From 92fa6c4e3a87918e6fb38b3e96913e13e5fc179f Mon Sep 17 00:00:00 2001
From: ForteDexe <57673412+ForteDexe@users.noreply.github.com>
Date: Sun, 25 Jan 2026 19:40:48 +0000
Subject: [PATCH 1/4] Add zoom-scaled sizing for highlighted icons and
 connection wires. Directional link toggles (in/out per type). And
 configurable file path display with subfolder levels for highlighted nodes in
 the codegraph HTML visualization.

 On branch dev
 Your branch is up to date with 'origin/dev'.

 Changes to be committed:
	modified:   .gitignore
	modified:   codegraph/templates/index.html
	modified:   codegraph/templates/main.js
	modified:   test_output.html
---
 .gitignore                     |   4 +-
 codegraph/templates/index.html |  10 +-
 codegraph/templates/main.js    | 157 +++++++++++++++++--
 test_output.html               | 277 ++++++++++++++++++++++++---------
 4 files changed, 362 insertions(+), 86 deletions(-)

diff --git a/.gitignore b/.gitignore
index f36439a..637d7d2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,4 +2,6 @@
 dist/
 codegraph.egg-info/
 codegraph/__pycache__/
-*/__pycache__/
\ No newline at end of file
+*/__pycache__/
+.vscode
+.conda
\ No newline at end of file
diff --git a/codegraph/templates/index.html b/codegraph/templates/index.html
index 16783d7..2eb01da 100644
--- a/codegraph/templates/index.html
+++ b/codegraph/templates/index.html
@@ -152,8 +152,16 @@ <h5>Show links</h5>
                 <label><input type="checkbox" id="show-link-dependency" checked> Dependencies</label>
             </div>
             <div class="display-section">
-                <h5>Font Settings</h5>
+                <h5>Highlight Settings</h5>
                 <label>Max highlighted font size: <input type="number" id="max-highlight-font" value="32" min="16" max="100"></label>
+                <label>Icon and wire scale factor: <input type="number" id="icon-wire-scale" value="1.0" min="0.1" max="5" step="0.1"></label>
+                <label>Subfolder levels: <input type="number" id="path-subfolder-levels" value="0" min="0" max="10"></label>
+                <div style="margin-top: 8px;">
+                    <label><input type="checkbox" id="highlight-link-mm-out" checked> Module → Module</label>
+                    <label><input type="checkbox" id="highlight-link-mm-in" checked> Module ← Module</label>
+                    <label><input type="checkbox" id="highlight-link-me-out" checked> Module → Entity</label>
+                    <label><input type="checkbox" id="highlight-link-me-in" checked> Module ← Entity</label>
+                </div>
             </div>
         </div>
     </div>
diff --git a/codegraph/templates/main.js b/codegraph/templates/main.js
index 87d7d6c..1b6cd08 100644
--- a/codegraph/templates/main.js
+++ b/codegraph/templates/main.js
@@ -225,6 +225,96 @@ function updateFontSizes(scale) {
     });
 }
 
+function updateIconWireSizes(scale) {
+    // Update node sizes with scaling
+    node.each(function(d) {
+        const el = d3.select(this);
+        const isHighlighted = el.classed('highlighted-main') || el.classed('highlighted');
+        const multiplier = isHighlighted ? iconWireScaleFactor / scale : 1;
+        if (d.type === "module") {
+            const baseSize = getNodeSize(d, 30);
+            const size = baseSize * multiplier;
+            const clampedSize = Math.max(10, Math.min(200, size));
+            el.select("rect")
+                .attr("width", clampedSize)
+                .attr("height", clampedSize)
+                .attr("x", -clampedSize / 2)
+                .attr("y", -clampedSize / 2);
+        } else if (d.type === "entity" || d.type === "external") {
+            const baseR = getNodeSize(d, 10);
+            const r = baseR * multiplier;
+            const clampedR = Math.max(5, Math.min(100, r));
+            el.select("circle").attr("r", clampedR);
+        }
+    });
+    // Update link stroke widths
+    link.each(function(d) {
+        const el = d3.select(this);
+        const isHighlighted = el.classed('highlighted');
+        const multiplier = isHighlighted ? iconWireScaleFactor / scale : 1;
+        const baseWidth = 2;
+        const width = baseWidth * multiplier;
+        const clampedWidth = Math.max(1, Math.min(10, width));
+        el.style("stroke-width", clampedWidth + "px");
+    });
+    // Update labels position
+    labels.attr("dy", d => {
+        const el = node.filter(n => n.id === d.id);
+        if (d.type === "module") {
+            const size = +el.select("rect").attr("width");
+            return size / 2 + 15;
+        } else {
+            const r = +el.select("circle").attr("r");
+            return r + 10;
+        }
+    });
+}
+
+function isLinkHighlighted(d, highlightedNodeId) {
+    const sourceId = typeof d.source === 'object' ? d.source.id : d.source;
+    const targetId = typeof d.target === 'object' ? d.target.id : d.target;
+    const isOut = sourceId === highlightedNodeId;
+    const isIn = targetId === highlightedNodeId;
+    if (d.type === 'module-module') {
+        if (isOut && highlightLinkFilters.mmOut) return true;
+        if (isIn && highlightLinkFilters.mmIn) return true;
+    } else if (d.type === 'module-entity') {
+        if (isOut && highlightLinkFilters.meOut) return true;
+        if (isIn && highlightLinkFilters.meIn) return true;
+    }
+    return false;
+}
+
+function formatPathForDisplay(fullPath, levels) {
+    if (!fullPath) return '';
+    
+    const parts = fullPath.split(/[\/\\]/);
+    if (levels <= 0) {
+        // Return just filename
+        return parts[parts.length - 1] || '';
+    }
+    
+    const startIndex = Math.max(0, parts.length - levels - 1);
+    return parts.slice(startIndex).join('/');
+}
+
+function updatePathDisplay() {
+    labels.text(function(d) {
+        const isHighlighted = d3.select(this).classed('highlighted-label');
+        const originalLabel = d.label || d.id;
+        
+        if (!isHighlighted) {
+            return originalLabel;
+        }
+        
+        const fullPath = d.fullPath || d.parent;
+        if (!fullPath) return originalLabel;
+        
+        const displayPath = formatPathForDisplay(fullPath, pathSubfolderLevels);
+        return displayPath || originalLabel;
+    });
+}
+
 const zoom = d3.zoom()
     .scaleExtent([0.05, 4])
     .on("zoom", (event) => {
@@ -232,6 +322,7 @@ const zoom = d3.zoom()
         currentScale = event.transform.k;
         // Adjust font sizes based on zoom scale
         updateFontSizes(currentScale);
+        updateIconWireSizes(currentScale);
     });
 
 svg.call(zoom);
@@ -391,6 +482,7 @@ function updateNodeSizes() {
 document.getElementById('size-by-code').addEventListener('change', function() {
     sizeByCode = this.checked;
     updateNodeSizes();
+    updateIconWireSizes(currentScale);
 });
 
 // Display filter state
@@ -438,6 +530,31 @@ document.getElementById('max-highlight-font').addEventListener('input', function
     // Update font sizes immediately
     updateFontSizes(currentScale);
 });
+document.getElementById('icon-wire-scale').addEventListener('input', function() {
+    iconWireScaleFactor = parseFloat(this.value) || 1.0;
+    // Update icon and wire sizes immediately
+    updateIconWireSizes(currentScale);
+});
+document.getElementById('highlight-link-mm-out').addEventListener('change', function() {
+    highlightLinkFilters.mmOut = this.checked;
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
+});
+document.getElementById('highlight-link-mm-in').addEventListener('change', function() {
+    highlightLinkFilters.mmIn = this.checked;
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
+});
+document.getElementById('highlight-link-me-out').addEventListener('change', function() {
+    highlightLinkFilters.meOut = this.checked;
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
+});
+document.getElementById('highlight-link-me-in').addEventListener('change', function() {
+    highlightLinkFilters.meIn = this.checked;
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
+});
+document.getElementById('path-subfolder-levels').addEventListener('input', function() {
+    pathSubfolderLevels = parseInt(this.value) || 0;
+    updatePathDisplay();
+});
 
 // Check if node should be hidden by display filter
 function isNodeFilteredOut(nodeData) {
@@ -718,8 +835,17 @@ const autocompleteList = document.getElementById('autocompleteList');
 let selectedAutocompleteIndex = -1;
 let currentHighlightedNode = null;
 let maxHighlightFontSize = 32;
+let iconWireScaleFactor = 1.0;
 let currentScale = 1;
 let filteredNodes = [];
+let highlightLinkFilters = {
+    mmOut: true,
+    mmIn: true,
+    meOut: true,
+    meIn: true
+};
+let showHighlightedPath = true;
+let pathSubfolderLevels = 0;
 
 // Build searchable index
 const searchIndex = graphData.nodes.map(n => ({
@@ -798,32 +924,33 @@ function zoomToFitNodes(nodeIds) {
 
 // Highlight a node and its connections
 function highlightNode(nodeId) {
-    const connectedNodes = getConnectedNodes(nodeId);
+    const connectedLinks = graphData.links.filter(d => isLinkHighlighted(d, nodeId));
+    const connectedNodes = new Set();
+    connectedLinks.forEach(l => {
+        const sourceId = typeof l.source === 'object' ? l.source.id : l.source;
+        const targetId = typeof l.target === 'object' ? l.target.id : l.target;
+        if (sourceId !== nodeId) connectedNodes.add(sourceId);
+        if (targetId !== nodeId) connectedNodes.add(targetId);
+    });
     currentHighlightedNode = nodeId;
 
     // Update nodes
-    node.classed('dimmed', d => !connectedNodes.has(d.id))
+    node.classed('dimmed', d => d.id !== nodeId && !connectedNodes.has(d.id))
         .classed('highlighted', d => connectedNodes.has(d.id) && d.id !== nodeId)
         .classed('highlighted-main', d => d.id === nodeId);
 
     // Update links
-    link.classed('dimmed', d => {
-        const sourceId = typeof d.source === 'object' ? d.source.id : d.source;
-        const targetId = typeof d.target === 'object' ? d.target.id : d.target;
-        return sourceId !== nodeId && targetId !== nodeId;
-    })
-    .classed('highlighted', d => {
-        const sourceId = typeof d.source === 'object' ? d.source.id : d.source;
-        const targetId = typeof d.target === 'object' ? d.target.id : d.target;
-        return sourceId === nodeId || targetId === nodeId;
-    });
+    link.classed('dimmed', d => !isLinkHighlighted(d, nodeId))
+        .classed('highlighted', d => isLinkHighlighted(d, nodeId));
 
     // Update labels
-    labels.classed('dimmed', d => !connectedNodes.has(d.id))
-        .classed('highlighted-label', d => connectedNodes.has(d.id));
+    labels.classed('dimmed', d => d.id !== nodeId && !connectedNodes.has(d.id))
+        .classed('highlighted-label', d => d.id === nodeId || connectedNodes.has(d.id));
 
     // Zoom to fit all connected nodes
     zoomToFitNodes(connectedNodes);
+    updateIconWireSizes(currentScale);
+    updatePathDisplay();
 }
 
 // Clear all highlighting
@@ -843,6 +970,8 @@ function clearHighlight() {
     searchInput.value = '';
     searchClear.classList.remove('visible');
     hideAutocomplete();
+    updateIconWireSizes(currentScale);
+    updatePathDisplay();
 }
 
 // Filter nodes based on search query
diff --git a/test_output.html b/test_output.html
index 92320dd..1f30fe0 100644
--- a/test_output.html
+++ b/test_output.html
@@ -729,8 +729,16 @@ <h5>Show links</h5>
                 <label><input type="checkbox" id="show-link-dependency" checked> Dependencies</label>
             </div>
             <div class="display-section">
-                <h5>Font Settings</h5>
+                <h5>Highlight Settings</h5>
                 <label>Max highlighted font size: <input type="number" id="max-highlight-font" value="32" min="16" max="100"></label>
+                <label>Icon and wire scale factor: <input type="number" id="icon-wire-scale" value="1.0" min="0.1" max="5" step="0.1"></label>
+                <label>Subfolder levels: <input type="number" id="path-subfolder-levels" value="0" min="0" max="10"></label>
+                <div style="margin-top: 8px;">
+                    <label><input type="checkbox" id="highlight-link-mm-out" checked> Module → Module</label>
+                    <label><input type="checkbox" id="highlight-link-mm-in" checked> Module ← Module</label>
+                    <label><input type="checkbox" id="highlight-link-me-out" checked> Module → Entity</label>
+                    <label><input type="checkbox" id="highlight-link-me-in" checked> Module ← Entity</label>
+                </div>
             </div>
         </div>
     </div>
@@ -1130,19 +1138,19 @@ <h5>Font Settings</h5>
       "lines": 66
     },
     {
-      "id": "test_package_install.py:test_d3_visualization_without_matplotlib",
-      "label": "test_d3_visualization_without_matplotlib",
+      "id": "test_package_install.py:test_codegraph_on_itself_without_matplotlib",
+      "label": "test_codegraph_on_itself_without_matplotlib",
       "type": "entity",
       "parent": "test_package_install.py",
-      "lines": 33,
+      "lines": 12,
       "entityType": "function"
     },
     {
-      "id": "test_package_install.py:test_codegraph_on_itself_without_matplotlib",
-      "label": "test_codegraph_on_itself_without_matplotlib",
+      "id": "test_package_install.py:test_d3_visualization_without_matplotlib",
+      "label": "test_d3_visualization_without_matplotlib",
       "type": "entity",
       "parent": "test_package_install.py",
-      "lines": 12,
+      "lines": 33,
       "entityType": "function"
     },
     {
@@ -1501,12 +1509,12 @@ <h5>Font Settings</h5>
     },
     {
       "source": "main.py:main",
-      "target": "core.py:CodeGraph",
+      "target": "vizualyzer.py:draw_graph",
       "type": "dependency"
     },
     {
       "source": "main.py:main",
-      "target": "vizualyzer.py:draw_graph",
+      "target": "core.py:CodeGraph",
       "type": "dependency"
     },
     {
@@ -1856,22 +1864,22 @@ <h5>Font Settings</h5>
     },
     {
       "source": "test_package_install.py",
-      "target": "test_package_install.py:test_d3_visualization_without_matplotlib",
+      "target": "test_package_install.py:test_codegraph_on_itself_without_matplotlib",
       "type": "module-entity"
     },
     {
-      "source": "test_package_install.py:test_d3_visualization_without_matplotlib",
-      "target": "vizualyzer.py:draw_graph",
+      "source": "test_package_install.py:test_codegraph_on_itself_without_matplotlib",
+      "target": "core.py:CodeGraph",
       "type": "dependency"
     },
     {
       "source": "test_package_install.py",
-      "target": "test_package_install.py:test_codegraph_on_itself_without_matplotlib",
+      "target": "test_package_install.py:test_d3_visualization_without_matplotlib",
       "type": "module-entity"
     },
     {
-      "source": "test_package_install.py:test_codegraph_on_itself_without_matplotlib",
-      "target": "core.py:CodeGraph",
+      "source": "test_package_install.py:test_d3_visualization_without_matplotlib",
+      "target": "vizualyzer.py:draw_graph",
       "type": "dependency"
     },
     {
@@ -1951,17 +1959,17 @@ <h5>Font Settings</h5>
     },
     {
       "source": "comma_imports.py:use_all",
-      "target": "module_a.py:func_a",
+      "target": "module_b.py:func_b",
       "type": "dependency"
     },
     {
       "source": "comma_imports.py:use_all",
-      "target": "module_c.py:func_c1",
+      "target": "module_a.py:func_a",
       "type": "dependency"
     },
     {
       "source": "comma_imports.py:use_all",
-      "target": "module_b.py:func_b",
+      "target": "module_c.py:func_c1",
       "type": "dependency"
     },
     {
@@ -1976,12 +1984,12 @@ <h5>Font Settings</h5>
     },
     {
       "source": "module_a.py:func_a",
-      "target": "module_c.py:func_c1",
+      "target": "module_b.py:func_b",
       "type": "dependency"
     },
     {
       "source": "module_a.py:func_a",
-      "target": "module_b.py:func_b",
+      "target": "module_c.py:func_c1",
       "type": "dependency"
     },
     {
@@ -2040,38 +2048,38 @@ <h5>Font Settings</h5>
       "type": "module-entity"
     },
     {
-      "source": "alias_imports.py",
-      "target": "module_b.py",
+      "source": "core.py",
+      "target": "utils.py",
       "type": "module-module"
     },
     {
-      "source": "comma_imports.py",
-      "target": "module_c.py",
+      "source": "test_codegraph.py",
+      "target": "core.py",
       "type": "module-module"
     },
     {
-      "source": "core.py",
-      "target": "parser.py",
+      "source": "main.py",
+      "target": "__init__.py",
       "type": "module-module"
     },
     {
-      "source": "test_codegraph.py",
-      "target": "core.py",
+      "source": "test_utils.py",
+      "target": "utils.py",
       "type": "module-module"
     },
     {
-      "source": "module_a.py",
-      "target": "module_b.py",
+      "source": "test_package_install.py",
+      "target": "main.py",
       "type": "module-module"
     },
     {
-      "source": "core.py",
-      "target": "utils.py",
+      "source": "module_a.py",
+      "target": "module_b.py",
       "type": "module-module"
     },
     {
-      "source": "main.py",
-      "target": "core.py",
+      "source": "test_graph_generation.py",
+      "target": "parser.py",
       "type": "module-module"
     },
     {
@@ -2079,19 +2087,24 @@ <h5>Font Settings</h5>
       "target": "__init__.py",
       "type": "module-module"
     },
+    {
+      "source": "test_graph_generation.py",
+      "target": "core.py",
+      "type": "module-module"
+    },
     {
       "source": "module_b.py",
       "target": "module_c.py",
       "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py",
+      "source": "main.py",
       "target": "core.py",
       "type": "module-module"
     },
     {
-      "source": "alias_imports.py",
-      "target": "module_a.py",
+      "source": "core.py",
+      "target": "parser.py",
       "type": "module-module"
     },
     {
@@ -2100,43 +2113,38 @@ <h5>Font Settings</h5>
       "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py",
-      "target": "vizualyzer.py",
-      "type": "module-module"
-    },
-    {
-      "source": "module_a.py",
+      "source": "comma_imports.py",
       "target": "module_c.py",
       "type": "module-module"
     },
     {
-      "source": "test_utils.py",
-      "target": "utils.py",
+      "source": "test_package_install.py",
+      "target": "core.py",
       "type": "module-module"
     },
     {
-      "source": "comma_imports.py",
-      "target": "module_b.py",
+      "source": "test_graph_generation.py",
+      "target": "vizualyzer.py",
       "type": "module-module"
     },
     {
-      "source": "main.py",
-      "target": "__init__.py",
+      "source": "alias_imports.py",
+      "target": "module_b.py",
       "type": "module-module"
     },
     {
-      "source": "test_package_install.py",
-      "target": "core.py",
+      "source": "alias_imports.py",
+      "target": "module_a.py",
       "type": "module-module"
     },
     {
       "source": "test_package_install.py",
-      "target": "main.py",
+      "target": "vizualyzer.py",
       "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py",
-      "target": "parser.py",
+      "source": "comma_imports.py",
+      "target": "module_b.py",
       "type": "module-module"
     },
     {
@@ -2145,8 +2153,8 @@ <h5>Font Settings</h5>
       "type": "module-module"
     },
     {
-      "source": "test_package_install.py",
-      "target": "vizualyzer.py",
+      "source": "module_a.py",
+      "target": "module_c.py",
       "type": "module-module"
     }
   ],
@@ -2380,6 +2388,96 @@ <h5>Font Settings</h5>
     });
 }
 
