langClass = getLanguageClass(chunkData.file_path);
+        html += `<pre><code class="hljs${langClass ? ' language-' + langClass : ''}">${escapeHtml(chunkData.content)}</code></pre>`;
+        html += '</div>';
+    } else {
+        html += '<p style="color: #8b949e; padding: 20px; text-align: center;">No content available for this chunk.</p>';
+    }
+
+    // === 3. Metadata Section ===
+    sections.push({ id: 'metadata', label: 'ℹ️ Metadata' });
+    html += '<div class="viewer-section" data-section="metadata">';
+    html += '<div class="viewer-section-title">ℹ️ Metadata</div>';
+    html += '<div class="viewer-info-grid">';
+
+    // Basic info
+    html += `<div class="viewer-info-row">`;
+    html += `<span class="viewer-info-label">Name:</span>`;
+    html += `<span class="viewer-info-value">${escapeHtml(chunkName)}</span>`;
+    html += `</div>`;
+
+    html += `<div class="viewer-info-row">`;
+    html += `<span class="viewer-info-label">Type:</span>`;
+    html += `<span class="viewer-info-value">${escapeHtml(chunkData.type || 'code')}</span>`;
+    html += `</div>`;
+
+    // File path (clickable - navigates to file node)
+    if (chunkData.file_path) {
+        const shortPath = chunkData.file_path.split('/').slice(-3).join('/');
+        const escapedPath = escapeHtml(chunkData.file_path).replace(/'/g, "\\'");
+        html += `<div class="viewer-info-row">`;
+        html += `<span class="viewer-info-label">File:</span>`;
+        html += `<span class="viewer-info-value clickable" onclick="navigateToFileByPath('${escapedPath}')" title="Click to navigate to file: ${escapeHtml(chunkData.file_path)}">.../${escapeHtml(shortPath)}</span>`;
+        html += `</div>`;
+    }
+
+    // Line numbers
+    if (chunkData.start_line && chunkData.end_line) {
+        html += `<div class="viewer-info-row">`;
+        html += `<span class="viewer-info-label">Lines:</span>`;
+        html += `<span class="viewer-info-value">${chunkData.start_line} - ${chunkData.end_line} (${chunkData.end_line - chunkData.start_line + 1} lines)</span>`;
+        html += `</div>`;
+    }
+
+    // Language
+    if (chunkData.language) {
+        html += `<div class="viewer-info-row">`;
+        html += `<span class="viewer-info-label">Language:</span>`;
+        html += `<span class="viewer-info-value">${escapeHtml(chunkData.language)}</span>`;
+        html += `</div>`;
+    }
+
+    // Complexity
+    if (chunkData.complexity !== undefined && chunkData.complexity !== null) {
+        const complexityColor = chunkData.complexity > 10 ? '#f85149' : chunkData.complexity > 5 ? '#d29922' : '#3fb950';
+        html += `<div class="viewer-info-row">`;
+        html += `<span class="viewer-info-label">Complexity:</span>`;
+        html += `<span class="viewer-info-value" style="color: ${complexityColor}">${chunkData.complexity.toFixed(1)}</span>`;
+        html += `</div>`;
+    }
+
+    html += '</div>';
+    html += '</div>';
+
+    // === 4. External Calls & Callers Section (Cross-file references) ===
+    const chunkId = chunkData.id;
+    const currentFilePath = chunkData.file_path;
+
+    if (chunkId) {
+        // Find all caller relationships
+        const allCallers = allLinks.filter(l => l.type === 'caller' && l.target === chunkId);
+        const allCallees = allLinks.filter(l => l.type === 'caller' && l.source === chunkId);
+
+        // Separate external (different file) from local (same file) relationships
+        // Use Maps to deduplicate by node.id
+        const externalCallersMap = new Map();
+        const localCallersMap = new Map();
+        allCallers.forEach(link => {
+            const callerNode = allNodes.find(n => n.id === link.source);
+            if (callerNode) {
+                if (callerNode.file_path !== currentFilePath) {
+                    if (!externalCallersMap.has(callerNode.id)) {
+                        externalCallersMap.set(callerNode.id, { link, node: callerNode });
+                    }
+                } else {
+                    if (!localCallersMap.has(callerNode.id)) {
+                        localCallersMap.set(callerNode.id, { link, node: callerNode });
+                    }
+                }
+            }
+        });
+        const externalCallers = Array.from(externalCallersMap.values());
+        const localCallers = Array.from(localCallersMap.values());
+
+        const externalCalleesMap = new Map();
+        const localCalleesMap = new Map();
+        allCallees.forEach(link => {
+            const calleeNode = allNodes.find(n => n.id === link.target);
+            if (calleeNode) {
+                if (calleeNode.file_path !== currentFilePath) {
+                    if (!externalCalleesMap.has(calleeNode.id)) {
+                        externalCalleesMap.set(calleeNode.id, { link, node: calleeNode });
+                    }
+                } else {
+                    if (!localCalleesMap.has(calleeNode.id)) {
+                        localCalleesMap.set(calleeNode.id, { link, node: calleeNode });
+                    }
+                }
+            }
+        });
+        const externalCallees = Array.from(externalCalleesMap.values());
+        const localCallees = Array.from(localCalleesMap.values());
+
+        // === External Callers Section (functions from other files that call this) ===
+        if (externalCallers.length > 0) {
+            sections.push({ id: 'external-callers', label: '📥 External Callers' });
+            html += '<div class="viewer-section" data-section="external-callers">';
+            html += '<div class="viewer-section-title">📥 External Callers <span style="color: #8b949e; font-weight: normal;">(functions from other files calling this)</span></div>';
+            html += '<div style="display: flex; flex-direction: column; gap: 6px;">';
+            externalCallers.slice(0, 10).forEach(({ link, node }) => {
+                const shortPath = node.file_path ? node.file_path.split('/').slice(-2).join('/') : '';
+                html += `<div class="external-call-item" onclick="focusNodeInTree('${link.source}')" title="${escapeHtml(node.file_path || '')}">`;
+                html += `<span class="external-call-icon">←</span>`;
+                html += `<span class="external-call-name">${escapeHtml(node.name || node.id.substring(0, 8))}</span>`;
+                html += `<span class="external-call-path">${escapeHtml(shortPath)}</span>`;
+                html += `</div>`;
+            });
+            if (externalCallers.length > 10) {
+                html += `<div style="color: #8b949e; font-size: 11px; padding-left: 20px;">+${externalCallers.length - 10} more external callers</div>`;
+            }
+            html += '</div></div>';
+        }
+
+        // === External Calls Section (functions in other files this calls) ===
+        if (externalCallees.length > 0) {
+            sections.push({ id: 'external-calls', label: '📤 External Calls' });
+            html += '<div class="viewer-section" data-section="external-calls">';
+            html += '<div class="viewer-section-title">📤 External Calls <span style="color: #8b949e; font-weight: normal;">(functions in other files this calls)</span></div>';
+            html += '<div style="display: flex; flex-direction: column; gap: 6px;">';
+            externalCallees.slice(0, 10).forEach(({ link, node }) => {
+                const shortPath = node.file_path ? node.file_path.split('/').slice(-2).join('/') : '';
+                html += `<div class="external-call-item" onclick="focusNodeInTree('${link.target}')" title="${escapeHtml(node.file_path || '')}">`;
+                html += `<span class="external-call-icon">→</span>`;
+                html += `<span class="external-call-name">${escapeHtml(node.name || node.id.substring(0, 8))}</span>`;
+                html += `<span class="external-call-path">${escapeHtml(shortPath)}</span>`;
+                html += `</div>`;
+            });
+            if (externalCallees.length > 10) {
+                html += `<div style="color: #8b949e; font-size: 11px; padding-left: 20px;">+${externalCallees.length - 10} more external calls</div>`;
+            }
+            html += '</div></div>';
+        }
+
+        // === Local (Same-File) Relationships Section ===
+        if (localCallers.length > 0 || localCallees.length > 0) {
+            sections.push({ id: 'local-references', label: '🔗 Local References' });
+            html += '<div class="viewer-section" data-section="local-references">';
+            html += '<div class="viewer-section-title">🔗 Local References <span style="color: #8b949e; font-weight: normal;">(same file)</span></div>';
+
+            if (localCallers.length > 0) {
+                html += '<div style="margin-bottom: 8px;">';
+                html += '<div style="color: #58a6ff; font-size: 11px; margin-bottom: 4px;">Called by:</div>';
+                html += '<div style="display: flex; flex-wrap: wrap; gap: 4px;">';
+                localCallers.slice(0, 8).forEach(({ link, node }) => {
+                    html += `<span class="relationship-tag caller" onclick="focusNodeInTree('${link.source}')" title="${escapeHtml(node.name || '')}">${escapeHtml(node.name || node.id.substring(0, 8))}</span>`;
+                });
+                if (localCallers.length > 8) {
+                    html += `<span style="color: #8b949e; font-size: 10px;">+${localCallers.length - 8} more</span>`;
+                }
+                html += '</div></div>';
+            }
+
+            if (localCallees.length > 0) {
+                html += '<div>';
+                html += '<div style="color: #f0883e; font-size: 11px; margin-bottom: 4px;">Calls:</div>';
+                html += '<div style="display: flex; flex-wrap: wrap; gap: 4px;">';
+                localCallees.slice(0, 8).forEach(({ link, node }) => {
+                    html += `<span class="relationship-tag callee" onclick="focusNodeInTree('${link.target}')" title="${escapeHtml(node.name || '')}">${escapeHtml(node.name || node.id.substring(0, 8))}</span>`;
+                });
+                if (localCallees.length > 8) {
+                    html += `<span style="color: #8b949e; font-size: 10px;">+${localCallees.length - 8} more</span>`;
+                }
+                html += '</div></div>';
+            }
+
+            html += '</div>';
+        }
+
+        // === Semantically Similar Section ===
+        const semanticLinks = allLinks.filter(l => l.type === 'semantic' && l.source === chunkId);
+        if (semanticLinks.length > 0) {
+            sections.push({ id: 'semantic', label: '🧠 Semantically Similar' });
+            html += '<div class="viewer-section" data-section="semantic">';
+            html += '<div class="viewer-section-title">🧠 Semantically Similar</div>';
+            html += '<div style="display: flex; flex-direction: column; gap: 4px;">';
+            semanticLinks.slice(0, 5).forEach(link => {
+                const similarNode = allNodes.find(n => n.id === link.target);
+                if (similarNode) {
+                    const similarity = (link.similarity * 100).toFixed(0);
+                    const label = similarNode.name || similarNode.id.substring(0, 8);
+                    html += `<div class="semantic-item" onclick="focusNodeInTree('${link.target}')" title="${escapeHtml(similarNode.file_path || '')}">`;
+                    html += `<span class="semantic-score">${similarity}%</span>`;
+                    html += `<span class="semantic-name">${escapeHtml(label)}</span>`;
+                    html += `<span class="semantic-type">${similarNode.type || ''}</span>`;
+                    html += `</div>`;
+                }
+            });
+            html += '</div>';
+            html += '</div>';
+        }
+    }
+
+    content.innerHTML = html;
+
+    // Apply syntax highlighting to code blocks
+    content.querySelectorAll('pre code').forEach((block) => {
+        if (typeof hljs !== 'undefined') {
+            hljs.highlightElement(block);
+        }
+    });
+
+    // Populate section dropdown for navigation
+    populateSectionDropdown(sections);
+}
+
+// Focus on a node in the tree (expand path, scroll, highlight)
+function focusNodeInTree(nodeId) {
+    console.log(`Focusing on node in tree: ${nodeId}`);
+
+    // Find the node in allNodes (the original data)