+function updateIconWireSizes(scale) {
+    // Update node sizes with scaling
+    node.each(function(d) {
+        const el = d3.select(this);
+        const isHighlighted = el.classed('highlighted-main') || el.classed('highlighted');
+        const multiplier = isHighlighted ? iconWireScaleFactor / scale : 1;
+        if (d.type === "module") {
+            const baseSize = getNodeSize(d, 30);
+            const size = baseSize * multiplier;
+            const clampedSize = Math.max(10, Math.min(200, size));
+            el.select("rect")
+                .attr("width", clampedSize)
+                .attr("height", clampedSize)
+                .attr("x", -clampedSize / 2)
+                .attr("y", -clampedSize / 2);
+        } else if (d.type === "entity" || d.type === "external") {
+            const baseR = getNodeSize(d, 10);
+            const r = baseR * multiplier;
+            const clampedR = Math.max(5, Math.min(100, r));
+            el.select("circle").attr("r", clampedR);
+        }
+    });
+    // Update link stroke widths
+    link.each(function(d) {
+        const el = d3.select(this);
+        const isHighlighted = el.classed('highlighted');
+        const multiplier = isHighlighted ? iconWireScaleFactor / scale : 1;
+        const baseWidth = 2;
+        const width = baseWidth * multiplier;
+        const clampedWidth = Math.max(1, Math.min(10, width));
+        el.style("stroke-width", clampedWidth + "px");
+    });
+    // Update labels position
+    labels.attr("dy", d => {
+        const el = node.filter(n => n.id === d.id);
+        if (d.type === "module") {
+            const size = +el.select("rect").attr("width");
+            return size / 2 + 15;
+        } else {
+            const r = +el.select("circle").attr("r");
+            return r + 10;
+        }
+    });
+}
+
+function isLinkHighlighted(d, highlightedNodeId) {
+    const sourceId = typeof d.source === 'object' ? d.source.id : d.source;
+    const targetId = typeof d.target === 'object' ? d.target.id : d.target;
+    const isOut = sourceId === highlightedNodeId;
+    const isIn = targetId === highlightedNodeId;
+    if (d.type === 'module-module') {
+        if (isOut && highlightLinkFilters.mmOut) return true;
+        if (isIn && highlightLinkFilters.mmIn) return true;
+    } else if (d.type === 'module-entity') {
+        if (isOut && highlightLinkFilters.meOut) return true;
+        if (isIn && highlightLinkFilters.meIn) return true;
+    }
+    return false;
+}
+
+function formatPathForDisplay(fullPath, levels) {
+    if (!fullPath) return '';
+    
+    const parts = fullPath.split(/[\/\\]/);
+    if (levels <= 0) {
+        // Return just filename
+        return parts[parts.length - 1] || '';
+    }
+    
+    const startIndex = Math.max(0, parts.length - levels - 1);
+    return parts.slice(startIndex).join('/');
+}
+
+function updatePathDisplay() {
+    labels.text(function(d) {
+        const isHighlighted = d3.select(this).classed('highlighted-label');
+        const originalLabel = d.label || d.id;
+        
+        if (!isHighlighted) {
+            return originalLabel;
+        }
+        
+        const fullPath = d.fullPath || d.parent;
+        if (!fullPath) return originalLabel;
+        
+        const displayPath = formatPathForDisplay(fullPath, pathSubfolderLevels);
+        return displayPath || originalLabel;
+    });
+}
+
 const zoom = d3.zoom()
     .scaleExtent([0.05, 4])
     .on("zoom", (event) => {
@@ -2387,6 +2485,7 @@ <h5>Font Settings</h5>
         currentScale = event.transform.k;
         // Adjust font sizes based on zoom scale
         updateFontSizes(currentScale);
+        updateIconWireSizes(currentScale);
     });
 
 svg.call(zoom);
@@ -2546,6 +2645,7 @@ <h5>Font Settings</h5>
 document.getElementById('size-by-code').addEventListener('change', function() {
     sizeByCode = this.checked;
     updateNodeSizes();
+    updateIconWireSizes(currentScale);
 });
 
 // Display filter state
@@ -2593,6 +2693,31 @@ <h5>Font Settings</h5>
     // Update font sizes immediately
     updateFontSizes(currentScale);
 });
+document.getElementById('icon-wire-scale').addEventListener('input', function() {
+    iconWireScaleFactor = parseFloat(this.value) || 1.0;
+    // Update icon and wire sizes immediately
+    updateIconWireSizes(currentScale);
+});
+document.getElementById('highlight-link-mm-out').addEventListener('change', function() {
+    highlightLinkFilters.mmOut = this.checked;
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
+});
+document.getElementById('highlight-link-mm-in').addEventListener('change', function() {
+    highlightLinkFilters.mmIn = this.checked;
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
+});
+document.getElementById('highlight-link-me-out').addEventListener('change', function() {
+    highlightLinkFilters.meOut = this.checked;
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
+});
+document.getElementById('highlight-link-me-in').addEventListener('change', function() {
+    highlightLinkFilters.meIn = this.checked;
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
+});
+document.getElementById('path-subfolder-levels').addEventListener('input', function() {
+    pathSubfolderLevels = parseInt(this.value) || 0;
+    updatePathDisplay();
+});
 
 // Check if node should be hidden by display filter
 function isNodeFilteredOut(nodeData) {
@@ -2873,8 +2998,17 @@ <h5>Font Settings</h5>
 let selectedAutocompleteIndex = -1;
 let currentHighlightedNode = null;
 let maxHighlightFontSize = 32;
+let iconWireScaleFactor = 1.0;
 let currentScale = 1;
 let filteredNodes = [];
+let highlightLinkFilters = {
+    mmOut: true,
+    mmIn: true,
+    meOut: true,
+    meIn: true
+};
+let showHighlightedPath = true;
+let pathSubfolderLevels = 0;
 
 // Build searchable index
 const searchIndex = graphData.nodes.map(n => ({
@@ -2953,32 +3087,33 @@ <h5>Font Settings</h5>
 
 // Highlight a node and its connections
 function highlightNode(nodeId) {
-    const connectedNodes = getConnectedNodes(nodeId);
+    const connectedLinks = graphData.links.filter(d => isLinkHighlighted(d, nodeId));
+    const connectedNodes = new Set();
+    connectedLinks.forEach(l => {
+        const sourceId = typeof l.source === 'object' ? l.source.id : l.source;
+        const targetId = typeof l.target === 'object' ? l.target.id : l.target;
+        if (sourceId !== nodeId) connectedNodes.add(sourceId);
+        if (targetId !== nodeId) connectedNodes.add(targetId);
+    });
     currentHighlightedNode = nodeId;
 
     // Update nodes
-    node.classed('dimmed', d => !connectedNodes.has(d.id))
+    node.classed('dimmed', d => d.id !== nodeId && !connectedNodes.has(d.id))
         .classed('highlighted', d => connectedNodes.has(d.id) && d.id !== nodeId)
         .classed('highlighted-main', d => d.id === nodeId);
 
     // Update links
-    link.classed('dimmed', d => {
-        const sourceId = typeof d.source === 'object' ? d.source.id : d.source;
-        const targetId = typeof d.target === 'object' ? d.target.id : d.target;
-        return sourceId !== nodeId && targetId !== nodeId;
-    })
-    .classed('highlighted', d => {
-        const sourceId = typeof d.source === 'object' ? d.source.id : d.source;
-        const targetId = typeof d.target === 'object' ? d.target.id : d.target;
-        return sourceId === nodeId || targetId === nodeId;
-    });
+    link.classed('dimmed', d => !isLinkHighlighted(d, nodeId))
+        .classed('highlighted', d => isLinkHighlighted(d, nodeId));
 
     // Update labels
-    labels.classed('dimmed', d => !connectedNodes.has(d.id))
-        .classed('highlighted-label', d => connectedNodes.has(d.id));
+    labels.classed('dimmed', d => d.id !== nodeId && !connectedNodes.has(d.id))
+        .classed('highlighted-label', d => d.id === nodeId || connectedNodes.has(d.id));
 
     // Zoom to fit all connected nodes
     zoomToFitNodes(connectedNodes);
+    updateIconWireSizes(currentScale);
+    updatePathDisplay();
 }
 
 // Clear all highlighting
@@ -2998,6 +3133,8 @@ <h5>Font Settings</h5>
     searchInput.value = '';
     searchClear.classList.remove('visible');
     hideAutocomplete();
+    updateIconWireSizes(currentScale);
+    updatePathDisplay();
 }
 
 // Filter nodes based on search query

From fc0c5286b9eebc66d78f118c64f45bc8eae6a645 Mon Sep 17 00:00:00 2001
From: ForteDexe <57673412+ForteDexe@users.noreply.github.com>
Date: Sun, 25 Jan 2026 19:49:53 +0000
Subject: [PATCH 2/4] Update version

 On branch dev
 Your branch is up to date with 'origin/dev'.

 Changes to be committed:
	modified:   codegraph/__init__.py
	modified:   pyproject.toml
---
 codegraph/__init__.py | 2 +-
 pyproject.toml        | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/codegraph/__init__.py b/codegraph/__init__.py
index c68196d..67bc602 100644
--- a/codegraph/__init__.py
+++ b/codegraph/__init__.py
@@ -1 +1 @@
-__version__ = "1.2.0"
+__version__ = "1.3.0"
diff --git a/pyproject.toml b/pyproject.toml
index e6bf148..e7b1c3e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,12 +1,12 @@
 [tool.poetry]
 name = "codegraph"
-version = "1.2.0"
+version = "1.3.0"
 license = "MIT"
 readme = "docs/README.rst"
-homepage = "https://github.com/xnuinside/codegraph"
-repository = "https://github.com/xnuinside/codegraph"
+homepage = "https://github.com/ForteDexe/codegraph"
+repository = "https://github.com/ForteDexe/codegraph"
 description = "Tool that create a graph of code to show dependencies between code entities (methods, classes and etc)."
-authors = ["xnuinside <xnuinside@gmail.com>"]
+authors = ["forted <forted.exe@gmail.com>"]
 classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",

From d3afc52085eac9e5f12a51b0acc599cd5d93804c Mon Sep 17 00:00:00 2001
From: ForteDexe <57673412+ForteDexe@users.noreply.github.com>
Date: Wed, 28 Jan 2026 07:40:36 +0000
Subject: [PATCH 3/4] Lot of reworks and improvements, check CHANGELOG.md

 Changes to be committed:
	modified:   CHANGELOG.md
	modified:   codegraph/__init__.py
	modified:   codegraph/core.py
	modified:   codegraph/main.py
	modified:   codegraph/parser.py
	modified:   codegraph/templates/index.html
	modified:   codegraph/templates/main.js
	modified:   codegraph/templates/styles.css
	modified:   codegraph/utils.py
	modified:   codegraph/vizualyzer.py
	modified:   pyproject.toml
	modified:   test_output.html
	modified:   tests/test_graph_generation.py
	new file:   tests/test_data/duplicate_names/src/main.py
	new file:   tests/test_data/duplicate_names/src/utils.py
	new file:   tests/test_data/duplicate_names/tests/__pycache__/test_main.cpython-311-pytest-8.3.3.pyc
	new file:   tests/test_data/duplicate_names/tests/sample_test.py
	new file:   tests/test_data/duplicate_names/tests/utils.py
---
 CHANGELOG.md                                  |   87 +
 HIDDENLOG.md                                  |   44 +
 codegraph/__init__.py                         |    2 +-
 codegraph/core.py                             |  287 +-
 codegraph/main.py                             |   25 +-
 codegraph/parser.py                           |   10 +-
 codegraph/templates/index.html                |   24 +-
 codegraph/templates/main.js                   |  354 ++-
 codegraph/templates/styles.css                |   54 +-
 codegraph/utils.py                            |   43 +-
 codegraph/vizualyzer.py                       |  215 +-
 pyproject.toml                                |    2 +-
 test_output.html                              | 2634 ++++++++++++-----
 tests/test_data/duplicate_names/src/main.py   |    7 +
 tests/test_data/duplicate_names/src/utils.py  |    8 +
 .../test_main.cpython-311-pytest-8.3.3.pyc    |  Bin 0 -> 714 bytes
 .../duplicate_names/tests/sample_test.py      |    7 +
 .../test_data/duplicate_names/tests/utils.py  |    8 +
 tests/test_graph_generation.py                |  134 +-
 19 files changed, 3141 insertions(+), 804 deletions(-)
 create mode 100644 HIDDENLOG.md
 create mode 100644 tests/test_data/duplicate_names/src/main.py
 create mode 100644 tests/test_data/duplicate_names/src/utils.py
 create mode 100644 tests/test_data/duplicate_names/tests/__pycache__/test_main.cpython-311-pytest-8.3.3.pyc
 create mode 100644 tests/test_data/duplicate_names/tests/sample_test.py
 create mode 100644 tests/test_data/duplicate_names/tests/utils.py

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e6bcd74..1819133 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,93 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.5.0] - 2026-01-28
+
+### Added
+
+**Focus Mode**
+- New "Focus Mode" checkbox in Highlight Settings panel
+- When enabled, hides all background (non-highlighted) nodes and links
+- Shows entire dependency chain regardless of display filters
+- Improves visibility when analyzing specific code paths
+
+**Navigation History**
+- Added back/forward navigation buttons with browser-style controls
+- Keyboard shortcuts: Alt+Left (back), Alt+Right (forward)
+- Tracks entity clicks for easy navigation through code exploration
+- Button states update based on history availability
+
+**External Import Nodes**
+- External imports (e.g., `os`, `sys`, `numpy`) now appear as nodes in the graph
+- Distinguished with special styling and external type
+- Helps visualize all project dependencies including standard library and third-party packages
+
+### Changed
+
+**Arrow Direction and Visualization**
+- Reversed arrow directions to better represent code flow
+- Module imports: arrows now point FROM importer TO imported module
+- Entity dependencies: arrows point FROM entity TO its dependencies
+- Improved arrow scaling: scales consistently with zoom level and icon size
+- Unified arrow head sizes and stroke widths across all link types
+- Dynamic arrow scaling in highlight mode with configurable maximum (18.75x scale factor)
+
+**Keyword Filtering Enhancements**
+- Keyword search now filters at entity level in addition to module level
+- Shows full dependency chains when entities match keywords
+- Handles import aliases correctly (e.g., `import pandas as pd`)
+- Improves search accuracy for finding specific functions/classes
+
+**UI Defaults and Behavior**
+- Default font size increased to 256 for better readability
+- Display panel now expanded by default
+- Classes and Functions checkboxes unchecked by default (show only modules)
+- Focus mode properly dims labels and icons of non-highlighted nodes
+- Improved link opacity handling in highlight and focus modes
+
+### Fixed
+
+**Display Filter Issues**
+- Fixed Classes/Functions nodes appearing in highlight mode when filters disabled
+- Corrected entity visibility logic to respect display panel settings
+- Entity links now properly hidden when corresponding filters are off
+
+**Import Handling**
+- Fixed import statement extraction from AST
+- Corrected handling of multi-line imports and comma-separated imports
+- Fixed alias imports (e.g., `import x as y`) appearing in tooltips
+
+**Highlight Mode**
+- Fixed entity-to-entity click highlighting for dependency relationships
+- Corrected link dimming in focus mode
+- Fixed label and icon dimming to match node highlight state
+
+**Arrow Scaling Consistency**
+- Fixed inconsistent arrow sizes at different zoom levels
+- Unified base stroke widths (2px for all link types)
+- Arrows now scale proportionally with icons in highlight mode
+- Applied proper clamping to prevent excessive arrow sizes
+
+## [1.4.0] - 2026-01-26
+
+### Fixed
+
+**Duplicate Filename Support**
+- Fixed critical issue where files with the same basename in different directories would collide
+- Now uses full relative paths as unique identifiers instead of just filenames
+- Module node IDs are now path-based (e.g., `src/utils`, `tests/utils`) without `.py` extension
+- Entity node IDs use format `path/module:entity_name` (e.g., `src/utils:helper`)
+- Module labels still display basenames for readability, with full paths in tooltips
+- Search box now shows file paths for modules to distinguish duplicates
+- CSV export shows basenames with `.py` extension for backward compatibility
+- Added comprehensive test suite for duplicate filename scenarios
+
+### Changed
+
+- Internal node identifiers now use relative paths for uniqueness
+- Module identification system refactored throughout core, parser, and visualization layers
+- Import resolution improved to correctly match dependencies with path-based identifiers
+
 ## [1.2.0] - 2026-01-18
 
 ### Added
diff --git a/HIDDENLOG.md b/HIDDENLOG.md
new file mode 100644
index 0000000..9cd1d9d
--- /dev/null
+++ b/HIDDENLOG.md
@@ -0,0 +1,44 @@
+1. Core Module (core.py)
+Updated parse_code_file() to pass full paths (instead of basename) to the parser
+Modified get_module_name() to return relative path-based keys (e.g., src/utils instead of utils)
+Changed get_code_objects() and CodeGraph.__init__() to track and pass base_paths
+Updated get_imports_and_entities_lines() to build module_names_set and names_map using relative paths
+2. Visualization Module (vizualyzer.py)
+Modified convert_to_d3_format() to generate unique node IDs from relative paths
+Module node IDs are now path-based (e.g., src/utils, tests/utils) without .py extension
+Entity node IDs use format path/module:entity_name (e.g., src/utils:helper)
+Updated entity_to_module mappings to use path-based identifiers
+Fixed dependency resolution loops to correctly attribute dependencies using relative paths
+Updated draw_graph(), draw_graph_matplotlib(), and export_to_csv() to accept and use base_paths
+CSV export now shows basenames with .py extension in the name column for backward compatibility
+3. Parser Module (parser.py)
+Updated create_objects_array() to accept full paths in the fname parameter
+Added base_paths parameter for future path-relative calculations
+4. Utilities Module (utils.py)
+Added get_relative_path() helper function to calculate relative paths from a list of base paths
+Normalizes path separators to forward slashes for cross-platform consistency
+5. Main Module (main.py)
+Updated to extract base_paths from CodeGraph instance
+Passes base_paths to all visualization functions
+6. Frontend (main.js)
+Already handles n.label || n.id pattern correctly
+Module nodes now display basename in labels while using path-based IDs internally
+fullPath attribute available in tooltips for disambiguation
+
+For modules: Shows the full file path (e.g., utils.py or utils.py)
+For entities: Shows the parent module (e.g., src/utils for src_helper function)
+
+Design Decisions Implemented:
+Clean relative paths for readability ✓
+
+Node IDs use sanitized relative paths: src/utils instead of utils.py
+Easy to read and understand in visualizations
+Basename for node labels + full path in tooltips ✓
+
+Module nodes show just the filename (e.g., utils) in the UI
+Full relative path available in the fullPath attribute for tooltips
+Users see familiar names while the system maintains unique identifiers
+Acceptable to break saved HTML files ✓
+
+Node ID format changed from module.py to module (relative path without extension)
+Existing visualizations will need to be regenerated
\ No newline at end of file
diff --git a/codegraph/__init__.py b/codegraph/__init__.py
index 67bc602..5b60188 100644
--- a/codegraph/__init__.py
+++ b/codegraph/__init__.py
@@ -1 +1 @@
-__version__ = "1.3.0"
+__version__ = "1.5.0"
diff --git a/codegraph/core.py b/codegraph/core.py
index 64ccd33..83e941d 100644
--- a/codegraph/core.py
+++ b/codegraph/core.py
@@ -2,7 +2,7 @@
 import os
 from argparse import Namespace
 from collections import defaultdict, deque
-from typing import Dict, List, Set, Text, Tuple
+from typing import Dict, List, Optional, Set, Text, Tuple
 
 from codegraph.parser import Import, create_objects_array
 from codegraph.utils import get_python_paths_list
@@ -13,35 +13,259 @@
 
 
 def read_file_content(path: Text) -> Text:
-    with open(path, "r+") as file_read:
-        return file_read.read()
+    try:
+        with open(path, "r", encoding="utf-8") as file_read:
+            return file_read.read()
+    except UnicodeDecodeError:
+        # Try with latin-1 as fallback, which accepts all byte values
+        with open(path, "r", encoding="latin-1") as file_read:
+            return file_read.read()
 