+    const targetNodeData = allNodes.find(n => n.id === nodeId);
+    if (!targetNodeData) {
+        console.log(`Node ${nodeId} not found in allNodes`);
+        return;
+    }
+
+    // Find the path to this node in the tree structure
+    // We need to find and expand all ancestors to make the node visible
+    const pathToNode = findPathToNode(treeData, nodeId);
+
+    if (pathToNode.length > 0) {
+        console.log(`Found path to node: ${pathToNode.map(n => n.name).join(' -> ')}`);
+
+        // Expand all nodes along the path (except the target node itself)
+        pathToNode.slice(0, -1).forEach(node => {
+            if (node._children) {
+                // Node is collapsed, expand it
+                console.log(`Expanding ${node.name} to reveal path`);
+                node.children = node._children;
+                node._children = null;
+            }
+        });
+
+        // Re-render the tree to show the expanded path
+        renderVisualization();
+
+        // After render, scroll to and highlight the target node
+        setTimeout(() => {
+            highlightNodeInTree(nodeId);
+        }, 100);
+    } else {
+        console.log(`Path to node ${nodeId} not found in tree - it may be orphaned`);
+    }
+
+    // Display the content in the viewer panel
+    if (chunkTypes.includes(targetNodeData.type)) {
+        displayChunkContent(targetNodeData);
+    } else if (targetNodeData.type === 'file') {
+        displayFileInfo(targetNodeData);
+    } else if (targetNodeData.type === 'directory') {
+        displayDirectoryInfo(targetNodeData);
+    }
+}
+
+// Find path from root to a specific node by ID
+function findPathToNode(node, targetId, path = []) {
+    if (!node) return [];
+
+    // Add current node to path
+    const currentPath = [...path, node];
+
+    // Check if this is the target
+    if (node.id === targetId) {
+        return currentPath;
+    }
+
+    // Check visible children
+    if (node.children) {
+        for (const child of node.children) {
+            const result = findPathToNode(child, targetId, currentPath);
+            if (result.length > 0) return result;
+        }
+    }
+
+    // Check hidden children
+    if (node._children) {
+        for (const child of node._children) {
+            const result = findPathToNode(child, targetId, currentPath);
+            if (result.length > 0) return result;
+        }
+    }
+
+    return [];
+}
+
+// Expand path to a node and highlight it (without triggering content display)
+function expandAndHighlightNode(nodeId) {
+    console.log('=== EXPAND AND HIGHLIGHT ===');
+    console.log('Target nodeId:', nodeId);
+
+    // Find the path to this node in the tree structure
+    const pathToNode = findPathToNode(treeData, nodeId);
+
+    if (pathToNode.length > 0) {
+        console.log('Found path:', pathToNode.map(n => n.name).join(' -> '));
+
+        // Expand all nodes along the path (except the target node itself)
+        let needsRerender = false;
+        pathToNode.slice(0, -1).forEach(node => {
+            if (node._children) {
+                console.log('Expanding:', node.name);
+                node.children = node._children;
+                node._children = null;
+                needsRerender = true;
+            }
+        });
+
+        if (needsRerender) {
+            renderVisualization();
+        }
+
+        // Highlight after a short delay to allow render to complete
+        setTimeout(() => {
+            highlightNodeInTree(nodeId);
+        }, 50);
+    } else {
+        console.log('Path not found - trying direct highlight');
+        highlightNodeInTree(nodeId);
+    }
+}
+
+// Highlight and scroll to a node in the rendered tree
+function highlightNodeInTree(nodeId, persistent = true) {
+    console.log('=== HIGHLIGHT NODE ===');
+    console.log('Looking for nodeId:', nodeId);
+
+    // Remove any existing highlight
+    d3.selectAll('.node-highlight').classed('node-highlight', false);
+    if (persistent) {
+        d3.selectAll('.node-selected').classed('node-selected', false);
+    }
+
+    // Find and highlight the target node in the rendered SVG
+    const svg = d3.select('#graph');
+    const allNodes = svg.selectAll('.node');
+    console.log('Total nodes in SVG:', allNodes.size());
+
+    const targetNode = allNodes.filter(d => d.data.id === nodeId);
+    console.log('Matching nodes found:', targetNode.size());
+
+    if (!targetNode.empty()) {
+        // Add highlight class (persistent = orange glow that stays)
+        if (persistent) {
+            targetNode.classed('node-selected', true);
+            console.log('Applied .node-selected class');
+        } else {
+            targetNode.classed('node-highlight', true);
+            console.log('Applied .node-highlight class');
+        }
+
+        // Pulse the node circle - scale up from current size
+        targetNode.select('circle')
+            .transition()
+            .duration(200)
+            .attr('r', d => getNodeRadius(d) * 1.5)  // Grow 50%
+            .transition()
+            .duration(200)
+            .attr('r', d => getNodeRadius(d) * 0.8)  // Shrink 20%
+            .transition()
+            .duration(200)
+            .attr('r', d => getNodeRadius(d));       // Return to normal
+
+        // Get the node's position for scrolling
+        const nodeTransform = targetNode.attr('transform');
+        const match = nodeTransform.match(/translate\\(([^,]+),([^)]+)\\)/);
+        if (match) {
+            const x = parseFloat(match[1]);
+            const y = parseFloat(match[2]);
+
+            // Pan the view to center on this node
+            const { width, height } = getViewportDimensions();
+            const zoom = d3.zoom().on('zoom', () => {});  // Get current zoom
+            const svg = d3.select('#graph');
+
+            // Calculate center offset
+            const centerX = width / 2 - x;
+            const centerY = height / 2 - y;
+
+            // Apply smooth transition to center on node
+            svg.transition()
+                .duration(500)
+                .call(
+                    d3.zoom().transform,
+                    d3.zoomIdentity.translate(centerX, centerY)
+                );
+        }
+
+        console.log(`Highlighted node ${nodeId}`);
+    } else {
+        console.log(`Node ${nodeId} not found in rendered tree`);
+    }
+}
+
+// Legacy function for backward compatibility
+function focusNode(nodeId) {
+    focusNodeInTree(nodeId);
+}
+
+function getChunkIcon(chunkType) {
+    const icons = {
+        'function': '⚡',
+        'class': '🏛️',
+        'method': '🔧',
+        'code': '📝',
+        'import': '📦',
+        'comment': '💬',
+        'docstring': '📖'
+    };
+    return icons[chunkType] || '📝';
+}
+
+function escapeHtml(text) {
+    const div = document.createElement('div');
+    div.textContent = text;
+    return div.innerHTML;
+}
+
+// Get language class for highlight.js based on file extension
+function getLanguageClass(filePath) {
+    if (!filePath) return '';
+    const ext = filePath.split('.').pop().toLowerCase();
+    const langMap = {
+        'py': 'python',
+        'js': 'javascript',
+        'ts': 'typescript',
+        'tsx': 'typescript',
+        'jsx': 'javascript',
+        'java': 'java',
+        'go': 'go',
+        'rs': 'rust',
+        'rb': 'ruby',
+        'php': 'php',
+        'c': 'c',
+        'cpp': 'cpp',
+        'cc': 'cpp',
+        'h': 'c',
+        'hpp': 'cpp',
+        'cs': 'csharp',
+        'swift': 'swift',
+        'kt': 'kotlin',
+        'scala': 'scala',
+        'sh': 'bash',
+        'bash': 'bash',
+        'zsh': 'bash',
+        'sql': 'sql',
+        'html': 'html',
+        'htm': 'html',
+        'css': 'css',
+        'scss': 'scss',
+        'less': 'less',
+        'json': 'json',
+        'yaml': 'yaml',
+        'yml': 'yaml',
+        'xml': 'xml',
+        'md': 'markdown',
+        'markdown': 'markdown',
+        'toml': 'ini',
+        'ini': 'ini',
+        'cfg': 'ini',
+        'lua': 'lua',
+        'r': 'r',
+        'dart': 'dart',
+        'ex': 'elixir',
+        'exs': 'elixir',
+        'erl': 'erlang',
+        'hs': 'haskell',
+        'clj': 'clojure',
+        'vim': 'vim',
+        'dockerfile': 'dockerfile'
+    };
+    return langMap[ext] || '';
+}
+
+// ============================================================================
+// LAYOUT TOGGLE
+// ============================================================================
+
+function toggleCallLines(show) {
+    showCallLines = show;
+    const lineGroup = d3.select('.external-lines-group');
+    if (!lineGroup.empty()) {
+        lineGroup.style('display', show ? 'block' : 'none');
+    }
+    console.log(`Call lines ${show ? 'shown' : 'hidden'}`);
+}
+
+function toggleLayout() {
+    const toggleCheckbox = document.getElementById('layout-toggle');
+    const labels = document.querySelectorAll('.toggle-label');
+
+    // Update layout based on checkbox state
+    currentLayout = toggleCheckbox.checked ? 'circular' : 'linear';
+
+    // Update label highlighting
+    labels.forEach((label, index) => {
+        if (index === 0) {
+            // Linear label (left)
+            label.classList.toggle('active', currentLayout === 'linear');
+        } else {
+            // Circular label (right)
+            label.classList.toggle('active', currentLayout === 'circular');
+        }
+    });
+
+    console.log(`Layout switched to: ${currentLayout}`);
+    renderVisualization();
+}
+
+// ============================================================================
+// FILE TYPE FILTER
+// ============================================================================
+
+// Code file extensions
+const codeExtensions = new Set([
+    '.py', '.js', '.ts', '.jsx', '.tsx', '.java', '.c', '.cpp', '.h', '.hpp',
+    '.cs', '.go', '.rs', '.rb', '.php', '.swift', '.kt', '.scala', '.r',
+    '.sh', '.bash', '.zsh', '.ps1', '.bat', '.sql', '.html', '.css', '.scss',
+    '.sass', '.less', '.vue', '.svelte', '.astro', '.elm', '.clj', '.ex', '.exs',
+    '.hs', '.ml', '.lua', '.pl', '.pm', '.m', '.mm', '.f', '.f90', '.for',
+    '.asm', '.s', '.v', '.vhd', '.sv', '.nim', '.zig', '.d', '.dart', '.groovy',
+    '.coffee', '.litcoffee', '.purs', '.rkt', '.scm', '.lisp', '.cl'
+]);
+
+// Doc file extensions
+const docExtensions = new Set([
+    '.md', '.markdown', '.rst', '.txt', '.adoc', '.asciidoc', '.org', '.tex',
+    '.rtf', '.doc', '.docx', '.pdf', '.json', '.yaml', '.yml', '.toml', '.ini',
+    '.cfg', '.conf', '.xml', '.csv', '.tsv', '.log', '.man', '.info', '.pod',
+    '.rdoc', '.textile', '.wiki'
+]);
+
+function getFileType(filename) {
+    if (!filename) return 'unknown';
+    const ext = '.' + filename.split('.').pop().toLowerCase();
+    if (codeExtensions.has(ext)) return 'code';
+    if (docExtensions.has(ext)) return 'docs';
+    return 'unknown';
+}
+
+function setFileFilter(filter) {
+    currentFileFilter = filter;
+
+    // Update button states
+    document.querySelectorAll('.filter-btn').forEach(btn => {
+        btn.classList.toggle('active', btn.dataset.filter === filter);
+    });
+
+    // Apply filter to the tree
+    applyFileFilter();
+
+    console.log(`File filter set to: ${filter}`);
+}
+
+function applyFileFilter() {
+    if (!treeData) return;
+
+    console.log('=== APPLYING FILE FILTER (VISIBILITY) ===');
+    console.log('Current filter:', currentFileFilter);
+
+    // Get all node elements in the visualization
+    const nodeElements = d3.selectAll('.node');
+    const linkElements = d3.selectAll('.link');
+
+    if (currentFileFilter === 'all') {
+        // Show everything
+        nodeElements.style('display', null);
+        linkElements.style('display', null);
+        console.log('Showing all nodes');
+        return;
+    }
+
+    // Build set of visible node IDs based on filter
+    const visibleIds = new Set();
+
+    // Recursive function to check if a node or any descendant matches filter
+    function checkNodeAndDescendants(node) {
+        let hasMatchingDescendant = false;
+
+        // Check children (both visible and collapsed)
+        const children = node.children || node._children || [];
+        children.forEach(child => {
+            if (checkNodeAndDescendants(child)) {
+                hasMatchingDescendant = true;