 
-def parse_code_file(path: Text) -> List:
+def parse_code_file(path: Text, base_paths: Optional[List] = None) -> List:
     """read module source and parse to get objects array"""
     source = read_file_content(path)
-    parsed_module = create_objects_array(source=source, fname=os.path.basename(path))
+    # Pass full path to parser to support duplicate filenames
+    parsed_module = create_objects_array(source=source, fname=path, base_paths=base_paths or [])
     return parsed_module
 
 
-def get_code_objects(paths_list: List) -> Dict:
+def get_code_objects(paths_list: List, base_paths: Optional[List] = None) -> Dict:
     """
         get all code files data for paths list
     :param paths_list: list with paths to code files to parse
+    :param base_paths: list of base paths for calculating relative paths
     :return:
     """
     all_data = {}
     for path in paths_list:
-        content = parse_code_file(path)
+        content = parse_code_file(path, base_paths)
         all_data[path] = content
     return all_data
 
 
 class CodeGraph:
     def __init__(self, args: Namespace):
-        self.paths_list = get_python_paths_list(args.paths)
+        self.base_paths = [os.path.abspath(p) for p in args.paths]
+        self.paths_list = get_python_paths_list(args.paths, max_depth=args.depth)
+        
+        # Filter by keyword if provided
+        if args.keyword:
+            self.paths_list = self._filter_by_keyword(self.paths_list, args.keyword)
+            if not self.paths_list:
+                print(f"Warning: No files found containing keyword '{args.keyword}'")
+        
         # get py modules list data
-        self.modules_data = get_code_objects(self.paths_list)
+        self.modules_data = get_code_objects(self.paths_list, self.base_paths)
+        
+        # Store raw imports before they get popped by get_imports_and_entities_lines
+        self.raw_imports = {}
+        for module_path, parsed_objects in self.modules_data.items():
+            for obj in parsed_objects:
+                if isinstance(obj, Import):
+                    self.raw_imports[module_path] = list(obj.modules)
+                    break
+        
+        # Apply entity-level filtering if keyword is specified
+        if args.keyword:
+            self._filter_entities_by_keyword(args.keyword)
+    
+    def _filter_entities_by_keyword(self, keyword: str):
+        """Filter entities within modules to only include those that use the keyword.
+        
+        Handles import aliases like 'import h13shotgrid as shotgrid' by tracking the alias name.
+        Also includes entities that call other entities using the keyword (dependency chain).
+        """
+        keyword_lower = keyword.lower()
+        
+        for module_path, parsed_objects in self.modules_data.items():
+            # Extract import statements and build alias mapping
+            import_aliases = {}  # Maps alias/module name to original module name
+            for obj in parsed_objects:
+                if isinstance(obj, Import):
+                    for module_import in obj.modules:
+                        # Handle "import module as alias"
+                        if " as " in module_import:
+                            original, alias = module_import.split(" as ")
+                            original = original.strip()
+                            alias = alias.strip()
+                            # Check if original matches keyword
+                            if keyword_lower in original.lower():
+                                import_aliases[alias.lower()] = original
+                                import_aliases[original.lower()] = original
+                        else:
+                            # Handle "import module" or "from X import Y"
+                            parts = module_import.split(".")
+                            base_module = parts[0]
+                            if keyword_lower in base_module.lower():
+                                import_aliases[base_module.lower()] = base_module
+            
+            # If no matching imports found, skip filtering for this module
+            if not import_aliases:
+                continue
+            
+            # Read file content to check entity usage
+            try:
+                content = read_file_content(module_path)
+                content_lower = content.lower()
+            except Exception:
+                continue
+            
+            # First pass: identify entities that directly use the keyword
+            entities_using_keyword = set()
+            entity_code_map = {}  # Map entity name to its code
+            entity_objects = []  # Non-import objects
+            
+            for obj in parsed_objects:
+                if isinstance(obj, Import):
+                    continue
+                    
+                entity_objects.append(obj)
+                entity_name = obj.name
+                
+                if hasattr(obj, 'lineno') and hasattr(obj, 'endno') and obj.lineno and obj.endno:
+                    # Extract entity's code section
+                    lines = content.split('\n')
+                    entity_code = '\n'.join(lines[obj.lineno - 1:obj.endno])
+                    entity_code_map[entity_name] = entity_code
+                    entity_code_lower = entity_code.lower()
+                    
+                    # Check if entity uses any of the import aliases
+                    for alias in import_aliases.keys():
+                        if alias in entity_code_lower:
+                            entities_using_keyword.add(entity_name)
+                            break
+            
+            # Second pass: find entities that call entities using the keyword (dependency chain)
+            # Keep iterating until no new entities are found
+            entities_to_keep = set(entities_using_keyword)
+            changed = True
+            max_iterations = 10  # Prevent infinite loops
+            iteration = 0
+            
+            while changed and iteration < max_iterations:
+                changed = False
+                iteration += 1
+                
+                for obj in entity_objects:
+                    entity_name = obj.name
+                    if entity_name in entities_to_keep:
+                        continue
+                    
+                    if entity_name in entity_code_map:
+                        entity_code_lower = entity_code_map[entity_name].lower()
+                        
+                        # Check if this entity calls any entity that's already in the keep set
+                        for kept_entity in entities_to_keep:
+                            # Look for function/method calls: kept_entity( or kept_entity.
+                            if f'{kept_entity.lower()}(' in entity_code_lower or f'{kept_entity.lower()}.' in entity_code_lower:
+                                entities_to_keep.add(entity_name)
+                                changed = True
+                                break
+            
+            # Build filtered objects list
+            filtered_objects = []
+            for obj in parsed_objects:
+                if isinstance(obj, Import):
+                    # Always keep Import objects
+                    filtered_objects.append(obj)
+                elif hasattr(obj, 'name') and obj.name in entities_to_keep:
+                    filtered_objects.append(obj)
+            
+            # Update modules_data with filtered entities
+            self.modules_data[module_path] = filtered_objects
+    
+    def _filter_by_keyword(self, paths_list: list, keyword: str) -> list:
+        """Filter paths to only include files containing the keyword or their direct dependencies."""
+        keyword_lower = keyword.lower()
+        matching_files = set()
+        
+        # First pass: find files containing the keyword
+        for path in paths_list:
+            # Check if keyword is in filename
+            if keyword_lower in os.path.basename(path).lower():
+                matching_files.add(path)
+                continue
+            
+            # Check if keyword is in file content or imports
+            try:
+                # Parse the file to extract imports using parse_code_file
+                parsed_objects = parse_code_file(path, self.base_paths)
+                
+                # Check if any import contains the keyword
+                for obj in parsed_objects:
+                    if isinstance(obj, Import):
+                        for module in obj.modules:
+                            # Extract the actual import name from "module.name" or "name"
+                            if " as " in module:
+                                module = module.split(" as ")[0]
+                            parts = module.split(".")
+                            # Check all parts of the import for the keyword
+                            for part in parts:
+                                if keyword_lower in part.lower():
+                                    matching_files.add(path)
+                                    break
+                            if path in matching_files:
+                                break
+                    if path in matching_files:
+                        break
+                
+                # Also check file content for the keyword
+                if path not in matching_files:
+                    content = read_file_content(path)
+                    if keyword_lower in content.lower():
+                        matching_files.add(path)
+            except Exception as e:
+                # Skip files that can't be parsed/read
+                logger.debug(f"Failed to parse {path}: {e}")
+                pass
+        
+        if not matching_files:
+            return []
+        
+        # Second pass: parse all files to find direct dependencies
+        # Parse all files to build import mapping
+        all_modules_data = {}
+        for path in paths_list:
+            try:
+                all_modules_data[path] = parse_code_file(path, self.base_paths)
+            except Exception:
+                all_modules_data[path] = []
+        
+        # Extract imports from parsed data
+        all_imports = {}
+        for path, parsed_objects in all_modules_data.items():
+            imports_list = []
+            for obj in parsed_objects:
+                if isinstance(obj, Import):
+                    for module in obj.modules:
+                        # Extract base import name
+                        if " as " in module:
+                            module = module.split(" as ")[0]
+                        imports_list.append(module)
+            all_imports[path] = imports_list
+        
+        # Build dependency graph
+        result_files = set(matching_files)
+        for match_file in matching_files:
+            # Add files that import the keyword (already added in first pass)
+            
+            # Find files that the matching file depends on or that depend on it
+            for file_path, imports in all_imports.items():
+                # Check if this file imports something from match_file
+                match_basename = os.path.basename(match_file).replace('.py', '')
+                for imp in imports:
+                    if match_basename in imp:
+                        result_files.add(file_path)
+                
+                # Check if match_file imports something from this file  
+                if match_file in all_imports:
+                    file_basename = os.path.basename(file_path).replace('.py', '')
+                    for imp in all_imports[match_file]:
+                        if file_basename in imp:
+                            result_files.add(file_path)
+        
+        return list(result_files)
 
     def get_lines_numbers(self):
         """
@@ -109,6 +333,9 @@ def usage_graph(self) -> Dict:
             for method_that_used in entities_usage_in_modules[module]:
                 method_usage_lines = entities_usage_in_modules[module][method_that_used]
                 for method_usage_line in method_usage_lines:
+                    # Skip if method_usage_line is None (parsing issue)
+                    if method_usage_line is None:
+                        continue
                     for entity in entities_lines[module]:
                         if entity[0] <= method_usage_line <= entity[1]:
                             dependencies[module][entities_lines[module][entity]].append(
@@ -158,9 +385,25 @@ def get_dependencies(self, file_path: str, distance: int) -> Dict[str, Set[str]]
         return dependencies
 
 
-def get_module_name(code_path: Text) -> Text:
-    module_name = os.path.basename(code_path).replace(".py", "")
-    return module_name
+def get_module_name(code_path: Text, base_paths: Optional[List] = None) -> Text:
+    """Get a unique module identifier using relative path.
+    
+    :param code_path: Full path to the module
+    :param base_paths: List of base paths for calculating relative path
+    :return: Relative path without .py extension (e.g., 'src/utils' or 'tests/utils')
+    """
+    from codegraph.utils import get_relative_path
+    
+    if base_paths:
+        rel_path = get_relative_path(code_path, base_paths)
+    else:
+        rel_path = os.path.basename(code_path)
+    
+    # Remove .py extension
+    if rel_path.endswith('.py'):
+        rel_path = rel_path[:-3]
+    
+    return rel_path
 
 
 def module_name_in_imports(imports: List, module_name: Text) -> bool:
@@ -182,11 +425,21 @@ def get_imports_and_entities_lines(  # noqa: C901
     imports = defaultdict(list)
     modules_ = code_objects.keys()
     names_map = {}
-    # Build a set of all module names for quick lookup
-    module_names_set = {os.path.basename(m).replace(".py", "") for m in modules_}
+    
+    # Get base paths from any parsed object's file attribute
+    # This is a bit of a workaround - ideally we'd pass base_paths as a parameter
+    base_paths = []
+    for path in modules_:
+        parent_dir = os.path.dirname(path)
+        if parent_dir and parent_dir not in base_paths:
+            # Add parent directories as potential base paths
+            base_paths.append(parent_dir)
+    
+    # Build a set of all module names for quick lookup (now using relative paths)
+    module_names_set = {get_module_name(m, base_paths) for m in modules_}
 
     for path in code_objects:
-        names_map[get_module_name(path)] = path
+        names_map[get_module_name(path, base_paths)] = path
         # for each module in list
         if code_objects[path] and isinstance(code_objects[path][-1], Import):
             # extract imports if exist
@@ -233,7 +486,9 @@ def get_imports_and_entities_lines(  # noqa: C901
 
         for entity in code_objects[path]:
             # create a dict with lines of start and end for each entity in module
-            entities_lines[path][(entity.lineno, entity.endno)] = entity.name
+            # Skip entities with None line numbers to prevent TypeError
+            if entity.lineno is not None and entity.endno is not None:
+                entities_lines[path][(entity.lineno, entity.endno)] = entity.name
     return entities_lines, imports, names_map
 
 
diff --git a/codegraph/main.py b/codegraph/main.py
index 93f8a91..4523a6b 100644
--- a/codegraph/main.py
+++ b/codegraph/main.py
@@ -40,7 +40,18 @@
     type=click.Path(),
     help="Export graph data to CSV file (specify output path)",
 )
-def cli(paths, object_only, file_path, distance, matplotlib, output, csv):
+@click.option(
+    "--depth",
+    type=int,
+    required=True,
+    help="Maximum subfolder depth to scan (1=original/sub1, 2=original/sub1/sub2, etc.)",
+)
+@click.option(
+    "--keyword",
+    type=str,
+    help="Filter to only show modules related to this keyword (reduces graph size for large codebases)",
+)
+def cli(paths, object_only, file_path, distance, matplotlib, output, csv, depth, keyword):
     """
     Tool that creates a graph of code to show dependencies between code entities (methods, classes, etc.).
     CodeGraph does not execute code, it is based only on lex and syntax parsing.
@@ -62,6 +73,8 @@ def cli(paths, object_only, file_path, distance, matplotlib, output, csv):
         matplotlib=matplotlib,
         output=output,
         csv=csv,
+        depth=depth,
+        keyword=keyword,
     )
     main(args)
 
@@ -70,6 +83,8 @@ def main(args):
     code_graph = core.CodeGraph(args)
     usage_graph = code_graph.usage_graph()
     entity_metadata = code_graph.get_entity_metadata()
+    base_paths = code_graph.base_paths
+    raw_imports = code_graph.raw_imports  # Raw imports before they get popped
 
     if args.file_path and args.distance:
         dependencies = code_graph.get_dependencies(args.file_path, args.distance)
@@ -81,14 +96,16 @@ def main(args):
     elif args.csv:
         import codegraph.vizualyzer as vz
 
-        vz.export_to_csv(usage_graph, entity_metadata=entity_metadata, output_path=args.csv)
+        vz.export_to_csv(usage_graph, entity_metadata=entity_metadata, 
+                        output_path=args.csv, base_paths=base_paths, raw_imports=raw_imports)
     else:
         import codegraph.vizualyzer as vz
 
         if args.matplotlib:
-            vz.draw_graph_matplotlib(usage_graph)
+            vz.draw_graph_matplotlib(usage_graph, base_paths=base_paths)
         else:
-            vz.draw_graph(usage_graph, entity_metadata=entity_metadata, output_path=args.output)
+            vz.draw_graph(usage_graph, entity_metadata=entity_metadata, 
+                         output_path=args.output, base_paths=base_paths, raw_imports=raw_imports)
 
 
 if __name__ == "__main__":
diff --git a/codegraph/parser.py b/codegraph/parser.py
index d58850f..060a9ec 100644
--- a/codegraph/parser.py
+++ b/codegraph/parser.py
@@ -88,9 +88,15 @@ def _nest_class(ob, class_name, lineno, super=None):
     return newclass
 
 
-def create_objects_array(fname, source):  # noqa: C901
+def create_objects_array(fname, source, base_paths=None):  # noqa: C901
     # todo: need to do optimization
-    """Return an object list for a particular module."""
+    """Return an object list for a particular module.
+    
+    :param fname: Full path to the file being parsed
+    :param source: Source code content
+    :param base_paths: List of base paths for calculating relative paths (optional)
+    :return: List of parsed objects
+    """
     tree = []
     f = io.StringIO(source)
 
diff --git a/codegraph/templates/index.html b/codegraph/templates/index.html
index 2eb01da..7a7cfc2 100644
--- a/codegraph/templates/index.html
+++ b/codegraph/templates/index.html
@@ -16,6 +16,8 @@
     <!-- Search box -->
     <div class="search-container">
         <div class="search-box">
+            <button class="nav-button" id="backButton" title="Back (Alt+Left)" disabled>◀</button>
+            <button class="nav-button" id="forwardButton" title="Forward (Alt+Right)" disabled>▶</button>
             <input type="text" class="search-input" id="searchInput" placeholder="Search nodes... (Ctrl+F)" autocomplete="off">
             <button class="search-clear" id="searchClear">&times;</button>
             <div class="autocomplete-list" id="autocompleteList"></div>
@@ -128,22 +130,22 @@ <h4>Massive Objects <span class="count" id="massive-count"></span></h4>
             <ul id="massive-list"></ul>
         </div>
     </div>
-    <div class="panel size-toggle collapsed" id="size-toggle-panel">
+    <div class="panel size-toggle" id="size-toggle-panel">
         <div class="panel-header">
             <h4>Display</h4>
-            <button class="panel-toggle" title="Expand">+</button>
+            <button class="panel-toggle" title="Collapse">-</button>
         </div>
         <div class="panel-content">
             <label>
-                <input type="checkbox" id="size-by-code" checked>
+                <input type="checkbox" id="size-by-code">
                 Size by lines of code
             </label>
             <div class="display-section">
                 <h5>Show nodes</h5>
-                <label><input type="checkbox" id="show-modules" checked> Modules</label>
-                <label><input type="checkbox" id="show-classes" checked> Classes</label>
-                <label><input type="checkbox" id="show-functions" checked> Functions</label>
                 <label><input type="checkbox" id="show-external" checked> External</label>
+                <label><input type="checkbox" id="show-modules" checked> Modules</label>
+                <label><input type="checkbox" id="show-classes"> Classes</label>
+                <label><input type="checkbox" id="show-functions"> Functions</label>
             </div>
             <div class="display-section">
                 <h5>Show links</h5>
@@ -153,14 +155,18 @@ <h5>Show links</h5>
             </div>
             <div class="display-section">
                 <h5>Highlight Settings</h5>
-                <label>Max highlighted font size: <input type="number" id="max-highlight-font" value="32" min="16" max="100"></label>
+                <label>
+                    <input type="checkbox" id="highlight-focus-mode">
+                    Focus mode (hide background, show all chain nodes)
+                </label>
+                <label>Max highlighted font size: <input type="number" id="max-highlight-font" value="256" min="16" max="512"></label>
                 <label>Icon and wire scale factor: <input type="number" id="icon-wire-scale" value="1.0" min="0.1" max="5" step="0.1"></label>
                 <label>Subfolder levels: <input type="number" id="path-subfolder-levels" value="0" min="0" max="10"></label>
                 <div style="margin-top: 8px;">
                     <label><input type="checkbox" id="highlight-link-mm-out" checked> Module → Module</label>
-                    <label><input type="checkbox" id="highlight-link-mm-in" checked> Module ← Module</label>
+                    <label><input type="checkbox" id="highlight-link-mm-in"> Module ← Module</label>
                     <label><input type="checkbox" id="highlight-link-me-out" checked> Module → Entity</label>
-                    <label><input type="checkbox" id="highlight-link-me-in" checked> Module ← Entity</label>
+                    <label><input type="checkbox" id="highlight-link-me-in"> Module ← Entity</label>
                 </div>
             </div>
         </div>
diff --git a/codegraph/templates/main.js b/codegraph/templates/main.js
index 1b6cd08..2df9b5c 100644
--- a/codegraph/templates/main.js
+++ b/codegraph/templates/main.js
@@ -145,7 +145,7 @@ document.getElementById('links-threshold').addEventListener('input', updateLinks
 updateLinksCount();
 
 // Size scaling state
-let sizeByCode = true;
+let sizeByCode = false;
 
 // Calculate max lines for scaling
 const maxLines = Math.max(...graphData.nodes.map(n => n.lines || 0), 1);
@@ -230,11 +230,14 @@ function updateIconWireSizes(scale) {
     node.each(function(d) {
         const el = d3.select(this);
         const isHighlighted = el.classed('highlighted-main') || el.classed('highlighted');
-        const multiplier = isHighlighted ? iconWireScaleFactor / scale : 1;
+        const isDimmed = el.classed('dimmed');
+        const multiplier = (isHighlighted && !isDimmed) ? iconWireScaleFactor / scale : 1;
         if (d.type === "module") {
             const baseSize = getNodeSize(d, 30);
             const size = baseSize * multiplier;
-            const clampedSize = Math.max(10, Math.min(200, size));
+            // Use scale factor to determine reasonable max (higher scale factor = higher max)
+            const maxSize = 200 * iconWireScaleFactor;
+            const clampedSize = Math.max(10, Math.min(maxSize, size));
             el.select("rect")
                 .attr("width", clampedSize)
                 .attr("height", clampedSize)
@@ -243,7 +246,9 @@ function updateIconWireSizes(scale) {
         } else if (d.type === "entity" || d.type === "external") {
             const baseR = getNodeSize(d, 10);
             const r = baseR * multiplier;
-            const clampedR = Math.max(5, Math.min(100, r));
+            // Use scale factor to determine reasonable max (higher scale factor = higher max)
+            const maxR = 100 * iconWireScaleFactor;
+            const clampedR = Math.max(5, Math.min(maxR, r));
             el.select("circle").attr("r", clampedR);
         }
     });
@@ -251,10 +256,18 @@ function updateIconWireSizes(scale) {
     link.each(function(d) {
         const el = d3.select(this);
         const isHighlighted = el.classed('highlighted');
-        const multiplier = isHighlighted ? iconWireScaleFactor / scale : 1;
+        const isDimmed = el.classed('dimmed');
+        
+        // Use same multiplier as icons - only highlighted arrows scale with zoom
+        const multiplier = (isHighlighted && !isDimmed) ? iconWireScaleFactor / scale : 1;
+        
+        // Use same base width for all link types for consistent arrow scaling
         const baseWidth = 2;
+        
         const width = baseWidth * multiplier;
-        const clampedWidth = Math.max(1, Math.min(10, width));
+        // Reduce max for better balance
+        const maxWidth = 18.75 * iconWireScaleFactor;
+        const clampedWidth = Math.max(1, Math.min(maxWidth, width));
         el.style("stroke-width", clampedWidth + "px");
     });
     // Update labels position
@@ -281,6 +294,10 @@ function isLinkHighlighted(d, highlightedNodeId) {
     } else if (d.type === 'module-entity') {
         if (isOut && highlightLinkFilters.meOut) return true;
         if (isIn && highlightLinkFilters.meIn) return true;
+    } else if (d.type === 'dependency') {
+        // Entity-to-entity or entity-to-external dependencies
+        // Always highlight these when the entity is selected
+        if (isOut || isIn) return true;
     }
     return false;
 }
@@ -349,10 +366,10 @@ const defs = svg.append("defs");
 defs.append("marker")
     .attr("id", "arrow-module-module")
     .attr("viewBox", "0 -5 10 10")
-    .attr("refX", 25)
+    .attr("refX", 18)
     .attr("refY", 0)
-    .attr("markerWidth", 8)
-    .attr("markerHeight", 8)
+    .attr("markerWidth", 6)
+    .attr("markerHeight", 6)
     .attr("orient", "auto")
     .append("path")
     .attr("fill", "#ff9800")
@@ -488,8 +505,8 @@ document.getElementById('size-by-code').addEventListener('change', function() {
 // Display filter state
 const displayFilters = {
     showModules: true,
-    showClasses: true,
-    showFunctions: true,
+    showClasses: false,
+    showFunctions: false,
     showExternal: true,
     showLinkModule: true,
     showLinkEntity: true,
@@ -500,30 +517,37 @@ const displayFilters = {
 document.getElementById('show-modules').addEventListener('change', function() {
     displayFilters.showModules = this.checked;
     updateDisplayFilters();
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
 });
 document.getElementById('show-classes').addEventListener('change', function() {
     displayFilters.showClasses = this.checked;
     updateDisplayFilters();
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
 });
 document.getElementById('show-functions').addEventListener('change', function() {
     displayFilters.showFunctions = this.checked;
     updateDisplayFilters();
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
 });
 document.getElementById('show-external').addEventListener('change', function() {
     displayFilters.showExternal = this.checked;
     updateDisplayFilters();
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
 });
 document.getElementById('show-link-module').addEventListener('change', function() {
     displayFilters.showLinkModule = this.checked;
     updateDisplayFilters();
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
 });
 document.getElementById('show-link-entity').addEventListener('change', function() {
     displayFilters.showLinkEntity = this.checked;
     updateDisplayFilters();
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
 });
 document.getElementById('show-link-dependency').addEventListener('change', function() {
     displayFilters.showLinkDependency = this.checked;
     updateDisplayFilters();
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
 });
 document.getElementById('max-highlight-font').addEventListener('input', function() {
     maxHighlightFontSize = parseInt(this.value) || 32;
@@ -535,6 +559,15 @@ document.getElementById('icon-wire-scale').addEventListener('input', function()
     // Update icon and wire sizes immediately
     updateIconWireSizes(currentScale);
 });
+document.getElementById('highlight-focus-mode').addEventListener('change', function() {
+    highlightFocusMode = this.checked;
+    if (currentHighlightedNode) {
+        highlightNode(currentHighlightedNode);
+    } else if (!this.checked) {
+        // When turning off focus mode without active highlight, restore display filters
+        updateDisplayFilters();
+    }
+});
 document.getElementById('highlight-link-mm-out').addEventListener('change', function() {
     highlightLinkFilters.mmOut = this.checked;
     if (currentHighlightedNode) highlightNode(currentHighlightedNode);
@@ -626,6 +659,9 @@ const labels = g.append("g")
 // Initialize font sizes
 updateFontSizes(1);
 
+// Apply initial display filters
+updateDisplayFilters();
+
 // Node interactions
 node.on("mouseover", function(event, d) {
     // Highlight connected links
@@ -832,17 +868,83 @@ const searchInput = document.getElementById('searchInput');
 const searchClear = document.getElementById('searchClear');
 const autocompleteList = document.getElementById('autocompleteList');
 
+// Navigation history
+let highlightHistory = [];
+let historyIndex = -1;
+let isNavigating = false; // Flag to prevent adding to history during navigation
+
+const backButton = document.getElementById('backButton');
+const forwardButton = document.getElementById('forwardButton');
+
+function updateNavigationButtons() {
+    backButton.disabled = historyIndex <= 0;
+    forwardButton.disabled = historyIndex >= highlightHistory.length - 1;
+}
+
+function addToHistory(nodeId) {
+    if (isNavigating) return; // Don't add to history during back/forward navigation
+    
+    // Remove any forward history when a new node is selected
+    highlightHistory = highlightHistory.slice(0, historyIndex + 1);
+    
+    // Add new node (avoid duplicates of the same node in a row)
+    if (highlightHistory[historyIndex] !== nodeId) {
+        highlightHistory.push(nodeId);
+        historyIndex++;
+    }
+    
+    updateNavigationButtons();
+}
+
+function navigateBack() {
+    if (historyIndex > 0) {
+        isNavigating = true;
+        historyIndex--;
+        const nodeId = highlightHistory[historyIndex];
+        highlightNode(nodeId);
+        isNavigating = false;
+        updateNavigationButtons();
+    }
+}
+
+function navigateForward() {
+    if (historyIndex < highlightHistory.length - 1) {
+        isNavigating = true;
+        historyIndex++;
+        const nodeId = highlightHistory[historyIndex];
+        highlightNode(nodeId);
+        isNavigating = false;
+        updateNavigationButtons();
+    }
+}
+
+backButton.addEventListener('click', navigateBack);
+forwardButton.addEventListener('click', navigateForward);
+
+// Keyboard shortcuts for navigation
+document.addEventListener('keydown', (e) => {
+    if (e.altKey && e.key === 'ArrowLeft') {
+        e.preventDefault();
+        navigateBack();
+    } else if (e.altKey && e.key === 'ArrowRight') {
+        e.preventDefault();
+        navigateForward();
+    }
+});
+
+
 let selectedAutocompleteIndex = -1;
 let currentHighlightedNode = null;
-let maxHighlightFontSize = 32;
+let maxHighlightFontSize = 256;
 let iconWireScaleFactor = 1.0;
 let currentScale = 1;
 let filteredNodes = [];
+let highlightFocusMode = false;
 let highlightLinkFilters = {
     mmOut: true,
-    mmIn: true,
+    mmIn: false,
     meOut: true,
-    meIn: true
+    meIn: false
 };
 let showHighlightedPath = true;
 let pathSubfolderLevels = 0;
@@ -853,7 +955,15 @@ const searchIndex = graphData.nodes.map(n => ({
     label: n.label || n.id,
     type: n.type,
     parent: n.parent || null,
-    searchText: ((n.label || n.id) + ' ' + (n.parent || '')).toLowerCase()
+    fullPath: n.fullPath || null,
+    // For modules, include both 'modulename' and 'modulename.py' as separate searchable terms, plus imports
+    // For entities, search by label and parent
+    searchText: n.type === 'module' 
+        ? (n.label || n.id).toLowerCase() + ' ' + 
+          (n.label || n.id).toLowerCase() + '.py ' + 
+          (n.fullPath || '').toLowerCase() + ' ' +
+          ((n.imports || []).join(' ')).toLowerCase()
+        : ((n.label || n.id) + ' ' + (n.parent || '')).toLowerCase()
 }));
 
 // Get connected nodes for a given node
@@ -924,7 +1034,19 @@ function zoomToFitNodes(nodeIds) {
 
 // Highlight a node and its connections
 function highlightNode(nodeId) {
-    const connectedLinks = graphData.links.filter(d => isLinkHighlighted(d, nodeId));
+    // Add to history (unless we're navigating)
+    addToHistory(nodeId);
+    
+    // In focus mode, build chain from ALL dependency links
+    // In normal mode, use filtered links based on highlight settings
+    const connectedLinks = highlightFocusMode 
+        ? graphData.links.filter(d => {
+            const sourceId = typeof d.source === 'object' ? d.source.id : d.source;
+            const targetId = typeof d.target === 'object' ? d.target.id : d.target;
+            return sourceId === nodeId || targetId === nodeId;
+          })
+        : graphData.links.filter(d => isLinkHighlighted(d, nodeId));
+    
     const connectedNodes = new Set();
     connectedLinks.forEach(l => {
         const sourceId = typeof l.source === 'object' ? l.source.id : l.source;
@@ -934,18 +1056,137 @@ function highlightNode(nodeId) {
     });
     currentHighlightedNode = nodeId;
 
-    // Update nodes
-    node.classed('dimmed', d => d.id !== nodeId && !connectedNodes.has(d.id))
-        .classed('highlighted', d => connectedNodes.has(d.id) && d.id !== nodeId)
-        .classed('highlighted-main', d => d.id === nodeId);
+    if (highlightFocusMode) {
+        // Focus mode: show all chain nodes (ignore filters), hide background nodes completely
+        node.each(function(d) {
+            const el = d3.select(this);
+            if (d.id === nodeId) {
+                el.classed('dimmed', false)
+                  .classed('highlighted', false)
+                  .classed('highlighted-main', true)
+                  .classed('node-hidden', false);
+            } else if (connectedNodes.has(d.id)) {
+                // Check if this node should be highlighted or dimmed
+                const shouldHighlight = connectedLinks.some(l => {
+                    const sourceId = typeof l.source === 'object' ? l.source.id : l.source;
+                    const targetId = typeof l.target === 'object' ? l.target.id : l.target;
+                    return (sourceId === d.id || targetId === d.id) && isLinkHighlighted(l, nodeId);
+                });
+                el.classed('dimmed', !shouldHighlight)
+                  .classed('highlighted', shouldHighlight)
+                  .classed('highlighted-main', false)
+                  .classed('node-hidden', false);
+            } else {
+                // Background nodes - completely hidden
+                el.classed('dimmed', false)
+                  .classed('highlighted', false)
+                  .classed('highlighted-main', false)
+                  .classed('node-hidden', true);
+            }
+        });
+    } else {
+        // Normal mode: respect filters, only dim background
+        // First, clear node-hidden from all nodes to undo focus mode
+        node.classed('node-hidden', d => isNodeFilteredOut(d) || isNodeHidden(d));
+        
+        // Then apply highlight classes only to visible nodes
+        node.filter(d => !isNodeFilteredOut(d) && !isNodeHidden(d))
+            .classed('dimmed', d => d.id !== nodeId && !connectedNodes.has(d.id))
+            .classed('highlighted', d => connectedNodes.has(d.id) && d.id !== nodeId)
+            .classed('highlighted-main', d => d.id === nodeId);
+    }
 
     // Update links
-    link.classed('dimmed', d => !isLinkHighlighted(d, nodeId))
-        .classed('highlighted', d => isLinkHighlighted(d, nodeId));
+    if (highlightFocusMode) {
+        // Focus mode: show only links between chain nodes
+        link.each(function(d) {
+            const el = d3.select(this);
+            const sourceId = typeof d.source === 'object' ? d.source.id : d.source;
+            const targetId = typeof d.target === 'object' ? d.target.id : d.target;
+            const sourceInChain = sourceId === nodeId || connectedNodes.has(sourceId);
+            const targetInChain = targetId === nodeId || connectedNodes.has(targetId);
+            
+            if (sourceInChain && targetInChain) {
+                // Link is part of the chain
+                const isHighlighted = isLinkHighlighted(d, nodeId);
+                el.classed('dimmed', !isHighlighted)
+                  .classed('highlighted', isHighlighted)
+                  .classed('link-hidden', false)
+                  .style('stroke-opacity', isHighlighted ? 1 : 0.4);
+            } else {
+                // Background link - completely hidden
+                el.classed('dimmed', false)
+                  .classed('highlighted', false)
+                  .classed('link-hidden', true)
+                  .style('stroke-opacity', null);
+            }
+        });
+    } else {
+        // Normal mode: filter out links connected to hidden nodes
+        // First, clear any inline stroke-opacity styles from focus mode
+        link.style('stroke-opacity', null);
+        
+        link.filter(d => {
+                // First check if the link type is filtered out
+                if (isLinkFilteredOut(d)) return false;
+                
+                const sourceId = typeof d.source === 'object' ? d.source.id : d.source;
+                const targetId = typeof d.target === 'object' ? d.target.id : d.target;
+                const sourceNode = graphData.nodes.find(n => n.id === sourceId);
+                const targetNode = graphData.nodes.find(n => n.id === targetId);
+                const sourceVisible = sourceNode && !isNodeFilteredOut(sourceNode) && !isNodeHidden(sourceNode);
+                const targetVisible = targetNode && !isNodeFilteredOut(targetNode) && !isNodeHidden(targetNode);
+                return sourceVisible && targetVisible;
+            })
+            .classed('dimmed', d => !isLinkHighlighted(d, nodeId))
+            .classed('highlighted', d => isLinkHighlighted(d, nodeId));
+        
+        // Reapply link-hidden to ALL links to ensure hidden links stay hidden (normal mode only)
+        link.classed('link-hidden', d => {
+            if (isLinkFilteredOut(d)) return true;
+            const sourceId = typeof d.source === 'object' ? d.source.id : d.source;
+            const targetId = typeof d.target === 'object' ? d.target.id : d.target;
+            const sourceNode = graphData.nodes.find(n => n.id === sourceId);
+            const targetNode = graphData.nodes.find(n => n.id === targetId);
+            if (sourceNode && isNodeFilteredOut(sourceNode)) return true;
+            if (targetNode && isNodeFilteredOut(targetNode)) return true;
+            if (d.type === 'module-module') return false;
+            if (sourceNode && isNodeHidden(sourceNode)) return true;
+            if (targetNode && isNodeHidden(targetNode)) return true;
+            if (d.type === 'module-entity' && collapsedNodes.has(sourceId)) return true;
+            if (d.type === 'dependency' && collapsedNodes.has(sourceId)) return true;
+            return false;
+        });
+    }
 
     // Update labels
-    labels.classed('dimmed', d => d.id !== nodeId && !connectedNodes.has(d.id))
-        .classed('highlighted-label', d => d.id === nodeId || connectedNodes.has(d.id));
+    if (highlightFocusMode) {
+        // Focus mode: show all chain labels (ignore filters), hide background labels
+        labels.each(function(d) {
+            const el = d3.select(this);
+            const nodeEl = node.filter(n => n.id === d.id);
+            const isNodeDimmed = nodeEl.classed('dimmed');
+            
+            if (d.id === nodeId || connectedNodes.has(d.id)) {
+                el.classed('dimmed', isNodeDimmed)
+                  .classed('highlighted-label', !isNodeDimmed)
+                  .classed('label-hidden', false);
+            } else {
+                el.classed('dimmed', false)
+                  .classed('highlighted-label', false)
+                  .classed('label-hidden', true);
+            }
+        });
+    } else {
+        // Normal mode: respect filters
+        // First, clear label-hidden from all labels and reapply based on filters
+        labels.classed('label-hidden', d => isNodeFilteredOut(d) || isNodeHidden(d));
+        
+        // Then apply highlight classes only to visible labels
+        labels.filter(d => !isNodeFilteredOut(d) && !isNodeHidden(d))
+            .classed('dimmed', d => d.id !== nodeId && !connectedNodes.has(d.id))
+            .classed('highlighted-label', d => d.id === nodeId || connectedNodes.has(d.id));
+    }
 
     // Zoom to fit all connected nodes
     zoomToFitNodes(connectedNodes);
@@ -957,15 +1198,26 @@ function highlightNode(nodeId) {
 function clearHighlight() {
     currentHighlightedNode = null;
 
+    // Clear highlight classes from all nodes and restore filter state
     node.classed('dimmed', false)
         .classed('highlighted', false)
         .classed('highlighted-main', false);
+    
+    // Restore node-hidden based on filters
+    node.classed('node-hidden', d => isNodeFilteredOut(d) || isNodeHidden(d));
 
     link.classed('dimmed', false)
         .classed('highlighted', false);
 