+            }
+        });
+
+        // Check if this node itself matches
+        let matches = false;
+        if (node.type === 'directory') {
+            // Directories are visible if they have matching descendants
+            matches = hasMatchingDescendant;
+        } else if (node.type === 'file') {
+            const fileType = getFileType(node.name);
+            matches = (fileType === currentFileFilter) || (fileType === 'unknown');
+        } else if (chunkTypes.includes(node.type)) {
+            // Chunks match if their parent file matches
+            // For simplicity, check file_path extension
+            if (node.file_path) {
+                const ext = node.file_path.substring(node.file_path.lastIndexOf('.'));
+                const fileType = getFileType(node.file_path);
+                matches = (fileType === currentFileFilter) || (fileType === 'unknown');
+            }
+        }
+
+        if (matches || hasMatchingDescendant) {
+            visibleIds.add(node.id);
+            return true;
+        }
+        return false;
+    }
+
+    checkNodeAndDescendants(treeData);
+    console.log(`Filter found ${visibleIds.size} visible nodes`);
+
+    // Apply visibility to DOM elements
+    nodeElements.style('display', function(d) {
+        return visibleIds.has(d.data.id) ? null : 'none';
+    });
+
+    // Hide links where either end is hidden
+    linkElements.style('display', function(d) {
+        const sourceVisible = visibleIds.has(d.source.data.id);
+        const targetVisible = visibleIds.has(d.target.data.id);
+        return (sourceVisible && targetVisible) ? null : 'none';
+    });
+
+    console.log('=== FILTER COMPLETE (VISIBILITY) ===');
+}
+
+// ============================================================================
+// VIEWER PANEL CONTROLS
+// ============================================================================
+
+let isViewerExpanded = false;
+
+function openViewerPanel() {
+    const panel = document.getElementById('viewer-panel');
+    const container = document.getElementById('main-container');
+
+    if (!isViewerOpen) {
+        panel.classList.add('open');
+        container.classList.add('viewer-open');
+        isViewerOpen = true;
+
+        // Re-render visualization to adjust to new viewport size
+        setTimeout(() => {
+            renderVisualization();
+        }, 300); // Wait for transition
+    }
+}
+
+function closeViewerPanel() {
+    const panel = document.getElementById('viewer-panel');
+    const container = document.getElementById('main-container');
+
+    panel.classList.remove('open');
+    panel.classList.remove('expanded');
+    container.classList.remove('viewer-open');
+    isViewerOpen = false;
+    isViewerExpanded = false;
+
+    // Update icon
+    const icon = document.getElementById('expand-icon');
+    if (icon) icon.textContent = '⬅';
+
+    // Re-render visualization to adjust to new viewport size
+    setTimeout(() => {
+        renderVisualization();
+    }, 300); // Wait for transition
+}
+
+function toggleViewerExpand() {
+    const panel = document.getElementById('viewer-panel');
+    const icon = document.getElementById('expand-icon');
+
+    isViewerExpanded = !isViewerExpanded;
+
+    if (isViewerExpanded) {
+        panel.classList.add('expanded');
+        if (icon) icon.textContent = '➡';
+    } else {
+        panel.classList.remove('expanded');
+        if (icon) icon.textContent = '⬅';
+    }
+
+    // Don't re-render graph on expand - only affects panel width
+    // Graph will adjust on close via closeViewerPanel()
+}
+
+function jumpToSection(sectionId) {
+    if (!sectionId) return;
+
+    const viewerContent = document.getElementById('viewer-content');
+    const sectionElement = viewerContent.querySelector(`[data-section="${sectionId}"]`);
+
+    if (sectionElement) {
+        sectionElement.scrollIntoView({ behavior: 'smooth', block: 'start' });
+
+        // Briefly highlight the section
+        sectionElement.style.transition = 'background-color 0.3s';
+        sectionElement.style.backgroundColor = 'rgba(88, 166, 255, 0.15)';
+        setTimeout(() => {
+            sectionElement.style.backgroundColor = '';
+        }, 1000);
+    }
+
+    // Reset dropdown to default
+    const dropdown = document.getElementById('section-dropdown');
+    if (dropdown) dropdown.value = '';
+}
+
+function populateSectionDropdown(sections) {
+    const dropdown = document.getElementById('section-dropdown');
+    if (!dropdown) return;
+
+    // Clear existing options except the first one
+    dropdown.innerHTML = '<option value="">Jump to section...</option>';
+
+    // Add section options
+    sections.forEach(section => {
+        const option = document.createElement('option');
+        option.value = section.id;
+        option.textContent = section.label;
+        dropdown.appendChild(option);
+    });
+
+    // Show/hide dropdown based on whether we have sections
+    const sectionNav = document.getElementById('section-nav');
+    if (sectionNav) {
+        sectionNav.style.display = sections.length > 1 ? 'block' : 'none';
+    }
+}
+
+// ============================================================================
+// NAVIGATION FUNCTIONS
+// ============================================================================
+
+function addToNavHistory(item) {
+    // Remove any forward history when adding new item
+    if (navigationIndex < navigationHistory.length - 1) {
+        navigationHistory = navigationHistory.slice(0, navigationIndex + 1);
+    }
+    navigationHistory.push(item);
+    navigationIndex = navigationHistory.length - 1;
+    console.log(`Navigation history: ${navigationHistory.length} items, index: ${navigationIndex}`);
+}
+
+function goBack() {
+    if (navigationIndex > 0) {
+        navigationIndex--;
+        const item = navigationHistory[navigationIndex];
+        console.log(`Going back to: ${item.type} - ${item.data.name}`);
+        if (item.type === 'directory') {
+            displayDirectoryInfo(item.data, false);  // false = don't add to history
+            focusNodeInTree(item.data.id);
+        } else if (item.type === 'file') {
+            displayFileInfo(item.data, false);  // false = don't add to history
+            focusNodeInTree(item.data.id);
+        } else if (item.type === 'chunk') {
+            displayChunkContent(item.data, false);  // false = don't add to history
+            focusNodeInTree(item.data.id);
+        }
+    }
+}
+
+function goForward() {
+    if (navigationIndex < navigationHistory.length - 1) {
+        navigationIndex++;
+        const item = navigationHistory[navigationIndex];
+        console.log(`Going forward to: ${item.type} - ${item.data.name}`);
+        if (item.type === 'directory') {
+            displayDirectoryInfo(item.data, false);  // false = don't add to history
+            focusNodeInTree(item.data.id);
+        } else if (item.type === 'file') {
+            displayFileInfo(item.data, false);  // false = don't add to history
+            focusNodeInTree(item.data.id);
+        } else if (item.type === 'chunk') {
+            displayChunkContent(item.data, false);  // false = don't add to history
+            focusNodeInTree(item.data.id);
+        }
+    }
+}
+
+function navigateToDirectory(dirData) {
+    console.log(`Navigating to directory: ${dirData.name}`);
+    // Focus on the node in the tree (expand path and highlight)
+    focusNodeInTree(dirData.id);
+}
+
+function navigateToFile(fileData) {
+    console.log(`Navigating to file: ${fileData.name}`);
+    // Focus on the node in the tree (expand path and highlight)
+    focusNodeInTree(fileData.id);
+}
+
+// Navigate to a file by its file path (used when clicking on file paths in chunk metadata)
+function navigateToFileByPath(filePath) {
+    console.log(`Navigating to file by path: ${filePath}`);
+
+    // Find the file node in allNodes that matches this path
+    const fileNode = allNodes.find(n => {
+        if (n.type !== 'file') return false;
+        // Match against various path properties
+        return n.path === filePath ||
+               n.file_path === filePath ||
+               (n.path && n.path.endsWith(filePath)) ||
+               (n.file_path && n.file_path.endsWith(filePath)) ||
+               filePath.endsWith(n.name);
+    });
+
+    if (fileNode) {
+        console.log(`Found file node: ${fileNode.name} (id: ${fileNode.id})`);
+        focusNodeInTree(fileNode.id);
+    } else {
+        console.log(`File node not found for path: ${filePath}`);
+        // Try to find by just the filename
+        const fileName = filePath.split('/').pop();
+        const fileByName = allNodes.find(n => n.type === 'file' && n.name === fileName);
+        if (fileByName) {
+            console.log(`Found file by name: ${fileByName.name}`);
+            focusNodeInTree(fileByName.id);
+        }
+    }
+}
+
+function renderNavigationBar(currentItem) {
+    let html = '<div class="navigation-bar">';
+
+    // Back/Forward buttons
+    const canGoBack = navigationIndex > 0;
+    const canGoForward = navigationIndex < navigationHistory.length - 1;
+
+    html += `<button class="nav-btn ${canGoBack ? '' : 'disabled'}" onclick="goBack()" ${canGoBack ? '' : 'disabled'} title="Go Back">←</button>`;
+    html += `<button class="nav-btn ${canGoForward ? '' : 'disabled'}" onclick="goForward()" ${canGoForward ? '' : 'disabled'} title="Go Forward">→</button>`;
+
+    // Breadcrumb trail
+    html += '<div class="breadcrumb-trail">';
+
+    // Build breadcrumb from path
+    if (currentItem && currentItem.id) {
+        const path = findPathToNode(treeData, currentItem.id);
+        path.forEach((node, index) => {
+            const isLast = index === path.length - 1;
+            const clickable = !isLast;
+
+            if (index > 0) {
+                html += '<span class="breadcrumb-separator">/</span>';
+            }
+
+            if (clickable) {
+                html += `<span class="breadcrumb-item clickable" onclick="focusNodeInTree('${node.id}')">${escapeHtml(node.name)}</span>`;
+            } else {
+                html += `<span class="breadcrumb-item current">${escapeHtml(node.name)}</span>`;
+            }
+        });
+    }
+
+    html += '</div>';
+    html += '</div>';
+
+    return html;
+}
+
+// ============================================================================
+// SEARCH FUNCTIONALITY
+// ============================================================================
+
+let searchDebounceTimer = null;
+let searchResults = [];
+let selectedSearchIndex = -1;
+
+function handleSearchInput(event) {
+    const query = event.target.value.trim();
+
+    // Debounce search - wait 150ms after typing stops
+    clearTimeout(searchDebounceTimer);
+    searchDebounceTimer = setTimeout(() => {
+        performSearch(query);
+    }, 150);
+}
+
+function handleSearchKeydown(event) {
+    const resultsContainer = document.getElementById('search-results');
+
+    switch(event.key) {
+        case 'ArrowDown':
+            event.preventDefault();
+            if (searchResults.length > 0) {
+                selectedSearchIndex = Math.min(selectedSearchIndex + 1, searchResults.length - 1);
+                updateSearchSelection();
+            }
+            break;
+        case 'ArrowUp':
+            event.preventDefault();
+            if (searchResults.length > 0) {
+                selectedSearchIndex = Math.max(selectedSearchIndex - 1, 0);
+                updateSearchSelection();
+            }
+            break;
+        case 'Enter':
+            event.preventDefault();
+            if (selectedSearchIndex >= 0 && selectedSearchIndex < searchResults.length) {
+                selectSearchResult(searchResults[selectedSearchIndex]);
+            }
+            break;
+        case 'Escape':
+            closeSearchResults();
+            document.getElementById('search-input').blur();
+            break;
+    }
+}
+
+function performSearch(query) {
+    const resultsContainer = document.getElementById('search-results');
+
+    if (!query || query.length < 2) {
+        closeSearchResults();
+        return;
+    }
+
+    const lowerQuery = query.toLowerCase();
+
+    // Search through all nodes (directories, files, and chunks)
+    searchResults = allNodes
+        .filter(node => {