+    // Clear highlight classes from all labels and restore filter state
     labels.classed('dimmed', false)
         .classed('highlighted-label', false);
+    
+    // Restore label-hidden based on filters
+    labels.classed('label-hidden', d => isNodeFilteredOut(d) || isNodeHidden(d));
+    
+    // Restore display filters
+    updateDisplayFilters();
 
     searchInput.value = '';
     searchClear.classList.remove('visible');
@@ -978,9 +1230,36 @@ function clearHighlight() {
 function filterNodes(query) {
     if (!query) return [];
     const lowerQuery = query.toLowerCase();
-    return searchIndex
-        .filter(n => n.searchText.includes(lowerQuery))
-        .slice(0, 10); // Limit to 10 results
+    const results = searchIndex.filter(n => n.searchText.includes(lowerQuery));
+    
+    // Sort results: prioritize exact label matches, then label starts with query, then path matches
+    results.sort((a, b) => {
+        const aLabel = (a.label || a.id).toLowerCase();
+        const bLabel = (b.label || b.id).toLowerCase();
+        const aLabelWithPy = aLabel + '.py';
+        const bLabelWithPy = bLabel + '.py';
+        
+        // Exact matches come first
+        if (aLabel === lowerQuery || aLabelWithPy === lowerQuery) return -1;
+        if (bLabel === lowerQuery || bLabelWithPy === lowerQuery) return 1;
+        
+        // Label starts with query comes next
+        const aStarts = aLabel.startsWith(lowerQuery) || aLabelWithPy.startsWith(lowerQuery);
+        const bStarts = bLabel.startsWith(lowerQuery) || bLabelWithPy.startsWith(lowerQuery);
+        if (aStarts && !bStarts) return -1;
+        if (!aStarts && bStarts) return 1;
+        
+        // Label contains query comes before path contains query
+        const aLabelContains = aLabel.includes(lowerQuery) || aLabelWithPy.includes(lowerQuery);
+        const bLabelContains = bLabel.includes(lowerQuery) || bLabelWithPy.includes(lowerQuery);
+        if (aLabelContains && !bLabelContains) return -1;
+        if (!aLabelContains && bLabelContains) return 1;
+        
+        // Otherwise alphabetical
+        return aLabel.localeCompare(bLabel);
+    });
+    
+    return results.slice(0, 50); // Limit to 50 results
 }
 
 // Render autocomplete list
@@ -993,13 +1272,20 @@ function renderAutocomplete(results) {
     filteredNodes = results;
     selectedAutocompleteIndex = -1;
 
-    autocompleteList.innerHTML = results.map((n, i) => `
-        <div class="autocomplete-item" data-index="${i}" data-id="${n.id}">
-            <span class="node-type ${n.type}">${n.type}</span>
-            <span class="node-name">${n.label}</span>
-            ${n.parent ? `<span class="node-parent">${n.parent}</span>` : ''}
-        </div>
-    `).join('');
+    autocompleteList.innerHTML = results.map((n, i) => {
+        // For modules, show fullPath; for entities, show parent
+        const pathInfo = n.type === 'module' && n.fullPath 
+            ? `<span class="node-parent">${n.fullPath}</span>`
+            : n.parent ? `<span class="node-parent">${n.parent}</span>` : '';
+        
+        return `
+            <div class="autocomplete-item" data-index="${i}" data-id="${n.id}">
+                <span class="node-type ${n.type}">${n.type}</span>
+                <span class="node-name">${n.label}</span>
+                ${pathInfo}
+            </div>
+        `;
+    }).join('');
 
     autocompleteList.classList.add('visible');
 
diff --git a/codegraph/templates/styles.css b/codegraph/templates/styles.css
index 9118783..c74ad08 100644
--- a/codegraph/templates/styles.css
+++ b/codegraph/templates/styles.css
@@ -55,20 +55,23 @@ body {
 }
 .link-module-module {
     stroke: #ff9800;
-    stroke-width: 3px;
+    stroke-width: 2px;
     stroke-opacity: 0.8;
 }
 .link-module-entity {
     stroke: #009c2c;
-    stroke-width: 1.5px;
+    stroke-width: 2px;
     stroke-dasharray: 5, 3;
 }
 .link-dependency {
     stroke: #d94a4a;
-    stroke-width: 1.5px;
+    stroke-width: 2px;
+}
+.link.highlighted.link-dependency {
+    stroke-opacity: 1 !important;
 }
 .link-hidden {
-    opacity: 0;
+    opacity: 0 !important;
 }
 .label {
     font-size: 11px;
@@ -98,6 +101,9 @@ body {
     transition: opacity 0.2s;
     border: 1px solid #555;
     max-width: 300px;
+    word-wrap: break-word;
+    word-break: break-all;
+    white-space: normal;
 }
 .tooltip .links-info {
     margin-top: 8px;
@@ -458,9 +464,32 @@ body {
 .search-box {
     position: relative;
     width: 100%;
+    display: flex;
+    gap: 8px;
+    align-items: center;
+}
+.nav-button {
+    background: rgba(0, 0, 0, 0.9);
+    border: 2px solid #444;
+    border-radius: 6px;
+    color: #fff;
+    padding: 10px 14px;
+    font-size: 14px;
+    cursor: pointer;
+    transition: border-color 0.2s, background 0.2s;
+    flex-shrink: 0;
+}
+.nav-button:hover:not(:disabled) {
+    border-color: #70b8ff;
+    background: rgba(112, 184, 255, 0.1);
+}
+.nav-button:disabled {
+    color: #555;
+    cursor: not-allowed;
+    opacity: 0.5;
 }
 .search-input {
-    width: 100%;
+    flex: 1;
     padding: 12px 40px 12px 16px;
     font-size: 14px;
     border: 2px solid #444;
@@ -556,14 +585,23 @@ body {
 }
 /* Dimmed state for non-highlighted nodes/links */
 .node.dimmed {
-    opacity: 0.15;
+    opacity: 0.2;
+}
+/* Hidden nodes must always be hidden, even if dimmed */
+.node.node-hidden {
+    opacity: 0 !important;
+    pointer-events: none;
 }
 .link.dimmed {
-    opacity: 0.05;
+    opacity: 0.4;
 }
 .label.dimmed {
     opacity: 0.1;
 }
+/* Hidden labels must always be hidden, even if dimmed */
+.label.label-hidden {
+    opacity: 0 !important;
+}
 /* Highlighted state */
 .node.highlighted {
     filter: brightness(1.3) drop-shadow(0 0 8px rgba(255, 255, 255, 0.5));
@@ -572,6 +610,6 @@ body {
     filter: brightness(1.5) drop-shadow(0 0 15px rgba(112, 184, 255, 0.8));
 }
 .link.highlighted {
-    stroke-opacity: 1;
+    stroke-opacity: 1 !important;
     filter: drop-shadow(0 0 3px rgba(255, 255, 255, 0.5));
 }
diff --git a/codegraph/utils.py b/codegraph/utils.py
index 79ba9de..b6234c7 100644
--- a/codegraph/utils.py
+++ b/codegraph/utils.py
@@ -1,12 +1,45 @@
 import glob
+import os
 from pathlib import Path
 from typing import List, Union
 
 
-def get_python_paths_list(paths: Union[str, List]) -> List[str]:
+def get_relative_path(file_path: str, base_paths: List[str]) -> str:
+    """
+    Get a relative path from file_path based on the closest matching base path.
+    If no base path matches, return the basename.
+    
+    :param file_path: Absolute path to the file
+    :param base_paths: List of base paths to calculate relative path from
+    :return: Relative path string
+    """
+    file_path = os.path.normpath(file_path)
+    
+    # Try to find the closest matching base path
+    best_rel_path = os.path.basename(file_path)
+    
+    for base_path in base_paths:
+        base_path = os.path.normpath(base_path)
+        try:
+            rel_path = os.path.relpath(file_path, base_path)
+            # Only use this if the file is actually under this base path
+            if not rel_path.startswith('..'):
+                # Use the shortest relative path found
+                if len(rel_path) < len(best_rel_path) or best_rel_path == os.path.basename(file_path):
+                    best_rel_path = rel_path
+        except (ValueError, TypeError):
+            # Can happen on Windows with different drives
+            continue
+    
+    # Normalize path separators to forward slashes for consistency
+    return best_rel_path.replace('\\', '/')
+
+
+def get_python_paths_list(paths: Union[str, List], max_depth: int = None) -> List[str]:
     """
         return list of paths to python files, that found in provided path
     :param paths: paths to folder or python file that need to tests
+    :param max_depth: maximum subfolder depth to scan (1=original/sub1, 2=original/sub1/sub2, etc.)
     :return:
     """
     if isinstance(paths, str):
@@ -23,8 +56,14 @@ def get_python_paths_list(paths: Union[str, List]) -> List[str]:
         path = Path(path).absolute()
         if not path.exists():
             raise ValueError(f"Path {path.as_posix()} does not exist")
+        # Get all Python files recursively, excluding hidden folders (starting with '.')
+        all_files = glob.glob(str(path / "**" / "*.py"), recursive=True)
         paths_list += [
             Path(p).as_posix()
-            for p in glob.glob(str(path / "**" / "*.py"), recursive=True)
+            for p in all_files
+            # Skip files in folders starting with '.' (like .conda, .vscode, .git, etc.)
+            # and respect max_depth if specified
+            if not any(part.startswith('.') for part in Path(p).relative_to(path).parts[:-1])
+            and (max_depth is None or len(Path(p).relative_to(path).parts) - 1 <= max_depth)
         ]
     return paths_list
diff --git a/codegraph/vizualyzer.py b/codegraph/vizualyzer.py
index 6bf08b7..acc002a 100644
--- a/codegraph/vizualyzer.py
+++ b/codegraph/vizualyzer.py
@@ -3,13 +3,18 @@
 import logging
 import os
 import webbrowser
-from typing import Dict, List
+from typing import Dict, List, Optional
 
 logger = logging.getLogger(__name__)
 
 
-def process_module_in_graph(module: Dict[str, list], module_links: list, G):
-    _module = os.path.basename(module)
+def process_module_in_graph(module: str, module_links: list, G, base_paths: Optional[List] = None):
+    from codegraph.utils import get_relative_path
+    
+    if base_paths:
+        _module = get_relative_path(module, base_paths)
+    else:
+        _module = os.path.basename(module)
 
     module_edges = []
 
@@ -27,7 +32,7 @@ def process_module_in_graph(module: Dict[str, list], module_links: list, G):
     return module_edges, sub_edges
 
 
-def draw_graph_matplotlib(modules_entities: Dict) -> None:
+def draw_graph_matplotlib(modules_entities: Dict, base_paths: Optional[List] = None) -> None:
     try:
         import matplotlib.pyplot as plt
         import networkx as nx
@@ -37,6 +42,8 @@ def draw_graph_matplotlib(modules_entities: Dict) -> None:
             "Install it with: pip install codegraph[matplotlib]"
         )
 
+    from codegraph.utils import get_relative_path
+
     G = nx.DiGraph()
 
     module_edges_all = []
@@ -45,14 +52,19 @@ def draw_graph_matplotlib(modules_entities: Dict) -> None:
 
     for module in modules_entities:
         new_module_edges_all, new_edges_all = process_module_in_graph(
-            module, modules_entities[module], G
+            module, modules_entities[module], G, base_paths
         )
 
         module_edges_all += new_module_edges_all
         sub_edges_all += new_edges_all
 
     pos = nx.spring_layout(G)
-    module_list = [os.path.basename(module) for module in modules_entities]
+    
+    # Use relative paths for module identifiers
+    if base_paths:
+        module_list = [get_relative_path(module, base_paths) for module in modules_entities]
+    else:
+        module_list = [os.path.basename(module) for module in modules_entities]
     module_list_labels = {module_name: module_name for module_name in module_list}
 
     entities_labels = {edge[1]: edge[1] for edge in module_edges_all}
@@ -115,59 +127,83 @@ def draw_graph_matplotlib(modules_entities: Dict) -> None:
     plt.show()
 
 
-def convert_to_d3_format(modules_entities: Dict, entity_metadata: Dict = None) -> Dict:
-    """Convert the modules_entities graph data to D3.js format."""
+def convert_to_d3_format(modules_entities: Dict, entity_metadata: Optional[Dict] = None, 
+                         base_paths: Optional[List] = None, raw_imports: Optional[Dict[str, List[str]]] = None) -> Dict:
+    """Convert the modules_entities graph data to D3.js format with path-based node IDs.
+    
+    Args:
+        modules_entities: Dict mapping module paths to their entities
+        entity_metadata: Optional metadata for entities
+        base_paths: List of base paths for calculating relative paths
+        raw_imports: Dict mapping module paths to their raw import statements
+    
+    Returns:
+        Dict with 'nodes', 'links', and 'unlinkedModules' for D3.js visualization
+    """
+    from codegraph.utils import get_relative_path
+    from codegraph.parser import Import
+    
     nodes: List[Dict] = []
     links: List[Dict] = []
     node_ids = set()
     module_links = set()  # Track module-to-module links
-    module_full_paths: Dict[str, str] = {}  # Map module name to full path
+    module_full_paths: Dict[str, str] = {}  # Map module_id to full relative path
+    
+    # Extract raw imports if provided
+    raw_imports_by_module = {}
+    if raw_imports:
+        for module_path, import_modules in raw_imports.items():
+            imports_list = []
+            for module in import_modules:
+                # Extract base import name (before " as ")
+                if " as " in module:
+                    module = module.split(" as ")[0]
+                # For "from X import Y" style, it's stored as "X.Y"
+                # Extract both the base module and full path
+                if "." in module:
+                    parts = module.split(".")
+                    imports_list.append(parts[0])  # Base module like 'h13shotgrid'
+                else:
+                    imports_list.append(module)
+            raw_imports_by_module[module_path] = imports_list
 
     if entity_metadata is None:
         entity_metadata = {}
 
-    # Find common root path for relative paths
-    all_paths = list(modules_entities.keys())
-    if all_paths:
-        common_prefix = os.path.commonpath(all_paths)
-        # Go up one level to include the root folder name
-        common_root = os.path.dirname(common_prefix)
-    else:
-        common_root = ""
-
     # First pass: build entity-to-module mapping and create ALL nodes
     entity_to_module: Dict[str, str] = {}
     for module_path, entities in modules_entities.items():
-        module_name = os.path.basename(module_path)
-        module_metadata = entity_metadata.get(module_path, {})
-
-        # Compute relative path from common root
-        if common_root:
-            relative_path = os.path.relpath(module_path, common_root)
+        # Use relative path as module identifier
+        if base_paths:
+            module_id = get_relative_path(module_path, base_paths).replace('.py', '')
+            relative_path = get_relative_path(module_path, base_paths)
         else:
-            relative_path = module_path
-
-        module_full_paths[module_name] = relative_path
+            module_id = os.path.basename(module_path).replace('.py', '')
+            relative_path = os.path.basename(module_path)
+        
+        module_metadata = entity_metadata.get(module_path, {})
+        module_full_paths[module_id] = relative_path
 
         # Calculate total lines in module
         total_lines = sum(m.get("lines", 0) for m in module_metadata.values())
 
-        # Add module node
-        if module_name not in node_ids:
+        # Add module node with path-based ID
+        if module_id not in node_ids:
             nodes.append({
-                "id": module_name,
+                "id": module_id,
+                "label": os.path.basename(module_path).replace('.py', ''),  # Display basename
                 "type": "module",
                 "collapsed": False,
                 "fullPath": relative_path,
                 "lines": total_lines
             })
-            node_ids.add(module_name)
+            node_ids.add(module_id)
 
         # Add entity nodes and build mapping
         for entity_name in entities.keys():
-            entity_id = f"{module_name}:{entity_name}"
-            entity_to_module[entity_name] = module_name
-            entity_to_module[f"{module_name.replace('.py', '')}.{entity_name}"] = module_name
+            entity_id = f"{module_id}:{entity_name}"
+            entity_to_module[entity_name] = module_id
+            entity_to_module[f"{module_id}.{entity_name}"] = module_id
 
             # Get entity metadata
             ent_meta = module_metadata.get(entity_name, {})
@@ -179,7 +215,7 @@ def convert_to_d3_format(modules_entities: Dict, entity_metadata: Dict = None) -
                     "id": entity_id,
                     "label": entity_name,
                     "type": "entity",
-                    "parent": module_name,
+                    "parent": module_id,
                     "lines": lines,
                     "entityType": entity_type
                 })
@@ -187,14 +223,31 @@ def convert_to_d3_format(modules_entities: Dict, entity_metadata: Dict = None) -
 
     # Second pass: create all links
     for module_path, entities in modules_entities.items():
-        module_name = os.path.basename(module_path)
+        # Use relative path as module identifier (consistent with first pass)
+        if base_paths:
+            module_id = get_relative_path(module_path, base_paths).replace('.py', '')
+        else:
+            module_id = os.path.basename(module_path).replace('.py', '')
+        
+        # Collect all import names for this module
+        module_imports = set()
 
         for entity_name, dependencies in entities.items():
-            entity_id = f"{module_name}:{entity_name}"
+            entity_id = f"{module_id}:{entity_name}"
+            
+            # Collect import names
+            for dep in dependencies:
+                # Parse dependency name to extract the actual import name
+                if "." in dep:
+                    parts = dep.split(".")
+                    import_name = parts[1] if len(parts) > 1 else parts[0]
+                else:
+                    import_name = dep
+                module_imports.add(import_name)
 
             # Link from module to entity
             links.append({
-                "source": module_name,
+                "source": module_id,
                 "target": entity_id,
                 "type": "module-entity"
             })
@@ -212,13 +265,13 @@ def convert_to_d3_format(modules_entities: Dict, entity_metadata: Dict = None) -
                     # Find the actual module from mapping
                     if dep in entity_to_module:
                         dep_module = entity_to_module[dep]
-                    elif f"{dep_module_name}.py" in node_ids:
-                        dep_module = f"{dep_module_name}.py"
+                    elif dep_module_name in node_ids:
+                        dep_module = dep_module_name
 
                 # Special case: module._ means importing from a module (re-export)
                 # This creates a module-to-module link
                 if dep_entity == "_" and dep_module:
-                    link_key = (module_name, dep_module)
+                    link_key = (dep_module, module_id)  # Arrow from imported module to importer
                     if link_key not in module_links:
                         module_links.add(link_key)
                     continue  # Don't create entity-level link for module imports
@@ -226,10 +279,14 @@ def convert_to_d3_format(modules_entities: Dict, entity_metadata: Dict = None) -
                 # Try to resolve dependency to existing entity
                 dep_target = None
                 for m_path, m_entities in modules_entities.items():
-                    m_name = os.path.basename(m_path)
+                    if base_paths:
+                        m_id = get_relative_path(m_path, base_paths).replace('.py', '')
+                    else:
+                        m_id = os.path.basename(m_path).replace('.py', '')
+                    
                     if dep_entity in m_entities:
-                        dep_target = f"{m_name}:{dep_entity}"
-                        dep_module = m_name
+                        dep_target = f"{m_id}:{dep_entity}"
+                        dep_module = m_id
                         break
 
                 if dep_target and dep_target in node_ids:
@@ -240,8 +297,8 @@ def convert_to_d3_format(modules_entities: Dict, entity_metadata: Dict = None) -
                         "type": "dependency"
                     })
                     # Add module-to-module link if different modules
-                    if dep_module and dep_module != module_name:
-                        link_key = (module_name, dep_module)
+                    if dep_module and dep_module != module_id:
+                        link_key = (dep_module, module_id)  # Arrow from imported module to importer
                         if link_key not in module_links:
                             module_links.add(link_key)
                 else:
@@ -259,9 +316,41 @@ def convert_to_d3_format(modules_entities: Dict, entity_metadata: Dict = None) -
                         "target": dep_entity,
                         "type": "dependency"
                     })
+        
+        # Add imports list to the module node
+        # Use raw imports from modules_data if available, otherwise use collected imports
+        imports_to_add = raw_imports_by_module.get(module_path, []) if raw_imports_by_module else list(module_imports)
+        for node in nodes:
+            if node["id"] == module_id and node["type"] == "module":
+                node["imports"] = imports_to_add
+                # Create external nodes for all imports that aren't in the codebase
+                for import_name in imports_to_add:
+                    if import_name not in node_ids:
+                        nodes.append({
+                            "id": import_name,
+                            "type": "external",
+                            "label": import_name,
+                            "fullPath": import_name
+                        })
+                        node_ids.add(import_name)
+                    # Create module-to-module link (from external to importer)
+                    link_key = (import_name, module_id)  # Arrow from external module to file
+                    if link_key not in module_links:
+                        module_links.add(link_key)
+                break
 
     # Add module-to-module links
     for source_module, target_module in module_links:
+        # Create external module node if target doesn't exist in the codebase
+        if target_module not in node_ids:
+            nodes.append({
+                "id": target_module,
+                "type": "external",
+                "label": target_module,
+                "fullPath": target_module
+            })
+            node_ids.add(target_module)
+        
         links.append({
             "source": source_module,
             "target": target_module,
@@ -313,15 +402,18 @@ def get_d3_html_template(graph_data: Dict) -> str:
     return html_content
 
 
-def draw_graph(modules_entities: Dict, entity_metadata: Dict = None, output_path: str = None) -> None:
+def draw_graph(modules_entities: Dict, entity_metadata: Optional[Dict] = None, output_path: Optional[str] = None, 
+               base_paths: Optional[List] = None, raw_imports: Optional[Dict[str, List[str]]] = None) -> None:
     """Generate interactive D3.js visualization and open in browser.
 
     Args:
         modules_entities: Graph data with modules and their entities.
         entity_metadata: Metadata for entities (lines of code, type).
         output_path: Path to save HTML file. Default: ./codegraph.html
+        base_paths: List of base paths for calculating relative paths.
+        raw_imports: Dict mapping module paths to their raw import statements.
     """
-    graph_data = convert_to_d3_format(modules_entities, entity_metadata)
+    graph_data = convert_to_d3_format(modules_entities, entity_metadata, base_paths, raw_imports)
     html_content = get_d3_html_template(graph_data)
 
     # Determine output path
@@ -343,18 +435,21 @@ def draw_graph(modules_entities: Dict, entity_metadata: Dict = None, output_path
     click.echo(f"Interactive graph saved and opened in browser: {output_path}")
 
 
-def export_to_csv(modules_entities: Dict, entity_metadata: Dict = None, output_path: str = None) -> None:
+def export_to_csv(modules_entities: Dict, entity_metadata: Optional[Dict] = None, 
+                  output_path: Optional[str] = None, base_paths: Optional[List] = None, raw_imports: Optional[Dict[str, List[str]]] = None) -> None:
     """Export graph data to CSV file.
 
     Args:
         modules_entities: Graph data with modules and their entities.
         entity_metadata: Metadata for entities (lines of code, type).
         output_path: Path to save CSV file. Default: ./codegraph.csv
+        base_paths: List of base paths for calculating relative paths.
+        raw_imports: Dict mapping module paths to their raw import statements.
     """
     import click
 
     # Get D3 format data to reuse link calculation logic
-    graph_data = convert_to_d3_format(modules_entities, entity_metadata)
+    graph_data = convert_to_d3_format(modules_entities, entity_metadata, base_paths, raw_imports)
     nodes = graph_data["nodes"]
     links = graph_data["links"]
 
@@ -396,16 +491,20 @@ def export_to_csv(modules_entities: Dict, entity_metadata: Dict = None, output_p
                 parent_module = ""
                 full_path = node.get("fullPath", "")
                 lines = node.get("lines", 0)
-                name = node_id
+                # Use label (basename with .py) for CSV export for backward compatibility
+                name = node.get("label", node_id) + ".py" if not node.get("label", node_id).endswith(".py") else node.get("label", node_id)
             elif node_type == "entity":
                 display_type = node.get("entityType", "function")
-                parent_module = node.get("parent", "")
-                # Find full path from parent module
-                full_path = ""
-                for n in nodes:
-                    if n["id"] == parent_module and n["type"] == "module":
-                        full_path = n.get("fullPath", "")
-                        break
+                parent_module_id = node.get("parent", "")
+                # For parent_module in CSV, use label + .py for backward compatibility
+                parent_module_node = next((n for n in nodes if n["id"] == parent_module_id and n["type"] == "module"), None)
+                if parent_module_node:
+                    parent_label = parent_module_node.get("label", parent_module_id)
+                    parent_module = parent_label + ".py" if not parent_label.endswith(".py") else parent_label
+                    full_path = parent_module_node.get("fullPath", "")
+                else:
+                    parent_module = parent_module_id
+                    full_path = ""
                 lines = node.get("lines", 0)
                 name = node.get("label", node_id)
             else:  # external
diff --git a/pyproject.toml b/pyproject.toml
index e7b1c3e..4f34796 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "codegraph"
-version = "1.3.0"
+version = "1.5.0"
 license = "MIT"
 readme = "docs/README.rst"
 homepage = "https://github.com/ForteDexe/codegraph"
diff --git a/test_output.html b/test_output.html
index 1f30fe0..c840d51 100644
--- a/test_output.html
+++ b/test_output.html
@@ -63,20 +63,23 @@
 }
 .link-module-module {
     stroke: #ff9800;
-    stroke-width: 3px;
+    stroke-width: 2px;
     stroke-opacity: 0.8;
 }
 .link-module-entity {
     stroke: #009c2c;
-    stroke-width: 1.5px;
+    stroke-width: 2px;
     stroke-dasharray: 5, 3;
 }
 .link-dependency {
     stroke: #d94a4a;
-    stroke-width: 1.5px;
+    stroke-width: 2px;
+}
+.link.highlighted.link-dependency {
+    stroke-opacity: 1 !important;
 }
 .link-hidden {
-    opacity: 0;
+    opacity: 0 !important;
 }
 .label {
     font-size: 11px;
@@ -106,6 +109,9 @@
     transition: opacity 0.2s;
     border: 1px solid #555;
     max-width: 300px;
+    word-wrap: break-word;
+    word-break: break-all;
+    white-space: normal;
 }
 .tooltip .links-info {
     margin-top: 8px;
@@ -466,9 +472,32 @@
 .search-box {
     position: relative;
     width: 100%;
+    display: flex;
+    gap: 8px;
+    align-items: center;
+}
+.nav-button {
+    background: rgba(0, 0, 0, 0.9);
+    border: 2px solid #444;
+    border-radius: 6px;
+    color: #fff;
+    padding: 10px 14px;
+    font-size: 14px;
+    cursor: pointer;
+    transition: border-color 0.2s, background 0.2s;
+    flex-shrink: 0;
+}
+.nav-button:hover:not(:disabled) {
+    border-color: #70b8ff;
+    background: rgba(112, 184, 255, 0.1);
+}
+.nav-button:disabled {
+    color: #555;
+    cursor: not-allowed;
+    opacity: 0.5;
 }
 .search-input {
-    width: 100%;
+    flex: 1;
     padding: 12px 40px 12px 16px;
     font-size: 14px;
     border: 2px solid #444;
@@ -564,14 +593,23 @@
 }
 /* Dimmed state for non-highlighted nodes/links */
 .node.dimmed {
-    opacity: 0.15;
+    opacity: 0.2;
+}
+/* Hidden nodes must always be hidden, even if dimmed */
+.node.node-hidden {
+    opacity: 0 !important;
+    pointer-events: none;
 }
 .link.dimmed {
-    opacity: 0.05;
+    opacity: 0.4;
 }
 .label.dimmed {
     opacity: 0.1;
 }
+/* Hidden labels must always be hidden, even if dimmed */
+.label.label-hidden {
+    opacity: 0 !important;
+}
 /* Highlighted state */
 .node.highlighted {
     filter: brightness(1.3) drop-shadow(0 0 8px rgba(255, 255, 255, 0.5));
@@ -580,7 +618,7 @@
     filter: brightness(1.5) drop-shadow(0 0 15px rgba(112, 184, 255, 0.8));
 }
 .link.highlighted {
-    stroke-opacity: 1;
+    stroke-opacity: 1 !important;
     filter: drop-shadow(0 0 3px rgba(255, 255, 255, 0.5));
 }
 