+            // Match against name
+            const nameMatch = node.name && node.name.toLowerCase().includes(lowerQuery);
+            // Match against file path
+            const pathMatch = node.file_path && node.file_path.toLowerCase().includes(lowerQuery);
+            // Match against ID (useful for finding specific chunks)
+            const idMatch = node.id && node.id.toLowerCase().includes(lowerQuery);
+            return nameMatch || pathMatch || idMatch;
+        })
+        .slice(0, 20);  // Limit to 20 results
+
+    // Sort results: exact matches first, then by type priority
+    const typePriority = { 'directory': 1, 'file': 2, 'class': 3, 'function': 4, 'method': 5 };
+    searchResults.sort((a, b) => {
+        // Exact name match gets highest priority
+        const aExact = a.name && a.name.toLowerCase() === lowerQuery ? 0 : 1;
+        const bExact = b.name && b.name.toLowerCase() === lowerQuery ? 0 : 1;
+        if (aExact !== bExact) return aExact - bExact;
+
+        // Then sort by type priority
+        const aPriority = typePriority[a.type] || 10;
+        const bPriority = typePriority[b.type] || 10;
+        if (aPriority !== bPriority) return aPriority - bPriority;
+
+        // Finally sort alphabetically
+        return (a.name || '').localeCompare(b.name || '');
+    });
+
+    selectedSearchIndex = searchResults.length > 0 ? 0 : -1;
+    renderSearchResults(query);
+}
+
+function renderSearchResults(query) {
+    const resultsContainer = document.getElementById('search-results');
+
+    if (searchResults.length === 0) {
+        resultsContainer.innerHTML = '<div class="search-no-results">No results found</div>';
+        resultsContainer.classList.add('visible');
+        return;
+    }
+
+    let html = '';
+
+    searchResults.forEach((node, index) => {
+        const icon = getSearchResultIcon(node.type);
+        const name = highlightMatch(node.name || node.id.substring(0, 20), query);
+        const path = node.file_path ? node.file_path.split('/').slice(-3).join('/') : '';
+        const type = node.type || 'unknown';
+        const selected = index === selectedSearchIndex ? 'selected' : '';
+
+        html += `<div class="search-result-item ${selected}"
+                      data-index="${index}"
+                      onclick="selectSearchResultByIndex(${index})"
+                      onmouseenter="hoverSearchResult(${index})">`;
+        html += `<span class="search-result-icon">${icon}</span>`;
+        html += `<div class="search-result-info">`;
+        html += `<div class="search-result-name">${name}</div>`;
+        if (path) {
+            html += `<div class="search-result-path">${escapeHtml(path)}</div>`;
+        }
+        html += `</div>`;
+        html += `<span class="search-result-type">${type}</span>`;
+        html += `</div>`;
+    });
+
+    html += '<div class="search-hint">↑↓ Navigate • Enter Select • Esc Close</div>';
+
+    resultsContainer.innerHTML = html;
+    resultsContainer.classList.add('visible');
+}
+
+function getSearchResultIcon(type) {
+    const icons = {
+        'directory': '📁',
+        'file': '📄',
+        'function': '⚡',
+        'class': '🏛️',
+        'method': '🔧',
+        'module': '📦',
+        'imports': '📦',
+        'text': '📝',
+        'code': '📝'
+    };
+    return icons[type] || '📄';
+}
+
+function highlightMatch(text, query) {
+    if (!text || !query) return escapeHtml(text || '');
+
+    const lowerText = text.toLowerCase();
+    const lowerQuery = query.toLowerCase();
+    const index = lowerText.indexOf(lowerQuery);
+
+    if (index === -1) return escapeHtml(text);
+
+    const before = text.substring(0, index);
+    const match = text.substring(index, index + query.length);
+    const after = text.substring(index + query.length);
+
+    return escapeHtml(before) + '<mark>' + escapeHtml(match) + '</mark>' + escapeHtml(after);
+}
+
+function updateSearchSelection() {
+    const items = document.querySelectorAll('.search-result-item');
+    items.forEach((item, index) => {
+        item.classList.toggle('selected', index === selectedSearchIndex);
+    });
+
+    // Scroll selected item into view
+    const selected = items[selectedSearchIndex];
+    if (selected) {
+        selected.scrollIntoView({ block: 'nearest', behavior: 'smooth' });
+    }
+}
+
+function hoverSearchResult(index) {
+    selectedSearchIndex = index;
+    updateSearchSelection();
+}
+
+function selectSearchResultByIndex(index) {
+    if (index >= 0 && index < searchResults.length) {
+        selectSearchResult(searchResults[index]);
+    }
+}
+
+function selectSearchResult(node) {
+    console.log(`Search selected: ${node.name} (${node.type})`);
+
+    // Close search dropdown
+    closeSearchResults();
+
+    // Clear input
+    document.getElementById('search-input').value = '';
+
+    // Focus on the node in the tree
+    focusNodeInTree(node.id);
+}
+
+function closeSearchResults() {
+    const resultsContainer = document.getElementById('search-results');
+    resultsContainer.classList.remove('visible');
+    searchResults = [];
+    selectedSearchIndex = -1;
+}
+
+// ============================================================================
+// THEME TOGGLE
+// ============================================================================
+
+function toggleTheme() {
+    const html = document.documentElement;
+    const currentTheme = html.getAttribute('data-theme') || 'dark';
+    const newTheme = currentTheme === 'dark' ? 'light' : 'dark';
+
+    // Update theme
+    if (newTheme === 'light') {
+        html.setAttribute('data-theme', 'light');
+    } else {
+        html.removeAttribute('data-theme');
+    }
+
+    // Save preference
+    localStorage.setItem('theme', newTheme);
+
+    // Update icon only
+    const themeIcon = document.getElementById('theme-icon');
+
+    if (newTheme === 'light') {
+        themeIcon.textContent = '☀️';
+    } else {
+        themeIcon.textContent = '🌙';
+    }
+
+    console.log(`Theme toggled to: ${newTheme}`);
+}
+
+function loadThemePreference() {
+    const savedTheme = localStorage.getItem('theme') || 'dark';
+    const html = document.documentElement;
+
+    if (savedTheme === 'light') {
+        html.setAttribute('data-theme', 'light');
+        const themeIcon = document.getElementById('theme-icon');
+        if (themeIcon) themeIcon.textContent = '☀️';
+    }
+
+    console.log(`Loaded theme preference: ${savedTheme}`);
+}
+
+// ============================================================================
+// ANALYSIS REPORTS
+// ============================================================================
+
+function getComplexityGrade(complexity) {
+    if (complexity === undefined || complexity === null) return 'N/A';
+    if (complexity <= 5) return 'A';
+    if (complexity <= 10) return 'B';
+    if (complexity <= 15) return 'C';
+    if (complexity <= 20) return 'D';
+    return 'F';
+}
+
+function getGradeColor(grade) {
+    const colors = {
+        'A': '#2ea043',
+        'B': '#1f6feb',
+        'C': '#d29922',
+        'D': '#f0883e',
+        'F': '#da3633',
+        'N/A': '#6e7681'
+    };
+    return colors[grade] || colors['N/A'];
+}
+
+function showComplexityReport() {
+    openViewerPanel();
+
+    const viewerTitle = document.getElementById('viewer-title');
+    const viewerContent = document.getElementById('viewer-content');
+
+    viewerTitle.textContent = '📊 Complexity Report';
+
+    // Collect all chunk nodes with complexity data
+    const chunksWithComplexity = [];
+
+    function collectChunks(node) {
+        if (chunkTypes.includes(node.type)) {
+            const complexity = node.complexity !== undefined ? node.complexity : null;
+            chunksWithComplexity.push({
+                name: node.name,
+                type: node.type,
+                file_path: node.file_path || 'Unknown',
+                start_line: node.start_line || 0,
+                end_line: node.end_line || 0,
+                complexity: complexity,
+                grade: getComplexityGrade(complexity),
+                node: node
+            });
+        }
+
+        // Recursively process children
+        const children = node.children || node._children || [];
+        children.forEach(child => collectChunks(child));
+    }
+
+    // Start from treeData root
+    if (treeData) {
+        collectChunks(treeData);
+    }
+
+    // Calculate statistics
+    const totalFunctions = chunksWithComplexity.length;
+    const validComplexity = chunksWithComplexity.filter(c => c.complexity !== null);
+    const avgComplexity = validComplexity.length > 0
+        ? (validComplexity.reduce((sum, c) => sum + c.complexity, 0) / validComplexity.length).toFixed(2)
+        : 'N/A';
+
+    // Count by grade
+    const gradeCounts = {
+        'A': 0, 'B': 0, 'C': 0, 'D': 0, 'F': 0, 'N/A': 0
+    };
+    chunksWithComplexity.forEach(c => {
+        gradeCounts[c.grade]++;
+    });
+
+    // Sort by complexity (highest first)
+    const sortedChunks = [...chunksWithComplexity].sort((a, b) => {
+        if (a.complexity === null) return 1;
+        if (b.complexity === null) return -1;
+        return b.complexity - a.complexity;
+    });
+
+    // Build HTML
+    let html = '<div class="complexity-report">';
+
+    // Summary Stats
+    html += '<div class="complexity-summary">';
+    html += '<div class="summary-grid">';
+    html += `<div class="summary-card">
+        <div class="summary-label">Total Functions</div>
+        <div class="summary-value">${totalFunctions}</div>
+    </div>`;
+    html += `<div class="summary-card">
+        <div class="summary-label">Average Complexity</div>
+        <div class="summary-value">${avgComplexity}</div>
+    </div>`;
+    html += `<div class="summary-card">
+        <div class="summary-label">With Complexity Data</div>
+        <div class="summary-value">${validComplexity.length}</div>
+    </div>`;
+    html += '</div>';
+
+    // Grade Distribution
+    html += '<div class="grade-distribution">';
+    html += '<div class="distribution-title">Grade Distribution</div>';
+    html += '<div class="distribution-bars">';
+
+    const maxCount = Math.max(...Object.values(gradeCounts));
+    ['A', 'B', 'C', 'D', 'F', 'N/A'].forEach(grade => {
+        const count = gradeCounts[grade];
+        const percentage = totalFunctions > 0 ? (count / totalFunctions * 100) : 0;
+        const barWidth = maxCount > 0 ? (count / maxCount * 100) : 0;
+        html += `
+            <div class="distribution-row">
+                <div class="distribution-grade" style="color: ${getGradeColor(grade)}">${grade}</div>
+                <div class="distribution-bar-container">
+                    <div class="distribution-bar" style="width: ${barWidth}%; background: ${getGradeColor(grade)}"></div>
+                </div>
+                <div class="distribution-count">${count} (${percentage.toFixed(1)}%)</div>
+            </div>
+        `;
+    });
+    html += '</div></div>';
+    html += '</div>';
+
+    // Complexity Hotspots Table
+    html += '<div class="complexity-hotspots">';
+    html += '<h3 class="section-title">Complexity Hotspots</h3>';
+
+    if (sortedChunks.length === 0) {
+        html += '<p style="color: var(--text-secondary); text-align: center; padding: 20px;">No functions found with complexity data.</p>';
+    } else {
+        html += '<div class="hotspots-table-container">';
+        html += '<table class="hotspots-table">';
+        html += `
+            <thead>
+                <tr>
+                    <th>Name</th>
+                    <th>File</th>
+                    <th>Lines</th>
+                    <th>Complexity</th>
+                    <th>Grade</th>
+                </tr>
+            </thead>
+            <tbody>
+        `;
+
+        sortedChunks.forEach(chunk => {
+            const lines = chunk.end_line > 0 ? chunk.end_line - chunk.start_line + 1 : 'N/A';
+            const complexityDisplay = chunk.complexity !== null ? chunk.complexity.toFixed(1) : 'N/A';
+            const gradeColor = getGradeColor(chunk.grade);
+
+            // Get relative file path
+            const fileName = chunk.file_path.split('/').pop() || chunk.file_path;
+            const lineRange = chunk.start_line > 0 ? `L${chunk.start_line}-${chunk.end_line}` : '';
+
+            html += `