@@ -593,6 +631,8 @@
     <!-- Search box -->
     <div class="search-container">
         <div class="search-box">
+            <button class="nav-button" id="backButton" title="Back (Alt+Left)" disabled>◀</button>
+            <button class="nav-button" id="forwardButton" title="Forward (Alt+Right)" disabled>▶</button>
             <input type="text" class="search-input" id="searchInput" placeholder="Search nodes... (Ctrl+F)" autocomplete="off">
             <button class="search-clear" id="searchClear">&times;</button>
             <div class="autocomplete-list" id="autocompleteList"></div>
@@ -705,22 +745,22 @@ <h4>Massive Objects <span class="count" id="massive-count"></span></h4>
             <ul id="massive-list"></ul>
         </div>
     </div>
-    <div class="panel size-toggle collapsed" id="size-toggle-panel">
+    <div class="panel size-toggle" id="size-toggle-panel">
         <div class="panel-header">
             <h4>Display</h4>
-            <button class="panel-toggle" title="Expand">+</button>
+            <button class="panel-toggle" title="Collapse">-</button>
         </div>
         <div class="panel-content">
             <label>
-                <input type="checkbox" id="size-by-code" checked>
+                <input type="checkbox" id="size-by-code">
                 Size by lines of code
             </label>
             <div class="display-section">
                 <h5>Show nodes</h5>
-                <label><input type="checkbox" id="show-modules" checked> Modules</label>
-                <label><input type="checkbox" id="show-classes" checked> Classes</label>
-                <label><input type="checkbox" id="show-functions" checked> Functions</label>
                 <label><input type="checkbox" id="show-external" checked> External</label>
+                <label><input type="checkbox" id="show-modules" checked> Modules</label>
+                <label><input type="checkbox" id="show-classes"> Classes</label>
+                <label><input type="checkbox" id="show-functions"> Functions</label>
             </div>
             <div class="display-section">
                 <h5>Show links</h5>
@@ -730,14 +770,18 @@ <h5>Show links</h5>
             </div>
             <div class="display-section">
                 <h5>Highlight Settings</h5>
-                <label>Max highlighted font size: <input type="number" id="max-highlight-font" value="32" min="16" max="100"></label>
+                <label>
+                    <input type="checkbox" id="highlight-focus-mode">
+                    Focus mode (hide background, show all chain nodes)
+                </label>
+                <label>Max highlighted font size: <input type="number" id="max-highlight-font" value="256" min="16" max="512"></label>
                 <label>Icon and wire scale factor: <input type="number" id="icon-wire-scale" value="1.0" min="0.1" max="5" step="0.1"></label>
                 <label>Subfolder levels: <input type="number" id="path-subfolder-levels" value="0" min="0" max="10"></label>
                 <div style="margin-top: 8px;">
                     <label><input type="checkbox" id="highlight-link-mm-out" checked> Module → Module</label>
-                    <label><input type="checkbox" id="highlight-link-mm-in" checked> Module ← Module</label>
+                    <label><input type="checkbox" id="highlight-link-mm-in"> Module ← Module</label>
                     <label><input type="checkbox" id="highlight-link-me-out" checked> Module → Entity</label>
-                    <label><input type="checkbox" id="highlight-link-me-in" checked> Module ← Entity</label>
+                    <label><input type="checkbox" id="highlight-link-me-in"> Module ← Entity</label>
                 </div>
             </div>
         </div>
@@ -747,1418 +791,2396 @@ <h5>Highlight Settings</h5>
         const graphData = {
   "nodes": [
     {
-      "id": "core.py",
+      "id": "codegraph/core",
+      "label": "core",
       "type": "module",
       "collapsed": false,
-      "fullPath": "codegraph\\codegraph\\core.py",
-      "lines": 347
-    },
-    {
-      "id": "core.py:parse_code_file",
+      "fullPath": "codegraph/core.py",
+      "lines": 601,
+      "imports": [
+        "codegraph",
+        "logging",
+        "codegraph",
+        "typing",
+        "collections",
+        "typing",
+        "collections",
+        "typing",
+        "codegraph",
+        "codegraph",
+        "codegraph",
+        "os",
+        "argparse",
+        "typing",
+        "typing",
+        "typing",
+        "codegraph",
+        "codegraph"
+      ]
+    },
+    {
+      "id": "codegraph/core:parse_code_file",
       "label": "parse_code_file",
       "type": "entity",
-      "parent": "core.py",
+      "parent": "codegraph/core",
       "lines": 5,
       "entityType": "function"
     },
     {
-      "id": "core.py:CodeGraph",
+      "id": "codegraph/core:CodeGraph",
       "label": "CodeGraph",
       "type": "entity",
-      "parent": "core.py",
-      "lines": 121,
+      "parent": "codegraph/core",
+      "lines": 341,
       "entityType": "class"
     },
     {
-      "id": "core.py:collect_entities_usage_in_modules",
+      "id": "codegraph/core:collect_entities_usage_in_modules",
       "label": "collect_entities_usage_in_modules",
       "type": "entity",
-      "parent": "core.py",
+      "parent": "codegraph/core",
       "lines": 32,
       "entityType": "function"
     },
     {
-      "id": "core.py:get_code_objects",
+      "id": "codegraph/core:get_code_objects",
       "label": "get_code_objects",
       "type": "entity",
-      "parent": "core.py",
-      "lines": 11,
+      "parent": "codegraph/core",
+      "lines": 12,
       "entityType": "function"
     },
     {
-      "id": "core.py:get_imports_and_entities_lines",
+      "id": "codegraph/core:get_imports_and_entities_lines",
       "label": "get_imports_and_entities_lines",
       "type": "entity",
-      "parent": "core.py",
-      "lines": 65,
+      "parent": "codegraph/core",
+      "lines": 77,
       "entityType": "function"
     },
     {
-      "id": "core.py:search_entities_from_list_in_code",
+      "id": "codegraph/core:search_entities_from_list_in_code",
       "label": "search_entities_from_list_in_code",
       "type": "entity",
-      "parent": "core.py",
+      "parent": "codegraph/core",
       "lines": 8,
       "entityType": "function"
     },
     {
-      "id": "core.py:search_entities_from_module_in_code",
+      "id": "codegraph/core:search_entities_from_module_in_code",
       "label": "search_entities_from_module_in_code",
       "type": "entity",
-      "parent": "core.py",
+      "parent": "codegraph/core",
       "lines": 20,
       "entityType": "function"
     },
     {
-      "id": "core.py:_",
+      "id": "codegraph/core:_",
       "label": "_",
       "type": "entity",
-      "parent": "core.py",
+      "parent": "codegraph/core",
       "lines": 0,
       "entityType": "function"
     },
     {
-      "id": "core.py:read_file_content",
+      "id": "codegraph/core:read_file_content",
       "label": "read_file_content",
       "type": "entity",
-      "parent": "core.py",
-      "lines": 5,
+      "parent": "codegraph/core",
+      "lines": 10,
       "entityType": "function"
     },
     {
-      "id": "core.py:get_module_name",
+      "id": "codegraph/core:get_module_name",
       "label": "get_module_name",
       "type": "entity",
-      "parent": "core.py",
-      "lines": 3,
+      "parent": "codegraph/core",
+      "lines": 19,
       "entityType": "function"
     },
     {
-      "id": "core.py:module_name_in_imports",
+      "id": "codegraph/core:module_name_in_imports",
       "label": "module_name_in_imports",
       "type": "entity",
-      "parent": "core.py",
+      "parent": "codegraph/core",
       "lines": 5,
       "entityType": "function"
     },
     {
-      "id": "core.py:populate_free_nodes",
+      "id": "codegraph/core:populate_free_nodes",
       "label": "populate_free_nodes",
       "type": "entity",
-      "parent": "core.py",
+      "parent": "codegraph/core",
       "lines": 57,
       "entityType": "function"
     },
     {
-      "id": "core.py:search_entity_usage",
+      "id": "codegraph/core:search_entity_usage",
       "label": "search_entity_usage",
       "type": "entity",
-      "parent": "core.py",
+      "parent": "codegraph/core",
       "lines": 15,
       "entityType": "function"
     },
     {
-      "id": "main.py",
+      "id": "codegraph/main",
+      "label": "main",
       "type": "module",
       "collapsed": false,
-      "fullPath": "codegraph\\codegraph\\main.py",
-      "lines": 43
-    },
-    {
-      "id": "main.py:main",
+      "fullPath": "codegraph/main.py",
+      "lines": 47,
+      "imports": [
+        "pprint",
+        "logging",
+        "sys",
+        "codegraph",
+        "argparse",
+        "click",
+        "codegraph",
+        "codegraph"
+      ]
+    },
+    {
+      "id": "codegraph/main:main",
       "label": "main",
       "type": "entity",
-      "parent": "main.py",
-      "lines": 27,
+      "parent": "codegraph/main",
+      "lines": 31,
       "entityType": "function"
     },
     {
-      "id": "main.py:_",
+      "id": "codegraph/main:_",
       "label": "_",
       "type": "entity",
-      "parent": "main.py",
+      "parent": "codegraph/main",
       "lines": 0,
       "entityType": "function"
     },
     {
-      "id": "main.py:cli",
+      "id": "codegraph/main:cli",
       "label": "cli",
       "type": "entity",
-      "parent": "main.py",
+      "parent": "codegraph/main",
       "lines": 16,
       "entityType": "function"
     },
     {
-      "id": "parser.py",
+      "id": "codegraph/parser",
+      "label": "parser",
       "type": "module",
       "collapsed": false,
-      "fullPath": "codegraph\\codegraph\\parser.py",
-      "lines": 283
-    },
-    {
-      "id": "parser.py:Function",
+      "fullPath": "codegraph/parser.py",
+      "lines": 289,
+      "imports": [
+        "token",
+        "tokenize",
+        "typing",
+        "typing",
+        "token",
+        "io",
+        "token",
+        "token"
+      ]
+    },
+    {
+      "id": "codegraph/parser:Function",
       "label": "Function",
       "type": "entity",
-      "parent": "parser.py",
+      "parent": "codegraph/parser",
       "lines": 7,
       "entityType": "class"
     },
     {
-      "id": "parser.py:AsyncFunction",
+      "id": "codegraph/parser:AsyncFunction",
       "label": "AsyncFunction",
       "type": "entity",
-      "parent": "parser.py",
+      "parent": "codegraph/parser",
       "lines": 7,
       "entityType": "class"
     },
     {
-      "id": "parser.py:Class",
+      "id": "codegraph/parser:Class",
       "label": "Class",
       "type": "entity",
-      "parent": "parser.py",
+      "parent": "codegraph/parser",
       "lines": 16,
       "entityType": "class"
     },
     {
-      "id": "parser.py:_nest_function",
+      "id": "codegraph/parser:_nest_function",
       "label": "_nest_function",
       "type": "entity",
-      "parent": "parser.py",
+      "parent": "codegraph/parser",
       "lines": 10,
       "entityType": "function"
     },
     {
-      "id": "parser.py:create_objects_array",
+      "id": "codegraph/parser:create_objects_array",
       "label": "create_objects_array",
       "type": "entity",
-      "parent": "parser.py",
-      "lines": 206,
+      "parent": "codegraph/parser",
+      "lines": 212,
       "entityType": "function"
     },
     {
-      "id": "parser.py:_nest_class",
+      "id": "codegraph/parser:_nest_class",
       "label": "_nest_class",
       "type": "entity",
-      "parent": "parser.py",
+      "parent": "codegraph/parser",
       "lines": 5,
       "entityType": "function"
     },
     {
-      "id": "parser.py:_Object",
+      "id": "codegraph/parser:_Object",
       "label": "_Object",
       "type": "entity",
-      "parent": "parser.py",
+      "parent": "codegraph/parser",
       "lines": 22,
       "entityType": "class"
     },
     {
-      "id": "parser.py:Import",
+      "id": "codegraph/parser:Import",
       "label": "Import",
       "type": "entity",
-      "parent": "parser.py",
+      "parent": "codegraph/parser",
       "lines": 10,
       "entityType": "class"
     },
     {
-      "id": "utils.py",
+      "id": "codegraph/utils",
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     },
     {
-      "source": "test_graph_generation.py:TestImportParsing",
-      "target": "parser.py:create_objects_array",
-      "type": "dependency"
+      "source": "argparse",
+      "target": "tests/test_package_install",
+      "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py:TestImportParsing",
-      "target": "parser.py:create_objects_array",
-      "type": "dependency"
+      "source": "codegraph/core",
+      "target": "tests/test_data/module_a",
+      "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py:TestImportParsing",
-      "target": "parser.py:create_objects_array",
-      "type": "dependency"
+      "source": "networkx",
+      "target": "codegraph/vizualyzer",
+      "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py:TestImportParsing",
-      "target": "parser.py:create_objects_array",
-      "type": "dependency"
+      "source": "codegraph/core",
+      "target": "tests/test_graph_generation",
+      "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py:TestImportParsing",
-      "target": "parser.py:create_objects_array",
-      "type": "dependency"
+      "source": "os",
+      "target": "tests/test_package_install",
+      "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py",
-      "target": "test_graph_generation.py:TestCodeGraphConnections",
-      "type": "module-entity"
+      "source": "pprint",
+      "target": "codegraph/main",
+      "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py:TestCodeGraphConnections",
-      "target": "core.py:CodeGraph",
-      "type": "dependency"
+      "source": "pathlib",
+      "target": "tests/test_codegraph",
+      "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py:TestCodeGraphConnections",
-      "target": "core.py:CodeGraph",
-      "type": "dependency"
+      "source": "csv",
+      "target": "codegraph/vizualyzer",
+      "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py",
-      "target": "test_graph_generation.py:TestCodeGraphOnItself",
-      "type": "module-entity"
+      "source": "tests/test_data/module_a",
+      "target": "tests/test_data/alias_imports",
+      "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py:TestCodeGraphOnItself",
-      "target": "core.py:CodeGraph",
-      "type": "dependency"
+      "source": "argparse",
+      "target": "tests/test_codegraph",
+      "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py:TestCodeGraphOnItself",
-      "target": "core.py:CodeGraph",
-      "type": "dependency"
+      "source": "tests/test_data/module_c",
+      "target": "tests/test_data/module_a",
+      "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py:TestCodeGraphOnItself",
-      "target": "core.py:CodeGraph",
-      "type": "dependency"
+      "source": "typing",
+      "target": "codegraph/core",
+      "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py",
-      "target": "test_graph_generation.py:TestCSVExport",
-      "type": "module-entity"
+      "source": "matplotlib",
+      "target": "codegraph/vizualyzer",
+      "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py:TestCSVExport",
-      "target": "core.py:CodeGraph",
-      "type": "dependency"
+      "source": "token",
+      "target": "codegraph/parser",
+      "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py",
-      "target": "test_graph_generation.py:_",
-      "type": "module-entity"
+      "source": "codegraph/core",
+      "target": "codegraph/vizualyzer",
+      "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py",
-      "target": "test_graph_generation.py:TestD3FormatConversion",
-      "type": "module-entity"
+      "source": "io",
+      "target": "codegraph/parser",
+      "type": "module-module"
     },
     {
-      "source": "test_package_install.py",
-      "target": "test_package_install.py:test_codegraph_on_itself_without_matplotlib",
-      "type": "module-entity"
+      "source": "logging",
+      "target": "codegraph/core",
+      "type": "module-module"
     },
     {
-      "source": "test_package_install.py:test_codegraph_on_itself_without_matplotlib",
-      "target": "core.py:CodeGraph",
-      "type": "dependency"
+      "source": "codegraph/parser",
+      "target": "tests/test_graph_generation",
+      "type": "module-module"
     },
     {
-      "source": "test_package_install.py",
-      "target": "test_package_install.py:test_d3_visualization_without_matplotlib",
-      "type": "module-entity"
+      "source": "argparse",
+      "target": "codegraph/main",
+      "type": "module-module"
     },
     {
-      "source": "test_package_install.py:test_d3_visualization_without_matplotlib",
-      "target": "vizualyzer.py:draw_graph",
-      "type": "dependency"
+      "source": "codegraph",
+      "target": "tests/test_utils",
+      "type": "module-module"
     },
     {
-      "source": "test_package_install.py",
-      "target": "test_package_install.py:_",
-      "type": "module-entity"
+      "source": "matplotlib",
+      "target": "tests/test_data/vizualyzer",
+      "type": "module-module"
     },
     {
-      "source": "test_package_install.py",
-      "target": "test_package_install.py:test_import_codegraph",
-      "type": "module-entity"
+      "source": "tests/test_data/module_b",
+      "target": "tests/test_data/module_a",
+      "type": "module-module"
     },
     {
-      "source": "test_package_install.py",
-      "target": "test_package_install.py:test_import_core",
-      "type": "module-entity"
+      "source": "tests",
+      "target": "tests/test_data/module_a",
+      "type": "module-module"
     },
     {
-      "source": "test_package_install.py",
-      "target": "test_package_install.py:test_import_vizualyzer",
-      "type": "module-entity"
+      "source": "codegraph/core",
+      "target": "tests/test_data/comma_imports",
+      "type": "module-module"
     },
     {
-      "source": "test_package_install.py",
-      "target": "test_package_install.py:test_cli_help",
-      "type": "module-entity"
+      "source": "logging",
+      "target": "codegraph/main",
+      "type": "module-module"
     },
     {
-      "source": "test_utils.py",
-      "target": "test_utils.py:test_get_python_paths_list_error",
-      "type": "module-entity"
+      "source": "typing",
+      "target": "codegraph/utils",
+      "type": "module-module"
     },
     {
-      "source": "test_utils.py:test_get_python_paths_list_error",
-      "target": "utils.py:get_python_paths_list",
-      "type": "dependency"
+      "source": "codegraph/core",
+      "target": "tests/test_data/alias_imports",
+      "type": "module-module"
     },
     {
-      "source": "test_utils.py",
-      "target": "test_utils.py:_",
-      "type": "module-entity"
+      "source": "pathlib",
+      "target": "tests/test_graph_generation",
+      "type": "module-module"
     },
     {
-      "source": "test_utils.py:_",
-      "target": "utils.py:get_python_paths_list",
-      "type": "dependency"
+      "source": "json",
+      "target": "codegraph/vizualyzer",
+      "type": "module-module"
     },
     {
-      "source": "test_utils.py",
-      "target": "test_utils.py:test_get_python_paths_list",
-      "type": "module-entity"
+      "source": "pathlib",
+      "target": "codegraph/utils",
+      "type": "module-module"
     },
     {
-      "source": "alias_imports.py",
-      "target": "alias_imports.py:use_aliases",
-      "type": "module-entity"
+      "source": "click",
+      "target": "codegraph/main",
+      "type": "module-module"
     },
     {
-      "source": "alias_imports.py:use_aliases",
-      "target": "module_b.py:func_b",
-      "type": "dependency"
+      "source": "codegraph",
+      "target": "tests/test_codegraph",
+      "type": "module-module"
     },
     {
-      "source": "alias_imports.py:use_aliases",
-      "target": "module_a.py:func_a",
-      "type": "dependency"
+      "source": "click",
+      "target": "tests/test_package_install",
+      "type": "module-module"
     },
     {
-      "source": "alias_imports.py",
-      "target": "alias_imports.py:_",
-      "type": "module-entity"
+      "source": "tests/test_data/module_c",
+      "target": "tests/test_data/comma_imports",
+      "type": "module-module"
     },
     {
-      "source": "comma_imports.py",
-      "target": "comma_imports.py:use_all",
-      "type": "module-entity"
+      "source": "networkx",
+      "target": "tests/test_data/vizualyzer",
+      "type": "module-module"
     },
     {
-      "source": "comma_imports.py:use_all",
-      "target": "module_b.py:func_b",
-      "type": "dependency"
+      "source": "os",
+      "target": "codegraph/utils",
+      "type": "module-module"
     },
     {
-      "source": "comma_imports.py:use_all",
-      "target": "module_a.py:func_a",
-      "type": "dependency"
+      "source": "typing",
+      "target": "codegraph/vizualyzer",
+      "type": "module-module"
     },
     {
-      "source": "comma_imports.py:use_all",
-      "target": "module_c.py:func_c1",
-      "type": "dependency"
+      "source": "codegraph",
+      "target": "codegraph/core",
+      "type": "module-module"
     },
     {
-      "source": "comma_imports.py",
-      "target": "comma_imports.py:_",
-      "type": "module-entity"
+      "source": "pytest",
+      "target": "tests/test_utils",
+      "type": "module-module"
     },
     {
-      "source": "module_a.py",
-      "target": "module_a.py:func_a",
-      "type": "module-entity"
+      "source": "codegraph/core",
+      "target": "tests/test_data/duplicate_names/src/main",
+      "type": "module-module"
     },
     {
-      "source": "module_a.py:func_a",
-      "target": "module_b.py:func_b",
-      "type": "dependency"
+      "source": "codegraph/parser",
+      "target": "codegraph/core",
+      "type": "module-module"
     },
     {
-      "source": "module_a.py:func_a",
-      "target": "module_c.py:func_c1",
-      "type": "dependency"
+      "source": "codegraph/vizualyzer",
+      "target": "tests/test_data/vizualyzer",
+      "type": "module-module"
     },
     {
-      "source": "module_a.py",
-      "target": "module_a.py:_",
-      "type": "module-entity"
+      "source": "tests/test_data/duplicate_names/tests/utils",
+      "target": "tests/test_data/duplicate_names/tests/sample_test",
+      "type": "module-module"
     },
     {
-      "source": "module_a.py",
-      "target": "module_a.py:func_a2",
-      "type": "module-entity"
+      "source": "sys",
+      "target": "codegraph/main",
+      "type": "module-module"
     },
     {
-      "source": "module_b.py",
-      "target": "module_b.py:func_b",
-      "type": "module-entity"
+      "source": "tempfile",
+      "target": "tests/test_package_install",
+      "type": "module-module"
     },
     {
-      "source": "module_b.py:func_b",
-      "target": "module_c.py:func_c2",
-      "type": "dependency"
+      "source": "os",
+      "target": "codegraph/vizualyzer",
+      "type": "module-module"
     },
     {
-      "source": "module_b.py",
-      "target": "module_b.py:_",
-      "type": "module-entity"
+      "source": "glob",
+      "target": "codegraph/utils",
+      "type": "module-module"
     },
     {
-      "source": "module_b.py",
-      "target": "module_b.py:func_b2",
-      "type": "module-entity"
+      "source": "codegraph",
+      "target": "codegraph/main",
+      "type": "module-module"
     },
     {
-      "source": "module_c.py",
-      "target": "module_c.py:func_c1",
-      "type": "module-entity"
+      "source": "logging",
+      "target": "codegraph/vizualyzer",
+      "type": "module-module"
     },
     {
-      "source": "module_c.py",
-      "target": "module_c.py:func_c2",
-      "type": "module-entity"
+      "source": "codegraph",
+      "target": "tests/test_package_install",
+      "type": "module-module"
     },
     {
-      "source": "vizualyzer.py",
-      "target": "vizualyzer.py:draw_graph",
-      "type": "module-entity"
+      "source": "codegraph/core",
+      "target": "tests/test_data/module_b",
+      "type": "module-module"
     },
     {
-      "source": "vizualyzer.py:draw_graph",
-      "target": "vizualyzer.py:process_module_in_graph",
-      "type": "dependency"
+      "source": "codegraph/core",
+      "target": "tests/test_utils",
+      "type": "module-module"
     },
     {
-      "source": "vizualyzer.py",
-      "target": "vizualyzer.py:process_module_in_graph",
-      "type": "module-entity"
+      "source": "tests/test_data/module_b",
+      "target": "tests/test_data/comma_imports",
+      "type": "module-module"
     },
     {
-      "source": "core.py",
-      "target": "utils.py",
+      "source": "codegraph/core",
+      "target": "codegraph/main",
       "type": "module-module"
     },
     {
-      "source": "test_codegraph.py",
-      "target": "core.py",
+      "source": "codegraph/core",
+      "target": "tests/test_data/duplicate_names/tests/sample_test",
       "type": "module-module"
     },
     {
-      "source": "main.py",
-      "target": "__init__.py",
+      "source": "tests",
+      "target": "tests/test_data/comma_imports",
       "type": "module-module"
     },
     {
-      "source": "test_utils.py",
-      "target": "utils.py",
+      "source": "codegraph/core",
+      "target": "tests/test_package_install",
       "type": "module-module"
     },
     {
-      "source": "test_package_install.py",
-      "target": "main.py",
+      "source": "tests/test_data/module_b",
+      "target": "tests/test_data/alias_imports",
       "type": "module-module"
     },
     {
-      "source": "module_a.py",
-      "target": "module_b.py",
+      "source": "argparse",
+      "target": "tests/test_graph_generation",
       "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py",
-      "target": "parser.py",
+      "source": "src",
+      "target": "tests/test_data/duplicate_names/src/main",
       "type": "module-module"
     },
     {
-      "source": "test_package_install.py",
-      "target": "__init__.py",
+      "source": "tests/test_data/module_c",
+      "target": "tests/test_data/module_b",
       "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py",
-      "target": "core.py",
+      "source": "pathlib",
+      "target": "tests/test_utils",
       "type": "module-module"
     },
     {
-      "source": "module_b.py",
-      "target": "module_c.py",
+      "source": "tokenize",
+      "target": "codegraph/parser",
       "type": "module-module"
     },
     {
-      "source": "main.py",
-      "target": "core.py",
+      "source": "tests",
+      "target": "tests/test_data/alias_imports",
       "type": "module-module"
     },
     {
-      "source": "core.py",
-      "target": "parser.py",
+      "source": "os",
+      "target": "tests/test_data/vizualyzer",
       "type": "module-module"
     },
     {
-      "source": "main.py",
-      "target": "vizualyzer.py",
+      "source": "codegraph/core",
+      "target": "tests/test_codegraph",
       "type": "module-module"
     },
     {
-      "source": "comma_imports.py",
-      "target": "module_c.py",
+      "source": "tests/test_data/module_a",
+      "target": "tests/test_data/comma_imports",
       "type": "module-module"
     },
     {
-      "source": "test_package_install.py",
-      "target": "core.py",
+      "source": "tests/test_data/duplicate_names/src/utils",
+      "target": "tests/test_data/duplicate_names/src/main",
       "type": "module-module"
     },
     {
-      "source": "test_graph_generation.py",
-      "target": "vizualyzer.py",
+      "source": "collections",
+      "target": "codegraph/core",
       "type": "module-module"
     },
     {
-      "source": "alias_imports.py",
-      "target": "module_b.py",
+      "source": "typing",
+      "target": "codegraph/parser",
       "type": "module-module"
     },
     {
-      "source": "alias_imports.py",
-      "target": "module_a.py",
+      "source": "codegraph",
+      "target": "codegraph/vizualyzer",
       "type": "module-module"
     },
     {
-      "source": "test_package_install.py",
-      "target": "vizualyzer.py",
+      "source": "codegraph/vizualyzer",
+      "target": "codegraph/main",
       "type": "module-module"
     },
     {
-      "source": "comma_imports.py",
-      "target": "module_b.py",
+      "source": "codegraph/vizualyzer",
+      "target": "tests/test_package_install",
       "type": "module-module"
     },
     {
-      "source": "comma_imports.py",
-      "target": "module_a.py",
+      "source": "typing",
+      "target": "tests/test_data/vizualyzer",
       "type": "module-module"
     },
     {
-      "source": "module_a.py",
-      "target": "module_c.py",
+      "source": "argparse",
+      "target": "codegraph/core",
+      "type": "module-module"
+    },
+    {
+      "source": "click",
+      "target": "codegraph/vizualyzer",
+      "type": "module-module"
+    },
+    {
+      "source": "tests",
+      "target": "tests/test_data/module_b",
       "type": "module-module"
     }
   ],
-  "unlinkedModules": []
+  "unlinkedModules": [
+    {
+      "id": "codegraph/__init__",
+      "fullPath": "codegraph/__init__.py"
+    },
+    {
+      "id": "tests/__init__",
+      "fullPath": "tests/__init__.py"
+    }
+  ]
 };
 
 // Panel drag and collapse functionality
@@ -2308,7 +3330,7 @@ <h5>Highlight Settings</h5>
 updateLinksCount();
 
 // Size scaling state
-let sizeByCode = true;
+let sizeByCode = false;
 