+                <tr class="hotspot-row" onclick='navigateToChunk(${JSON.stringify(chunk.name)})'>
+                    <td class="hotspot-name">${escapeHtml(chunk.name)}</td>
+                    <td class="hotspot-file" title="${escapeHtml(chunk.file_path)}">${escapeHtml(fileName)}</td>
+                    <td class="hotspot-lines">${lines}</td>
+                    <td class="hotspot-complexity">${complexityDisplay}</td>
+                    <td class="hotspot-grade">
+                        <span class="grade-badge" style="background: ${gradeColor}">${chunk.grade}</span>
+                    </td>
+                </tr>
+            `;
+        });
+
+        html += '</tbody></table></div>';
+    }
+
+    html += '</div>'; // complexity-hotspots
+    html += '</div>'; // complexity-report
+
+    viewerContent.innerHTML = html;
+
+    // Hide section dropdown for reports (no code sections)
+    const sectionNav = document.getElementById('section-nav');
+    if (sectionNav) {
+        sectionNav.style.display = 'none';
+    }
+}
+
+function navigateToChunk(chunkName) {
+    // Find the chunk node in the tree
+    function findChunk(node) {
+        if (chunkTypes.includes(node.type) && node.name === chunkName) {
+            return node;
+        }
+        const children = node.children || node._children || [];
+        for (const child of children) {
+            const found = findChunk(child);
+            if (found) return found;
+        }
+        return null;
+    }
+
+    if (treeData) {
+        const chunk = findChunk(treeData);
+        if (chunk) {
+            // Display the chunk content
+            displayChunkContent(chunk);
+
+            // Highlight the node in the visualization
+            highlightNode(chunk.id);
+        }
+    }
+}
+
+function escapeHtml(text) {
+    const div = document.createElement('div');
+    div.textContent = text;
+    return div.innerHTML;
+}
+
+function highlightNode(nodeId) {
+    // Remove existing highlights
+    d3.selectAll('.node').classed('node-highlight', false);
+
+    // Add highlight to the target node
+    d3.selectAll('.node')
+        .filter(d => d.data.id === nodeId)
+        .classed('node-highlight', true);
+}
+
+// ============================================================================
+// CODE SMELLS DETECTION AND REPORTING
+// ============================================================================
+
+function detectCodeSmells(nodes) {
+    const smells = [];
+
+    function analyzeNode(node) {
+        // Only analyze code chunks
+        if (!chunkTypes.includes(node.type)) {
+            const children = node.children || node._children || [];
+            children.forEach(child => analyzeNode(child));
+            return;
+        }
+
+        const lineCount = (node.end_line && node.start_line)
+            ? node.end_line - node.start_line + 1
+            : 0;
+        const complexity = node.complexity || 0;
+
+        // 1. Long Method - Functions with > 50 lines
+        if (node.type === 'function' || node.type === 'method') {
+            if (lineCount > 100) {
+                smells.push({
+                    type: 'Long Method',
+                    severity: 'error',
+                    node: node,
+                    details: `${lineCount} lines (very long)`
+                });
+            } else if (lineCount > 50) {
+                smells.push({
+                    type: 'Long Method',
+                    severity: 'warning',
+                    node: node,
+                    details: `${lineCount} lines`
+                });
+            }
+        }
+
+        // 2. High Complexity - Functions with complexity > 15
+        if ((node.type === 'function' || node.type === 'method') && complexity > 0) {
+            if (complexity > 20) {
+                smells.push({
+                    type: 'High Complexity',
+                    severity: 'error',
+                    node: node,
+                    details: `Complexity: ${complexity.toFixed(1)} (very complex)`
+                });
+            } else if (complexity > 15) {
+                smells.push({
+                    type: 'High Complexity',
+                    severity: 'warning',
+                    node: node,
+                    details: `Complexity: ${complexity.toFixed(1)}`
+                });
+            }
+        }
+
+        // 3. Deep Nesting - Proxy using complexity > 20
+        if ((node.type === 'function' || node.type === 'method') && complexity > 20) {
+            smells.push({
+                type: 'Deep Nesting',
+                severity: complexity > 25 ? 'error' : 'warning',
+                node: node,
+                details: `Complexity: ${complexity.toFixed(1)} (likely deep nesting)`
+            });
+        }
+
+        // 4. God Class - Classes with > 20 methods or > 500 lines
+        if (node.type === 'class') {
+            const children = node.children || node._children || [];
+            const methodCount = children.filter(c => c.type === 'method').length;
+
+            if (methodCount > 30 || lineCount > 800) {
+                smells.push({
+                    type: 'God Class',
+                    severity: 'error',
+                    node: node,
+                    details: `${methodCount} methods, ${lineCount} lines (very large)`
+                });
+            } else if (methodCount > 20 || lineCount > 500) {
+                smells.push({
+                    type: 'God Class',
+                    severity: 'warning',
+                    node: node,
+                    details: `${methodCount} methods, ${lineCount} lines`
+                });
+            }
+        }
+
+        // Recursively process children
+        const children = node.children || node._children || [];
+        children.forEach(child => analyzeNode(child));
+    }
+
+    if (nodes) {
+        analyzeNode(nodes);
+    }
+
+    return smells;
+}
+
+function showCodeSmells() {
+    openViewerPanel();
+
+    const viewerTitle = document.getElementById('viewer-title');
+    const viewerContent = document.getElementById('viewer-content');
+
+    viewerTitle.textContent = '🔍 Code Smells';
+
+    // Detect all code smells
+    const allSmells = detectCodeSmells(treeData);
+
+    // Count by type and severity
+    const smellCounts = {
+        'Long Method': { total: 0, warning: 0, error: 0 },
+        'High Complexity': { total: 0, warning: 0, error: 0 },
+        'Deep Nesting': { total: 0, warning: 0, error: 0 },
+        'God Class': { total: 0, warning: 0, error: 0 }
+    };
+
+    let totalWarnings = 0;
+    let totalErrors = 0;
+
+    allSmells.forEach(smell => {
+        smellCounts[smell.type].total++;
+        smellCounts[smell.type][smell.severity]++;
+        if (smell.severity === 'warning') totalWarnings++;
+        if (smell.severity === 'error') totalErrors++;
+    });
+
+    // Build HTML
+    let html = '<div class="code-smells-report">';
+
+    // Summary Cards
+    html += '<div class="smell-summary-grid">';
+    html += `
+        <div class="smell-summary-card">
+            <div class="smell-card-header">
+                <span class="smell-card-icon">🔍</span>
+                <div class="smell-card-title">Total Smells</div>
+            </div>
+            <div class="smell-card-count">${allSmells.length}</div>
+        </div>
+        <div class="smell-summary-card warning">
+            <div class="smell-card-header">
+                <span class="smell-card-icon">⚠️</span>
+                <div class="smell-card-title">Warnings</div>
+            </div>
+            <div class="smell-card-count" style="color: var(--warning)">${totalWarnings}</div>
+        </div>
+        <div class="smell-summary-card error">
+            <div class="smell-card-header">
+                <span class="smell-card-icon">🚨</span>
+                <div class="smell-card-title">Errors</div>
+            </div>
+            <div class="smell-card-count" style="color: var(--error)">${totalErrors}</div>
+        </div>
+    `;
+    html += '</div>';
+
+    // Filters
+    html += '<div class="smell-filters">';
+    html += '<div class="filter-title">Filter by Type</div>';
+    html += '<div class="filter-checkboxes">';
+
+    Object.keys(smellCounts).forEach(type => {
+        const count = smellCounts[type].total;
+        html += `
+            <div class="filter-checkbox-item">
+                <input type="checkbox" id="filter-${type.replace(/\\s+/g, '-')}"
+                       checked onchange="filterCodeSmells()">
+                <label class="filter-checkbox-label" for="filter-${type.replace(/\\s+/g, '-')}">${type}</label>
+                <span class="filter-checkbox-count">${count}</span>
+            </div>
+        `;
+    });
+
+    html += '</div></div>';
+
+    // Smells Table
+    html += '<div id="smells-table-wrapper">';
+    html += '<h3 class="section-title">Detected Code Smells</h3>';
+
+    if (allSmells.length === 0) {
+        html += '<p style="color: var(--text-secondary); text-align: center; padding: 20px;">No code smells detected! Great job! 🎉</p>';
+    } else {
+        html += '<div class="smells-table-container">';
+        html += '<table class="smells-table">';
+        html += `
+            <thead>
+                <tr>
+                    <th>Type</th>
+                    <th>Severity</th>
+                    <th>Name</th>
+                    <th>File</th>
+                    <th>Details</th>
+                </tr>
+            </thead>
+            <tbody id="smells-table-body">
+        `;
+
+        // Sort by severity (error first) then by type
+        const sortedSmells = [...allSmells].sort((a, b) => {
+            if (a.severity !== b.severity) {
+                return a.severity === 'error' ? -1 : 1;
+            }
+            return a.type.localeCompare(b.type);
+        });
+
+        sortedSmells.forEach(smell => {
+            const fileName = smell.node.file_path ? smell.node.file_path.split('/').pop() : 'Unknown';
+            const severityIcon = smell.severity === 'error' ? '🚨' : '⚠️';
+
+            html += `
+                <tr class="smell-row" data-smell-type="${smell.type.replace(/\\s+/g, '-')}"
+                    onclick='navigateToChunk(${JSON.stringify(smell.node.name)})'>
+                    <td><span class="smell-type-badge">${escapeHtml(smell.type)}</span></td>
+                    <td><span class="severity-badge ${smell.severity}">${severityIcon} ${smell.severity.toUpperCase()}</span></td>
+                    <td class="smell-name">${escapeHtml(smell.node.name)}</td>
+                    <td class="smell-file" title="${escapeHtml(smell.node.file_path || '')}">${escapeHtml(fileName)}</td>
+                    <td class="smell-details">${escapeHtml(smell.details)}</td>
+                </tr>
+            `;
+        });
+
+        html += '</tbody></table></div>';
+    }
+
+    html += '</div>'; // smells-table-wrapper
+    html += '</div>'; // code-smells-report
+
+    viewerContent.innerHTML = html;
+
+    // Hide section dropdown for reports (no code sections)
+    const sectionNav = document.getElementById('section-nav');
+    if (sectionNav) {
+        sectionNav.style.display = 'none';
+    }
+}
+
+function filterCodeSmells() {
+    const rows = document.querySelectorAll('.smell-row');
+
+    rows.forEach(row => {
+        const smellType = row.getAttribute('data-smell-type');
+        const checkbox = document.getElementById(`filter-${smellType}`);
+
+        if (checkbox && checkbox.checked) {
+            row.style.display = '';
+        } else {
+            row.style.display = 'none';
+        }
+    });
+}
+
+// ============================================================================
+// DEPENDENCIES ANALYSIS AND REPORTING
+// ============================================================================
+
+function showDependencies() {
+    openViewerPanel();
+
+    const viewerTitle = document.getElementById('viewer-title');
+    const viewerContent = document.getElementById('viewer-content');
+
+    viewerTitle.textContent = '🔗 Code Structure';
+
+    // Code file extensions (exclude docs like .md, .txt, .rst)
+    const codeExtensions = ['.py', '.js', '.ts', '.jsx', '.tsx', '.go', '.rs', '.java', '.c', '.cpp', '.h', '.hpp', '.cs', '.rb', '.php', '.swift', '.kt', '.scala', '.ex', '.exs', '.clj', '.vue', '.svelte'];
+
+    function isCodeFile(filePath) {
+        const ext = filePath.substring(filePath.lastIndexOf('.')).toLowerCase();
+        return codeExtensions.includes(ext);
+    }
+
+    // Build directory structure from nodes (code files only)
+    const dirStructure = new Map();
+
+    allNodes.forEach(node => {
+        if (node.type === 'file' && node.file_path && isCodeFile(node.file_path)) {
+            const parts = node.file_path.split('/');
+            const fileName = parts.pop();
+            const dirPath = parts.join('/') || '/';
+
+            if (!dirStructure.has(dirPath)) {
+                dirStructure.set(dirPath, []);
+            }
+            dirStructure.get(dirPath).push({
+                name: fileName,
+                path: node.file_path,
+                chunks: allNodes.filter(n => n.file_path === node.file_path && n.type !== 'file').length
+            });
+        }
+    });
+
+    // Calculate stats
+    const totalDirs = dirStructure.size;
+    const totalFiles = Array.from(dirStructure.values()).reduce((sum, files) => sum + files.length, 0);
+    const totalChunks = allNodes.filter(n => n.type !== 'file' && n.type !== 'directory').length;
+
+    let html = `
+        <div class="report-section">
+            <h3>📁 Directory Overview</h3>
+            <p style="color: var(--text-secondary); margin-bottom: 15px;">Showing code organization by directory structure.</p>
+            <div class="metrics-grid">
+                <div class="metric-card">
+                    <div class="metric-value">${totalDirs}</div>
+                    <div class="metric-label">Directories</div>
+                </div>
+                <div class="metric-card">
+                    <div class="metric-value">${totalFiles}</div>
+                    <div class="metric-label">Files</div>
+                </div>
+                <div class="metric-card">
+                    <div class="metric-value">${totalChunks}</div>
+                    <div class="metric-label">Code Chunks</div>
+                </div>
+            </div>
+        </div>
+        <div class="report-section">
+            <h3>📂 Directory Structure</h3>
+    `;
+
+    // Sort directories
+    const sortedDirs = Array.from(dirStructure.entries()).sort((a, b) => a[0].localeCompare(b[0]));
+
+    sortedDirs.forEach(([dir, files]) => {
+        const dirDisplay = dir === '/' ? 'Root' : dir;
+        const totalChunksInDir = files.reduce((sum, f) => sum + f.chunks, 0);
+
+        html += `
+            <div class="dependency-item" style="margin-bottom: 20px; padding: 12px; background: var(--bg-secondary); border-radius: 6px; border-left: 3px solid var(--accent-blue);">
+                <div style="display: flex; justify-content: space-between; align-items: center; margin-bottom: 8px;">
+                    <strong style="color: var(--accent-blue);">📁 ${escapeHtml(dirDisplay)}</strong>
+                    <span style="color: var(--text-secondary); font-size: 12px;">${files.length} files, ${totalChunksInDir} chunks</span>
+                </div>
+                <ul style="margin: 0; padding: 0 0 0 20px; list-style: none;">
+        `;
+
+        files.sort((a, b) => a.name.localeCompare(b.name)).forEach(file => {
+            html += `<li style="padding: 4px 0; color: var(--text-primary);">
+                📄 ${escapeHtml(file.name)}
+                <span style="color: var(--text-secondary); font-size: 11px;">(${file.chunks} chunks)</span>
+            </li>`;
+        });
+
+        html += `</ul></div>`;
+    });
+
+    html += '</div>';
+
+    viewerContent.innerHTML = html;
+
+    // Hide section dropdown for reports (no code sections)
+    const sectionNav = document.getElementById('section-nav');
+    if (sectionNav) {
+        sectionNav.style.display = 'none';
+    }
+}
+
+function buildFileDependencyGraph() {
+    // Map: file_path -> { dependsOn: Set<file_path>, usedBy: Set<file_path> }
+    const fileDeps = new Map();
+
+    allLinks.forEach(link => {
+        if (link.type === 'caller') {
+            const sourceNode = allNodes.find(n => n.id === link.source);
+            const targetNode = allNodes.find(n => n.id === link.target);
+
+            if (sourceNode && targetNode && sourceNode.file_path && targetNode.file_path) {
+                // Skip self-references (same file)
+                if (sourceNode.file_path === targetNode.file_path) {
+                    return;
+                }
+
+                // sourceNode calls targetNode → source depends on target
+                if (!fileDeps.has(sourceNode.file_path)) {
+                    fileDeps.set(sourceNode.file_path, { dependsOn: new Set(), usedBy: new Set() });
+                }
+                if (!fileDeps.has(targetNode.file_path)) {
+                    fileDeps.set(targetNode.file_path, { dependsOn: new Set(), usedBy: new Set() });
+                }
+
+                fileDeps.get(sourceNode.file_path).dependsOn.add(targetNode.file_path);
+                fileDeps.get(targetNode.file_path).usedBy.add(sourceNode.file_path);
+            }
+        }
+    });
+
+    return fileDeps;
+}
+
+function findCircularDeps(fileDeps) {
+    // Simple cycle detection using DFS
+    const cycles = [];
+    const visited = new Set();
+    const recStack = new Set();
+    const pathStack = [];
+
+    function dfs(filePath) {
+        visited.add(filePath);
+        recStack.add(filePath);
+        pathStack.push(filePath);
+
+        const deps = fileDeps.get(filePath);
+        if (deps && deps.dependsOn) {
+            for (const depFile of deps.dependsOn) {
+                if (!visited.has(depFile)) {
+                    dfs(depFile);
+                } else if (recStack.has(depFile)) {
+                    // Found a cycle
+                    const cycleStartIndex = pathStack.indexOf(depFile);
+                    if (cycleStartIndex !== -1) {
+                        const cycle = pathStack.slice(cycleStartIndex);
+                        cycle.push(depFile); // Complete the cycle
+                        // Check if this cycle is already recorded
+                        const cycleStr = cycle.sort().join('|');
+                        if (!cycles.some(c => c.sort().join('|') === cycleStr)) {
+                            cycles.push([...cycle]);
+                        }
+                    }
+                }
+            }
+        }
+
+        pathStack.pop();
+        recStack.delete(filePath);
+    }
+
+    for (const filePath of fileDeps.keys()) {
+        if (!visited.has(filePath)) {
+            dfs(filePath);
+        }
+    }
+
+    return cycles;
+}
+
+function toggleDependencyDetails(rowId, index) {
+    const detailsRow = document.getElementById(`${rowId}-details`);
+    const btn = document.querySelector(`#${rowId} .expand-btn`);
+
+    if (detailsRow.style.display === 'none') {
+        detailsRow.style.display = '';
+        btn.textContent = '▲';
+    } else {
+        detailsRow.style.display = 'none';
+        btn.textContent = '▼';
+    }
+}
+
+// ============================================================================
+// TRENDS / METRICS SNAPSHOT
+// ============================================================================
+
+function showTrends() {
+    openViewerPanel();
+
+    const viewerTitle = document.getElementById('viewer-title');
+    const viewerContent = document.getElementById('viewer-content');
+
+    viewerTitle.textContent = '📈 Codebase Metrics Snapshot';
+
+    // Calculate metrics from current codebase
+    const metrics = calculateCodebaseMetrics();
+
+    // Build HTML
+    let html = '<div class="trends-report">';
+
+    // Snapshot Banner
+    html += '<div class="snapshot-banner">';
+    html += '<div class="snapshot-header">';
+    html += '<div class="snapshot-icon">📊</div>';
+    html += '<div class="snapshot-info">';
+    html += '<div class="snapshot-title">Codebase Metrics Snapshot</div>';
+    html += `<div class="snapshot-timestamp">Generated: ${new Date().toLocaleString('en-US', {
+        month: 'short',
+        day: 'numeric',
+        year: 'numeric',
+        hour: 'numeric',
+        minute: '2-digit',
+        hour12: true
+    })}</div>`;
+    html += '</div></div>';
+    html += '<div class="snapshot-description">';
+    html += 'This snapshot serves as the baseline for future trend tracking. ';
+    html += 'With git history analysis, you could track how these metrics evolve over time.';
+    html += '</div>';
+    html += '</div>';
+
+    // Key Metrics Cards
+    html += '<div class="metrics-section">';
+    html += '<h3 class="section-title">Key Metrics</h3>';
+    html += '<div class="metrics-grid">';
+
+    html += `<div class="metric-card">
+        <div class="metric-icon">📝</div>
+        <div class="metric-value">${metrics.totalLines.toLocaleString()}</div>
+        <div class="metric-label">Lines of Code</div>
+    </div>`;
+
+    html += `<div class="metric-card">
+        <div class="metric-icon">⚡</div>
+        <div class="metric-value">${metrics.totalFunctions}</div>
+        <div class="metric-label">Functions/Methods</div>
+    </div>`;
+
+    html += `<div class="metric-card">
+        <div class="metric-icon">🎯</div>
+        <div class="metric-value">${metrics.totalClasses}</div>
+        <div class="metric-label">Classes</div>
+    </div>`;
+
+    html += `<div class="metric-card">
+        <div class="metric-icon">📄</div>
+        <div class="metric-value">${metrics.totalFiles}</div>
+        <div class="metric-label">Files</div>
+    </div>`;
+
+    html += '</div></div>';
+
+    // Code Health Score
+    html += '<div class="health-section">';
+    html += '<h3 class="section-title">Code Health Score</h3>';
+    html += '<div class="health-card">';
+
+    const healthInfo = getHealthScoreInfo(metrics.healthScore);
+    html += `<div class="health-score-display">
+        <div class="health-score-value">${metrics.healthScore}/100</div>
+        <div class="health-score-label">${healthInfo.emoji} ${healthInfo.label}</div>
+    </div>`;
+
+    html += '<div class="health-progress-container">';
+    html += `<div class="health-progress-bar" style="width: ${metrics.healthScore}%; background: ${healthInfo.color}"></div>`;
+    html += '</div>';
+
+    html += `<div class="health-description">${healthInfo.description}</div>`;
+    html += '</div></div>';
+
+    // Complexity Distribution
+    html += '<div class="distribution-section">';
+    html += '<h3 class="section-title">Complexity Distribution</h3>';
+    html += '<div class="distribution-chart">';
+
+    const complexityDist = metrics.complexityDistribution;
+    const maxPct = Math.max(...Object.values(complexityDist));
+
+    ['A', 'B', 'C', 'D', 'F'].forEach(grade => {
+        const pct = complexityDist[grade] || 0;
+        const barWidth = maxPct > 0 ? (pct / maxPct * 100) : 0;
+        const color = getGradeColor(grade);
+        const range = getComplexityRange(grade);
+
+        html += `<div class="distribution-bar-row">
+            <div class="distribution-bar-label">
+                <span class="distribution-grade" style="color: ${color}">${grade}</span>
+                <span class="distribution-range">${range}</span>
+            </div>
+            <div class="distribution-bar-container">
+                <div class="distribution-bar-fill" style="width: ${barWidth}%; background: ${color}"></div>
+            </div>
+            <div class="distribution-bar-value">${pct.toFixed(1)}%</div>
+        </div>`;
+    });
+
+    html += '</div></div>';
+
+    // Function Size Distribution
+    html += '<div class="size-distribution-section">';
+    html += '<h3 class="section-title">Function Size Distribution</h3>';
+    html += '<div class="distribution-chart">';
+
+    const sizeDist = metrics.sizeDistribution;
+    const maxSizePct = Math.max(...Object.values(sizeDist));
+
+    [
+        { key: 'small', label: 'Small (1-20 lines)', color: '#238636' },
+        { key: 'medium', label: 'Medium (21-50 lines)', color: '#1f6feb' },
+        { key: 'large', label: 'Large (51-100 lines)', color: '#d29922' },
+        { key: 'veryLarge', label: 'Very Large (100+ lines)', color: '#da3633' }
+    ].forEach(({ key, label, color }) => {
+        const pct = sizeDist[key] || 0;
+        const barWidth = maxSizePct > 0 ? (pct / maxSizePct * 100) : 0;
+
+        html += `<div class="distribution-bar-row">
+            <div class="distribution-bar-label">
+                <span class="size-label">${label}</span>
+            </div>
+            <div class="distribution-bar-container">
+                <div class="distribution-bar-fill" style="width: ${barWidth}%; background: ${color}"></div>
+            </div>
+            <div class="distribution-bar-value">${pct.toFixed(1)}%</div>
+        </div>`;
+    });
+
+    html += '</div></div>';
+
+    // Historical Trends Section
+    html += '<div class="trends-section">';
+    html += '<h3 class="section-title">📊 Historical Trends</h3>';
+
+    // Check if trend data is available
+    if (window.graphTrendData && window.graphTrendData.entries && window.graphTrendData.entries.length > 0) {
+        const trendEntries = window.graphTrendData.entries;
+
+        // Render trend charts
+        html += '<div class="trends-container">';
+        html += '<div id="health-score-chart" class="trend-chart"></div>';
+        html += '<div id="complexity-chart" class="trend-chart"></div>';
+        html += '<div id="files-chunks-chart" class="trend-chart"></div>';
+        html += '</div>';
+
+        html += `<div class="trend-info">Showing ${trendEntries.length} data points from ${trendEntries[0].date} to ${trendEntries[trendEntries.length - 1].date}</div>`;
+    } else {
+        // No trend data yet - show placeholder
+        html += '<div class="future-placeholder">';
+        html += '<div class="future-icon">📊</div>';
+        html += '<div class="future-title">No Historical Data Yet</div>';
+        html += '<div class="future-description">';
+        html += 'Trend data will be collected automatically after each indexing operation. ';
+        html += 'Run <code>mcp-vector-search index</code> to generate the first snapshot.';
+        html += '</div>';
+        html += '</div>';
+    }
+
+    html += '</div>'; // trends-section
+
+    html += '</div>'; // trends-report
+
+    viewerContent.innerHTML = html;
+
+    // Hide section dropdown for reports (no code sections)
+    const sectionNav = document.getElementById('section-nav');
+    if (sectionNav) {
+        sectionNav.style.display = 'none';
+    }
+
+    // Render D3 charts if trend data is available
+    if (window.graphTrendData && window.graphTrendData.entries && window.graphTrendData.entries.length > 0) {
+        renderTrendCharts(window.graphTrendData.entries);
+    }
+}
+
+// ============================================================================
+// REMEDIATION REPORT GENERATION
+// ============================================================================
+
+function generateRemediationReport() {
+    // Gather complexity data (metrics are stored directly on nodes, not in a metrics object)
+    const complexityData = [];
+    allNodes.forEach(node => {
+        if (node.complexity !== undefined && node.complexity !== null) {
+            const complexity = node.complexity;
+            let grade = 'A';
+            if (complexity > 40) grade = 'F';
+            else if (complexity > 30) grade = 'D';
+            else if (complexity > 20) grade = 'C';
+            else if (complexity > 10) grade = 'B';
+
+            // Calculate lines from start_line and end_line
+            const lines = (node.end_line && node.start_line) ? (node.end_line - node.start_line + 1) : 0;
+
+            if (grade !== 'A' && grade !== 'B') {  // Only include C, D, F
+                complexityData.push({
+                    name: node.name || node.id,
+                    file: node.file_path || 'Unknown',
+                    type: node.type || 'unknown',
+                    complexity: complexity,
+                    grade: grade,
+                    lines: lines
+                });
+            }
+        }
+    });
+
+    // Gather code smell data
+    const smells = [];
+    allNodes.forEach(node => {
+        const file = node.file_path || 'Unknown';
+        const name = node.name || node.id;
+        const lines = (node.end_line && node.start_line) ? (node.end_line - node.start_line + 1) : 0;
+        const complexity = node.complexity || 0;
+        const depth = node.depth || 0;
+
+        // Long Method
+        if (lines > 50) {
+            smells.push({
+                file, name,
+                smell: 'Long Method',
+                severity: lines > 100 ? 'error' : 'warning',
+                detail: `${lines} lines (recommended: <50)`
+            });
+        }
+
+        // High Complexity
+        if (complexity > 15) {
+            smells.push({
+                file, name,
+                smell: 'High Complexity',
+                severity: complexity > 25 ? 'error' : 'warning',
+                detail: `Complexity: ${complexity} (recommended: <15)`
+            });
+        }
+
+        // Deep Nesting (using depth field)
+        if (depth > 4) {
+            smells.push({
+                file, name,
+                smell: 'Deep Nesting',
+                severity: depth > 6 ? 'error' : 'warning',
+                detail: `Depth: ${depth} (recommended: <4)`
+            });
+        }
+
+        // God Class (for classes only)
+        if (node.type === 'class' && lines > 300) {
+            smells.push({
+                file, name,
+                smell: 'God Class',
+                severity: 'error',
+                detail: `${lines} lines - consider breaking into smaller classes`
+            });
+        }
+    });
+
+    // Sort by severity (errors first) then by file
+    complexityData.sort((a, b) => {
+        const gradeOrder = { F: 0, D: 1, C: 2 };
+        return (gradeOrder[a.grade] || 99) - (gradeOrder[b.grade] || 99);
+    });
+
+    smells.sort((a, b) => {
+        if (a.severity !== b.severity) {
+            return a.severity === 'error' ? -1 : 1;
+        }
+        return a.file.localeCompare(b.file);
+    });
+
+    // Generate Markdown
+    const date = new Date().toISOString().split('T')[0];
+    let markdown = `# Code Remediation Report
+Generated: ${date}
+
+## Summary
+
+- **High Complexity Items**: ${complexityData.length}
+- **Code Smells Detected**: ${smells.length}
+- **Critical Issues (Errors)**: ${smells.filter(s => s.severity === 'error').length}
+
+---
+
+## 🔴 Priority: High Complexity Code
+
+These functions/methods have complexity scores that make them difficult to maintain and test.
+
+| Grade | Name | File | Complexity | Lines |
+|-------|------|------|------------|-------|
+`;
+
+    complexityData.forEach(item => {
+        const gradeEmoji = item.grade === 'F' ? '🔴' : item.grade === 'D' ? '🟠' : '🟡';
+        markdown += `| ${gradeEmoji} ${item.grade} | \\`${item.name}\\` | ${item.file} | ${item.complexity} | ${item.lines} |\\n`;
+    });
+
+    markdown += `
+---
+
+## 🔍 Code Smells
+
+### Critical Issues (Errors)
+
+`;
+
+    const errors = smells.filter(s => s.severity === 'error');
+    if (errors.length === 0) {
+        markdown += '_No critical issues found._\\n';
+    } else {
+        markdown += '| Smell | Name | File | Detail |\\n|-------|------|------|--------|\\n';
+        errors.forEach(s => {
+            markdown += `| 🔴 ${s.smell} | \\`${s.name}\\` | ${s.file} | ${s.detail} |\\n`;
+        });
+    }
+
+    markdown += `
+### Warnings
+
+`;
+
+    const warnings = smells.filter(s => s.severity === 'warning');
+    if (warnings.length === 0) {
+        markdown += '_No warnings found._\\n';
+    } else {
+        markdown += '| Smell | Name | File | Detail |\\n|-------|------|------|--------|\\n';
+        warnings.forEach(s => {
+            markdown += `| 🟡 ${s.smell} | \\`${s.name}\\` | ${s.file} | ${s.detail} |\\n`;
+        });
+    }
+
+    markdown += `
+---
+
+## Recommended Actions
+
+1. **Start with Grade F items** - These have the highest complexity and are hardest to maintain
+2. **Address Critical code smells** - God Classes and deeply nested code should be refactored
+3. **Break down long methods** - Extract helper functions to reduce complexity
+4. **Add tests before refactoring** - Ensure behavior is preserved
+
+---
+
+_Generated by MCP Vector Search Visualization_
+`;
+
+    // Save the file with dialog (or fallback to download)
+    const blob = new Blob([markdown], { type: 'text/markdown' });
+    const defaultFilename = `remediation-report-${date}.md`;
+
+    async function saveWithDialog() {
+        try {
+            // Use File System Access API if available (shows save dialog)
+            if ('showSaveFilePicker' in window) {
+                const handle = await window.showSaveFilePicker({
+                    suggestedName: defaultFilename,
+                    types: [{
+                        description: 'Markdown files',
+                        accept: { 'text/markdown': ['.md'] }
+                    }]
+                });
+                const writable = await handle.createWritable();
+                await writable.write(blob);
+                await writable.close();
+                return handle.name;
+            }
+        } catch (err) {
+            if (err.name === 'AbortError') {
+                return null; // User cancelled
+            }
+            console.warn('Save dialog failed, falling back to download:', err);
+        }
+
+        // Fallback: standard download
+        const url = URL.createObjectURL(blob);
+        const a = document.createElement('a');
+        a.href = url;
+        a.download = defaultFilename;
+        document.body.appendChild(a);
+        a.click();
+        document.body.removeChild(a);
+        URL.revokeObjectURL(url);
+        return defaultFilename;
+    }
+
+    saveWithDialog().then(savedFilename => {
+        if (savedFilename === null) {
+            // User cancelled - don't show confirmation
+            return;
+        }
+
+        // Show confirmation
+        openViewerPanel();
+        document.getElementById('viewer-title').textContent = '📋 Report Saved';
+        document.getElementById('viewer-content').innerHTML = `
+            <div class="report-section">
+                <h3>✅ Remediation Report Generated</h3>
+                <p>The report has been saved as <code>${escapeHtml(savedFilename)}</code></p>
+            <div class="metrics-grid">
+                <div class="metric-card">
+                    <div class="metric-value">${complexityData.length}</div>
+                    <div class="metric-label">Complexity Issues</div>
+                </div>
+                <div class="metric-card">
+                    <div class="metric-value">${smells.length}</div>
+                    <div class="metric-label">Code Smells</div>
+                </div>
+                <div class="metric-card">
+                    <div class="metric-value">${errors.length}</div>
+                    <div class="metric-label">Critical Errors</div>
+                </div>
+            </div>
+            <p style="margin-top: 15px; color: var(--text-secondary);">Share this report with your team for prioritized remediation.</p>
+        </div>
+    `;
+
+        // Hide section dropdown for reports (no code sections)
+        const sectionNav = document.getElementById('section-nav');
+        if (sectionNav) {
+            sectionNav.style.display = 'none';
+        }
+    });
+}
+
+// Render trend line charts using D3
+function renderTrendCharts(entries) {
+    // Chart dimensions
+    const margin = {top: 20, right: 30, bottom: 40, left: 50};
+    const width = 600 - margin.left - margin.right;
+    const height = 250 - margin.top - margin.bottom;
+
+    // Parse dates
+    const parseDate = d3.timeParse('%Y-%m-%d');
+    entries.forEach(d => {
+        d.parsedDate = parseDate(d.date);
+    });
+
+    // 1. Health Score Chart
+    renderLineChart('#health-score-chart', entries, {
+        title: 'Health Score Over Time',
+        width, height, margin,
+        yAccessor: d => d.metrics.health_score || 0,
+        yLabel: 'Health Score',
+        color: '#238636',
+        yDomain: [0, 100]
+    });
+
+    // 2. Average Complexity Chart
+    renderLineChart('#complexity-chart', entries, {
+        title: 'Average Complexity Over Time',
+        width, height, margin,
+        yAccessor: d => d.metrics.avg_complexity || 0,
+        yLabel: 'Avg Complexity',
+        color: '#d29922',
+        yDomain: [0, d3.max(entries, d => d.metrics.avg_complexity || 0) * 1.1]
+    });
+
+    // 3. Files and Chunks Chart (dual line)
+    renderDualLineChart('#files-chunks-chart', entries, {
+        title: 'Files and Chunks Over Time',
+        width, height, margin,
+        y1Accessor: d => d.metrics.total_files || 0,
+        y2Accessor: d => d.metrics.total_chunks || 0,
+        y1Label: 'Files',
+        y2Label: 'Chunks',
+        color1: '#1f6feb',
+        color2: '#8957e5'
+    });
+}
+
+// Render single line chart
+function renderLineChart(selector, data, config) {
+    const svg = d3.select(selector)
+        .append('svg')
+        .attr('width', config.width + config.margin.left + config.margin.right)
+        .attr('height', config.height + config.margin.top + config.margin.bottom)
+        .append('g')
+        .attr('transform', `translate(${config.margin.left},${config.margin.top})`);
+
+    // Add title
+    svg.append('text')
+        .attr('x', config.width / 2)
+        .attr('y', -5)
+        .attr('text-anchor', 'middle')
+        .style('font-size', '14px')
+        .style('font-weight', 'bold')
+        .text(config.title);
+
+    // Create scales
+    const xScale = d3.scaleTime()
+        .domain(d3.extent(data, d => d.parsedDate))
+        .range([0, config.width]);
+
+    const yScale = d3.scaleLinear()
+        .domain(config.yDomain || [0, d3.max(data, config.yAccessor)])
+        .range([config.height, 0]);
+
+    // Create line generator
+    const line = d3.line()
+        .x(d => xScale(d.parsedDate))
+        .y(d => yScale(config.yAccessor(d)))
+        .curve(d3.curveMonotoneX);
+
+    // Add X axis
+    svg.append('g')
+        .attr('transform', `translate(0,${config.height})`)
+        .call(d3.axisBottom(xScale).ticks(5).tickFormat(d3.timeFormat('%b %d')))
+        .selectAll('text')
+        .style('font-size', '11px');
+
+    // Add Y axis
+    svg.append('g')
+        .call(d3.axisLeft(yScale).ticks(5))
+        .selectAll('text')
+        .style('font-size', '11px');
+
+    // Add Y axis label
+    svg.append('text')
+        .attr('transform', 'rotate(-90)')
+        .attr('y', 0 - config.margin.left + 10)
+        .attr('x', 0 - (config.height / 2))
+        .attr('dy', '1em')
+        .style('text-anchor', 'middle')
+        .style('font-size', '12px')
+        .text(config.yLabel);
+
+    // Add line path
+    svg.append('path')
+        .datum(data)
+        .attr('fill', 'none')
+        .attr('stroke', config.color)
+        .attr('stroke-width', 2)
+        .attr('d', line);
+
+    // Add dots
+    svg.selectAll('.dot')
+        .data(data)
+        .enter().append('circle')
+        .attr('class', 'dot')
+        .attr('cx', d => xScale(d.parsedDate))
+        .attr('cy', d => yScale(config.yAccessor(d)))
+        .attr('r', 4)
+        .attr('fill', config.color)
+        .style('cursor', 'pointer')
+        .append('title')
+        .text(d => `${d.date}: ${config.yAccessor(d).toFixed(1)}`);
+}
+
+// Render dual line chart (two Y axes)
+function renderDualLineChart(selector, data, config) {
+    const svg = d3.select(selector)
+        .append('svg')
+        .attr('width', config.width + config.margin.left + config.margin.right)
+        .attr('height', config.height + config.margin.top + config.margin.bottom)
+        .append('g')
+        .attr('transform', `translate(${config.margin.left},${config.margin.top})`);
+
+    // Add title
+    svg.append('text')
+        .attr('x', config.width / 2)
+        .attr('y', -5)
+        .attr('text-anchor', 'middle')
+        .style('font-size', '14px')
+        .style('font-weight', 'bold')
+        .text(config.title);
+
+    // Create scales
+    const xScale = d3.scaleTime()
+        .domain(d3.extent(data, d => d.parsedDate))
+        .range([0, config.width]);
+
+    const y1Scale = d3.scaleLinear()
+        .domain([0, d3.max(data, config.y1Accessor) * 1.1])
+        .range([config.height, 0]);
+
+    const y2Scale = d3.scaleLinear()
+        .domain([0, d3.max(data, config.y2Accessor) * 1.1])
+        .range([config.height, 0]);
+
+    // Create line generators
+    const line1 = d3.line()
+        .x(d => xScale(d.parsedDate))
+        .y(d => y1Scale(config.y1Accessor(d)))
+        .curve(d3.curveMonotoneX);
+
+    const line2 = d3.line()
+        .x(d => xScale(d.parsedDate))
+        .y(d => y2Scale(config.y2Accessor(d)))
+        .curve(d3.curveMonotoneX);
+
+    // Add X axis
+    svg.append('g')
+        .attr('transform', `translate(0,${config.height})`)
+        .call(d3.axisBottom(xScale).ticks(5).tickFormat(d3.timeFormat('%b %d')))
+        .selectAll('text')
+        .style('font-size', '11px');
+
+    // Add Y1 axis (left)
+    svg.append('g')
+        .call(d3.axisLeft(y1Scale).ticks(5))
+        .selectAll('text')
+        .style('font-size', '11px')
+        .style('fill', config.color1);
+
+    // Add Y2 axis (right)
+    svg.append('g')
+        .attr('transform', `translate(${config.width},0)`)
+        .call(d3.axisRight(y2Scale).ticks(5))
+        .selectAll('text')
+        .style('font-size', '11px')
+        .style('fill', config.color2);
+
+    // Add line 1
+    svg.append('path')
+        .datum(data)
+        .attr('fill', 'none')
+        .attr('stroke', config.color1)
+        .attr('stroke-width', 2)
+        .attr('d', line1);
+
+    // Add line 2
+    svg.append('path')
+        .datum(data)
+        .attr('fill', 'none')
+        .attr('stroke', config.color2)
+        .attr('stroke-width', 2)
+        .attr('stroke-dasharray', '5,5')
+        .attr('d', line2);
+
+    // Add legend
+    const legend = svg.append('g')
+        .attr('transform', `translate(${config.width - 120}, 10)`);
+
+    legend.append('line')
+        .attr('x1', 0).attr('x2', 20)
+        .attr('y1', 5).attr('y2', 5)
+        .attr('stroke', config.color1)
+        .attr('stroke-width', 2);
+    legend.append('text')
+        .attr('x', 25).attr('y', 9)
+        .style('font-size', '11px')
+        .text(config.y1Label);
+
+    legend.append('line')
+        .attr('x1', 0).attr('x2', 20)
+        .attr('y1', 20).attr('y2', 20)
+        .attr('stroke', config.color2)
+        .attr('stroke-width', 2)
+        .attr('stroke-dasharray', '5,5');
+    legend.append('text')
+        .attr('x', 25).attr('y', 24)
+        .style('font-size', '11px')
+        .text(config.y2Label);
+}
+
+function calculateCodebaseMetrics() {
+    const metrics = {
+        totalLines: 0,
+        totalFunctions: 0,
+        totalClasses: 0,
+        totalFiles: 0,
+        complexityDistribution: { A: 0, B: 0, C: 0, D: 0, F: 0 },
+        sizeDistribution: { small: 0, medium: 0, large: 0, veryLarge: 0 },
+        healthScore: 0
+    };
+
+    const chunksWithComplexity = [];
+
+    function analyzeNode(node) {
+        // Count files
+        if (node.type === 'file') {
+            metrics.totalFiles++;
+        }
+
+        // Count classes
+        if (node.type === 'class') {
+            metrics.totalClasses++;
+        }
+
+        // Count functions and methods
+        if (node.type === 'function' || node.type === 'method') {
+            metrics.totalFunctions++;
+
+            // Calculate lines
+            const lineCount = (node.end_line && node.start_line)
+                ? node.end_line - node.start_line + 1
+                : 0;
+            metrics.totalLines += lineCount;
+
+            // Size distribution
+            if (lineCount <= 20) {
+                metrics.sizeDistribution.small++;
+            } else if (lineCount <= 50) {
+                metrics.sizeDistribution.medium++;
+            } else if (lineCount <= 100) {
+                metrics.sizeDistribution.large++;
+            } else {
+                metrics.sizeDistribution.veryLarge++;
+            }
+
+            // Complexity distribution
+            if (node.complexity !== undefined && node.complexity !== null) {
+                const grade = getComplexityGrade(node.complexity);
+                if (grade in metrics.complexityDistribution) {
+                    metrics.complexityDistribution[grade]++;
+                }
+                chunksWithComplexity.push(node);
+            }
+        }
+
+        // Recursively process children
+        const children = node.children || node._children || [];
+        children.forEach(child => analyzeNode(child));
+    }
+
+    if (treeData) {
+        analyzeNode(treeData);
+    }
+
+    // Convert complexity counts to percentages
+    const totalWithComplexity = chunksWithComplexity.length;
+    if (totalWithComplexity > 0) {
+        Object.keys(metrics.complexityDistribution).forEach(grade => {
+            metrics.complexityDistribution[grade] =
+                (metrics.complexityDistribution[grade] / totalWithComplexity) * 100;
+        });
+    }
+
+    // Convert size counts to percentages
+    const totalFuncs = metrics.totalFunctions;
+    if (totalFuncs > 0) {
+        Object.keys(metrics.sizeDistribution).forEach(size => {
+            metrics.sizeDistribution[size] =
+                (metrics.sizeDistribution[size] / totalFuncs) * 100;
+        });
+    }
+
+    // Calculate health score
+    metrics.healthScore = calculateHealthScore(chunksWithComplexity);
+
+    return metrics;
+}
+
+function calculateHealthScore(chunks) {
+    if (chunks.length === 0) return 100;
+
+    let score = 0;
+    chunks.forEach(chunk => {
+        const grade = getComplexityGrade(chunk.complexity);
+        const gradeScores = { A: 100, B: 80, C: 60, D: 40, F: 20 };
+        score += gradeScores[grade] || 50;
+    });
+
+    return Math.round(score / chunks.length);
+}
+
+function getHealthScoreInfo(score) {
+    if (score >= 80) {
+        return {
+            emoji: '🟢',
+            label: 'Excellent',
+            color: '#238636',
+            description: 'Your codebase has excellent complexity distribution with most code in the A-B range.'
+        };
+    } else if (score >= 60) {
+        return {
+            emoji: '🟡',
+            label: 'Good',
+            color: '#d29922',
+            description: 'Your codebase is in good shape, but could benefit from refactoring some complex functions.'
+        };
+    } else if (score >= 40) {
+        return {
+            emoji: '🟠',
+            label: 'Needs Attention',
+            color: '#f0883e',
+            description: 'Your codebase has significant complexity issues that should be addressed soon.'
+        };
+    } else {
+        return {
+            emoji: '🔴',
+            label: 'Critical',
+            color: '#da3633',
+            description: 'Your codebase has critical complexity issues requiring immediate refactoring.'
+        };
+    }
+}
+
+function getComplexityRange(grade) {
+    const ranges = {
+        'A': '1-5',
+        'B': '6-10',
+        'C': '11-15',
+        'D': '16-20',
+        'F': '21+'
+    };
+    return ranges[grade] || '';
+}
+
+function showComingSoon(reportName) {
+    alert(`${reportName} - Coming Soon!\n\nThis feature will display detailed ${reportName.toLowerCase()} in a future release.`);
+}
+
+// ============================================================================
+// INITIALIZATION
+// ============================================================================
+
+// Load data and initialize UI when page loads
+document.addEventListener('DOMContentLoaded', () => {
+    console.log('=== PAGE INITIALIZATION ===');
+    console.log('DOMContentLoaded event fired');
+
+    // Load theme preference before anything else
+    loadThemePreference();
+
+    // Initialize toggle label highlighting
+    const labels = document.querySelectorAll('.toggle-label');
+    console.log(`Found ${labels.length} toggle labels`);
+    if (labels[0]) {
+        labels[0].classList.add('active');
+        console.log('Activated first toggle label (linear mode)');
+    }
+
+    // Close search results when clicking outside
+    document.addEventListener('click', (event) => {
+        const searchContainer = document.querySelector('.search-container');
+        if (searchContainer && !searchContainer.contains(event.target)) {
+            closeSearchResults();
+        }
+    });
+
+    // Load graph data
+    console.log('Calling loadGraphData()...');
+    loadGraphData();
+    console.log('=== END PAGE INITIALIZATION ===');
+});
+"""