 // Calculate max lines for scaling
 const maxLines = Math.max(...graphData.nodes.map(n => n.lines || 0), 1);
@@ -2393,11 +3415,14 @@ <h5>Highlight Settings</h5>
     node.each(function(d) {
         const el = d3.select(this);
         const isHighlighted = el.classed('highlighted-main') || el.classed('highlighted');
-        const multiplier = isHighlighted ? iconWireScaleFactor / scale : 1;
+        const isDimmed = el.classed('dimmed');
+        const multiplier = (isHighlighted && !isDimmed) ? iconWireScaleFactor / scale : 1;
         if (d.type === "module") {
             const baseSize = getNodeSize(d, 30);
             const size = baseSize * multiplier;
-            const clampedSize = Math.max(10, Math.min(200, size));
+            // Use scale factor to determine reasonable max (higher scale factor = higher max)
+            const maxSize = 200 * iconWireScaleFactor;
+            const clampedSize = Math.max(10, Math.min(maxSize, size));
             el.select("rect")
                 .attr("width", clampedSize)
                 .attr("height", clampedSize)
@@ -2406,7 +3431,9 @@ <h5>Highlight Settings</h5>
         } else if (d.type === "entity" || d.type === "external") {
             const baseR = getNodeSize(d, 10);
             const r = baseR * multiplier;
-            const clampedR = Math.max(5, Math.min(100, r));
+            // Use scale factor to determine reasonable max (higher scale factor = higher max)
+            const maxR = 100 * iconWireScaleFactor;
+            const clampedR = Math.max(5, Math.min(maxR, r));
             el.select("circle").attr("r", clampedR);
         }
     });
@@ -2414,10 +3441,18 @@ <h5>Highlight Settings</h5>
     link.each(function(d) {
         const el = d3.select(this);
         const isHighlighted = el.classed('highlighted');
-        const multiplier = isHighlighted ? iconWireScaleFactor / scale : 1;
+        const isDimmed = el.classed('dimmed');
+        
+        // Use same multiplier as icons - only highlighted arrows scale with zoom
+        const multiplier = (isHighlighted && !isDimmed) ? iconWireScaleFactor / scale : 1;
+        
+        // Use same base width for all link types for consistent arrow scaling
         const baseWidth = 2;
+        
         const width = baseWidth * multiplier;
-        const clampedWidth = Math.max(1, Math.min(10, width));
+        // Reduce max for better balance
+        const maxWidth = 18.75 * iconWireScaleFactor;
+        const clampedWidth = Math.max(1, Math.min(maxWidth, width));
         el.style("stroke-width", clampedWidth + "px");
     });
     // Update labels position
@@ -2444,6 +3479,10 @@ <h5>Highlight Settings</h5>
     } else if (d.type === 'module-entity') {
         if (isOut && highlightLinkFilters.meOut) return true;
         if (isIn && highlightLinkFilters.meIn) return true;
+    } else if (d.type === 'dependency') {
+        // Entity-to-entity or entity-to-external dependencies
+        // Always highlight these when the entity is selected
+        if (isOut || isIn) return true;
     }
     return false;
 }
@@ -2512,10 +3551,10 @@ <h5>Highlight Settings</h5>
 defs.append("marker")
     .attr("id", "arrow-module-module")
     .attr("viewBox", "0 -5 10 10")
-    .attr("refX", 25)
+    .attr("refX", 18)
     .attr("refY", 0)
-    .attr("markerWidth", 8)
-    .attr("markerHeight", 8)
+    .attr("markerWidth", 6)
+    .attr("markerHeight", 6)
     .attr("orient", "auto")
     .append("path")
     .attr("fill", "#ff9800")
@@ -2651,8 +3690,8 @@ <h5>Highlight Settings</h5>
 // Display filter state
 const displayFilters = {
     showModules: true,
-    showClasses: true,
-    showFunctions: true,
+    showClasses: false,
+    showFunctions: false,
     showExternal: true,
     showLinkModule: true,
     showLinkEntity: true,
@@ -2663,30 +3702,37 @@ <h5>Highlight Settings</h5>
 document.getElementById('show-modules').addEventListener('change', function() {
     displayFilters.showModules = this.checked;
     updateDisplayFilters();
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
 });
 document.getElementById('show-classes').addEventListener('change', function() {
     displayFilters.showClasses = this.checked;
     updateDisplayFilters();
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
 });
 document.getElementById('show-functions').addEventListener('change', function() {
     displayFilters.showFunctions = this.checked;
     updateDisplayFilters();
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
 });
 document.getElementById('show-external').addEventListener('change', function() {
     displayFilters.showExternal = this.checked;
     updateDisplayFilters();
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
 });
 document.getElementById('show-link-module').addEventListener('change', function() {
     displayFilters.showLinkModule = this.checked;
     updateDisplayFilters();
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
 });
 document.getElementById('show-link-entity').addEventListener('change', function() {
     displayFilters.showLinkEntity = this.checked;
     updateDisplayFilters();
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
 });
 document.getElementById('show-link-dependency').addEventListener('change', function() {
     displayFilters.showLinkDependency = this.checked;
     updateDisplayFilters();
+    if (currentHighlightedNode) highlightNode(currentHighlightedNode);
 });
 document.getElementById('max-highlight-font').addEventListener('input', function() {
     maxHighlightFontSize = parseInt(this.value) || 32;
@@ -2698,6 +3744,15 @@ <h5>Highlight Settings</h5>
     // Update icon and wire sizes immediately
     updateIconWireSizes(currentScale);
 });
+document.getElementById('highlight-focus-mode').addEventListener('change', function() {
+    highlightFocusMode = this.checked;
+    if (currentHighlightedNode) {
+        highlightNode(currentHighlightedNode);
+    } else if (!this.checked) {
+        // When turning off focus mode without active highlight, restore display filters
+        updateDisplayFilters();
+    }
+});
 document.getElementById('highlight-link-mm-out').addEventListener('change', function() {
     highlightLinkFilters.mmOut = this.checked;
     if (currentHighlightedNode) highlightNode(currentHighlightedNode);
@@ -2789,6 +3844,9 @@ <h5>Highlight Settings</h5>
 // Initialize font sizes
 updateFontSizes(1);
 
+// Apply initial display filters
+updateDisplayFilters();
+
 // Node interactions
 node.on("mouseover", function(event, d) {
     // Highlight connected links
@@ -2995,17 +4053,83 @@ <h5>Highlight Settings</h5>
 const searchClear = document.getElementById('searchClear');
 const autocompleteList = document.getElementById('autocompleteList');
 
+// Navigation history
+let highlightHistory = [];
+let historyIndex = -1;
+let isNavigating = false; // Flag to prevent adding to history during navigation
+
+const backButton = document.getElementById('backButton');
+const forwardButton = document.getElementById('forwardButton');
+
+function updateNavigationButtons() {
+    backButton.disabled = historyIndex <= 0;
+    forwardButton.disabled = historyIndex >= highlightHistory.length - 1;
+}
+
+function addToHistory(nodeId) {
+    if (isNavigating) return; // Don't add to history during back/forward navigation
+    
+    // Remove any forward history when a new node is selected
+    highlightHistory = highlightHistory.slice(0, historyIndex + 1);
+    
+    // Add new node (avoid duplicates of the same node in a row)
+    if (highlightHistory[historyIndex] !== nodeId) {
+        highlightHistory.push(nodeId);
+        historyIndex++;
+    }
+    
+    updateNavigationButtons();
+}
+
+function navigateBack() {
+    if (historyIndex > 0) {
+        isNavigating = true;
+        historyIndex--;
+        const nodeId = highlightHistory[historyIndex];
+        highlightNode(nodeId);
+        isNavigating = false;
+        updateNavigationButtons();
+    }
+}
+
+function navigateForward() {
+    if (historyIndex < highlightHistory.length - 1) {
+        isNavigating = true;
+        historyIndex++;
+        const nodeId = highlightHistory[historyIndex];
+        highlightNode(nodeId);
+        isNavigating = false;
+        updateNavigationButtons();
+    }
+}
+
+backButton.addEventListener('click', navigateBack);
+forwardButton.addEventListener('click', navigateForward);
+
+// Keyboard shortcuts for navigation
+document.addEventListener('keydown', (e) => {
+    if (e.altKey && e.key === 'ArrowLeft') {
+        e.preventDefault();
+        navigateBack();
+    } else if (e.altKey && e.key === 'ArrowRight') {
+        e.preventDefault();
+        navigateForward();
+    }
+});
+
+
 let selectedAutocompleteIndex = -1;
 let currentHighlightedNode = null;
-let maxHighlightFontSize = 32;
+let maxHighlightFontSize = 256;
 let iconWireScaleFactor = 1.0;
 let currentScale = 1;
 let filteredNodes = [];
+let highlightFocusMode = false;
 let highlightLinkFilters = {
     mmOut: true,
-    mmIn: true,
+    mmIn: false,
     meOut: true,
-    meIn: true
+    meIn: false
 };
 let showHighlightedPath = true;
 let pathSubfolderLevels = 0;
@@ -3016,7 +4140,15 @@ <h5>Highlight Settings</h5>
     label: n.label || n.id,
     type: n.type,
     parent: n.parent || null,
-    searchText: ((n.label || n.id) + ' ' + (n.parent || '')).toLowerCase()
+    fullPath: n.fullPath || null,
+    // For modules, include both 'modulename' and 'modulename.py' as separate searchable terms, plus imports
+    // For entities, search by label and parent
+    searchText: n.type === 'module' 
+        ? (n.label || n.id).toLowerCase() + ' ' + 
+          (n.label || n.id).toLowerCase() + '.py ' + 
+          (n.fullPath || '').toLowerCase() + ' ' +
+          ((n.imports || []).join(' ')).toLowerCase()
+        : ((n.label || n.id) + ' ' + (n.parent || '')).toLowerCase()
 }));
 
 // Get connected nodes for a given node
@@ -3087,7 +4219,19 @@ <h5>Highlight Settings</h5>
 
 // Highlight a node and its connections
 function highlightNode(nodeId) {
-    const connectedLinks = graphData.links.filter(d => isLinkHighlighted(d, nodeId));
+    // Add to history (unless we're navigating)
+    addToHistory(nodeId);
+    
+    // In focus mode, build chain from ALL dependency links
+    // In normal mode, use filtered links based on highlight settings
+    const connectedLinks = highlightFocusMode 
+        ? graphData.links.filter(d => {
+            const sourceId = typeof d.source === 'object' ? d.source.id : d.source;
+            const targetId = typeof d.target === 'object' ? d.target.id : d.target;
+            return sourceId === nodeId || targetId === nodeId;
+          })
+        : graphData.links.filter(d => isLinkHighlighted(d, nodeId));
+    
     const connectedNodes = new Set();
     connectedLinks.forEach(l => {
         const sourceId = typeof l.source === 'object' ? l.source.id : l.source;
@@ -3097,18 +4241,137 @@ <h5>Highlight Settings</h5>
     });
     currentHighlightedNode = nodeId;
 
-    // Update nodes
-    node.classed('dimmed', d => d.id !== nodeId && !connectedNodes.has(d.id))
-        .classed('highlighted', d => connectedNodes.has(d.id) && d.id !== nodeId)
-        .classed('highlighted-main', d => d.id === nodeId);
+    if (highlightFocusMode) {
+        // Focus mode: show all chain nodes (ignore filters), hide background nodes completely
+        node.each(function(d) {
+            const el = d3.select(this);
+            if (d.id === nodeId) {
+                el.classed('dimmed', false)
+                  .classed('highlighted', false)
+                  .classed('highlighted-main', true)
+                  .classed('node-hidden', false);
+            } else if (connectedNodes.has(d.id)) {
+                // Check if this node should be highlighted or dimmed
+                const shouldHighlight = connectedLinks.some(l => {
+                    const sourceId = typeof l.source === 'object' ? l.source.id : l.source;
+                    const targetId = typeof l.target === 'object' ? l.target.id : l.target;
+                    return (sourceId === d.id || targetId === d.id) && isLinkHighlighted(l, nodeId);
+                });
+                el.classed('dimmed', !shouldHighlight)
+                  .classed('highlighted', shouldHighlight)
+                  .classed('highlighted-main', false)
+                  .classed('node-hidden', false);
+            } else {
+                // Background nodes - completely hidden
+                el.classed('dimmed', false)
+                  .classed('highlighted', false)
+                  .classed('highlighted-main', false)
+                  .classed('node-hidden', true);
+            }
+        });
+    } else {
+        // Normal mode: respect filters, only dim background
+        // First, clear node-hidden from all nodes to undo focus mode
+        node.classed('node-hidden', d => isNodeFilteredOut(d) || isNodeHidden(d));
+        
+        // Then apply highlight classes only to visible nodes
+        node.filter(d => !isNodeFilteredOut(d) && !isNodeHidden(d))
+            .classed('dimmed', d => d.id !== nodeId && !connectedNodes.has(d.id))
+            .classed('highlighted', d => connectedNodes.has(d.id) && d.id !== nodeId)
+            .classed('highlighted-main', d => d.id === nodeId);
+    }
 
     // Update links
-    link.classed('dimmed', d => !isLinkHighlighted(d, nodeId))
-        .classed('highlighted', d => isLinkHighlighted(d, nodeId));
+    if (highlightFocusMode) {
+        // Focus mode: show only links between chain nodes
+        link.each(function(d) {
+            const el = d3.select(this);
+            const sourceId = typeof d.source === 'object' ? d.source.id : d.source;
+            const targetId = typeof d.target === 'object' ? d.target.id : d.target;
+            const sourceInChain = sourceId === nodeId || connectedNodes.has(sourceId);
+            const targetInChain = targetId === nodeId || connectedNodes.has(targetId);
+            
+            if (sourceInChain && targetInChain) {
+                // Link is part of the chain
+                const isHighlighted = isLinkHighlighted(d, nodeId);
+                el.classed('dimmed', !isHighlighted)
+                  .classed('highlighted', isHighlighted)
+                  .classed('link-hidden', false)
+                  .style('stroke-opacity', isHighlighted ? 1 : 0.4);
+            } else {
+                // Background link - completely hidden
+                el.classed('dimmed', false)
+                  .classed('highlighted', false)
+                  .classed('link-hidden', true)
+                  .style('stroke-opacity', null);
+            }
+        });
+    } else {
+        // Normal mode: filter out links connected to hidden nodes
+        // First, clear any inline stroke-opacity styles from focus mode
+        link.style('stroke-opacity', null);
+        
+        link.filter(d => {
+                // First check if the link type is filtered out
+                if (isLinkFilteredOut(d)) return false;
+                
+                const sourceId = typeof d.source === 'object' ? d.source.id : d.source;
+                const targetId = typeof d.target === 'object' ? d.target.id : d.target;
+                const sourceNode = graphData.nodes.find(n => n.id === sourceId);
+                const targetNode = graphData.nodes.find(n => n.id === targetId);
+                const sourceVisible = sourceNode && !isNodeFilteredOut(sourceNode) && !isNodeHidden(sourceNode);
+                const targetVisible = targetNode && !isNodeFilteredOut(targetNode) && !isNodeHidden(targetNode);
+                return sourceVisible && targetVisible;
+            })
+            .classed('dimmed', d => !isLinkHighlighted(d, nodeId))
+            .classed('highlighted', d => isLinkHighlighted(d, nodeId));
+        
+        // Reapply link-hidden to ALL links to ensure hidden links stay hidden (normal mode only)
+        link.classed('link-hidden', d => {
+            if (isLinkFilteredOut(d)) return true;
+            const sourceId = typeof d.source === 'object' ? d.source.id : d.source;
+            const targetId = typeof d.target === 'object' ? d.target.id : d.target;
+            const sourceNode = graphData.nodes.find(n => n.id === sourceId);
+            const targetNode = graphData.nodes.find(n => n.id === targetId);
+            if (sourceNode && isNodeFilteredOut(sourceNode)) return true;
+            if (targetNode && isNodeFilteredOut(targetNode)) return true;
+            if (d.type === 'module-module') return false;
+            if (sourceNode && isNodeHidden(sourceNode)) return true;
+            if (targetNode && isNodeHidden(targetNode)) return true;
+            if (d.type === 'module-entity' && collapsedNodes.has(sourceId)) return true;
+            if (d.type === 'dependency' && collapsedNodes.has(sourceId)) return true;
+            return false;
+        });
+    }
 
     // Update labels
-    labels.classed('dimmed', d => d.id !== nodeId && !connectedNodes.has(d.id))
-        .classed('highlighted-label', d => d.id === nodeId || connectedNodes.has(d.id));
+    if (highlightFocusMode) {
+        // Focus mode: show all chain labels (ignore filters), hide background labels
+        labels.each(function(d) {
+            const el = d3.select(this);
+            const nodeEl = node.filter(n => n.id === d.id);
+            const isNodeDimmed = nodeEl.classed('dimmed');
+            
+            if (d.id === nodeId || connectedNodes.has(d.id)) {
+                el.classed('dimmed', isNodeDimmed)
+                  .classed('highlighted-label', !isNodeDimmed)
+                  .classed('label-hidden', false);
+            } else {
+                el.classed('dimmed', false)
+                  .classed('highlighted-label', false)
+                  .classed('label-hidden', true);
+            }
+        });
+    } else {
+        // Normal mode: respect filters
+        // First, clear label-hidden from all labels and reapply based on filters
+        labels.classed('label-hidden', d => isNodeFilteredOut(d) || isNodeHidden(d));
+        
+        // Then apply highlight classes only to visible labels
+        labels.filter(d => !isNodeFilteredOut(d) && !isNodeHidden(d))
+            .classed('dimmed', d => d.id !== nodeId && !connectedNodes.has(d.id))
+            .classed('highlighted-label', d => d.id === nodeId || connectedNodes.has(d.id));
+    }
 
     // Zoom to fit all connected nodes
     zoomToFitNodes(connectedNodes);
@@ -3120,15 +4383,26 @@ <h5>Highlight Settings</h5>
 function clearHighlight() {
     currentHighlightedNode = null;
 
+    // Clear highlight classes from all nodes and restore filter state
     node.classed('dimmed', false)
         .classed('highlighted', false)
         .classed('highlighted-main', false);
+    
+    // Restore node-hidden based on filters
+    node.classed('node-hidden', d => isNodeFilteredOut(d) || isNodeHidden(d));
 
     link.classed('dimmed', false)
         .classed('highlighted', false);
 
+    // Clear highlight classes from all labels and restore filter state
     labels.classed('dimmed', false)
         .classed('highlighted-label', false);
+    
+    // Restore label-hidden based on filters
+    labels.classed('label-hidden', d => isNodeFilteredOut(d) || isNodeHidden(d));
+    
+    // Restore display filters
+    updateDisplayFilters();
 
     searchInput.value = '';
     searchClear.classList.remove('visible');
@@ -3141,9 +4415,36 @@ <h5>Highlight Settings</h5>
 function filterNodes(query) {
     if (!query) return [];
     const lowerQuery = query.toLowerCase();
-    return searchIndex
-        .filter(n => n.searchText.includes(lowerQuery))
-        .slice(0, 10); // Limit to 10 results
+    const results = searchIndex.filter(n => n.searchText.includes(lowerQuery));
+    
+    // Sort results: prioritize exact label matches, then label starts with query, then path matches
+    results.sort((a, b) => {
+        const aLabel = (a.label || a.id).toLowerCase();
+        const bLabel = (b.label || b.id).toLowerCase();
+        const aLabelWithPy = aLabel + '.py';
+        const bLabelWithPy = bLabel + '.py';
+        
+        // Exact matches come first
+        if (aLabel === lowerQuery || aLabelWithPy === lowerQuery) return -1;
+        if (bLabel === lowerQuery || bLabelWithPy === lowerQuery) return 1;
+        
+        // Label starts with query comes next
+        const aStarts = aLabel.startsWith(lowerQuery) || aLabelWithPy.startsWith(lowerQuery);
+        const bStarts = bLabel.startsWith(lowerQuery) || bLabelWithPy.startsWith(lowerQuery);
+        if (aStarts && !bStarts) return -1;
+        if (!aStarts && bStarts) return 1;
+        
+        // Label contains query comes before path contains query
+        const aLabelContains = aLabel.includes(lowerQuery) || aLabelWithPy.includes(lowerQuery);
+        const bLabelContains = bLabel.includes(lowerQuery) || bLabelWithPy.includes(lowerQuery);
+        if (aLabelContains && !bLabelContains) return -1;
+        if (!aLabelContains && bLabelContains) return 1;
+        
+        // Otherwise alphabetical
+        return aLabel.localeCompare(bLabel);
+    });
+    
+    return results.slice(0, 50); // Limit to 50 results
 }
 
 // Render autocomplete list
@@ -3156,13 +4457,20 @@ <h5>Highlight Settings</h5>
     filteredNodes = results;
     selectedAutocompleteIndex = -1;
 
-    autocompleteList.innerHTML = results.map((n, i) => `
-        <div class="autocomplete-item" data-index="${i}" data-id="${n.id}">
-            <span class="node-type ${n.type}">${n.type}</span>
-            <span class="node-name">${n.label}</span>
-            ${n.parent ? `<span class="node-parent">${n.parent}</span>` : ''}
-        </div>
-    `).join('');
+    autocompleteList.innerHTML = results.map((n, i) => {
+        // For modules, show fullPath; for entities, show parent
+        const pathInfo = n.type === 'module' && n.fullPath 
+            ? `<span class="node-parent">${n.fullPath}</span>`
+            : n.parent ? `<span class="node-parent">${n.parent}</span>` : '';
+        
+        return `
+            <div class="autocomplete-item" data-index="${i}" data-id="${n.id}">
+                <span class="node-type ${n.type}">${n.type}</span>
+                <span class="node-name">${n.label}</span>
+                ${pathInfo}
+            </div>
+        `;
+    }).join('');
 
     autocompleteList.classList.add('visible');
 
diff --git a/tests/test_data/duplicate_names/src/main.py b/tests/test_data/duplicate_names/src/main.py
new file mode 100644
index 0000000..57fabcb
--- /dev/null
+++ b/tests/test_data/duplicate_names/src/main.py
@@ -0,0 +1,7 @@
+from src.utils import src_helper, common_function
+
+def main():
+    """Main function that uses src utils"""
+    result = src_helper()
+    common = common_function()
+    return result + common
diff --git a/tests/test_data/duplicate_names/src/utils.py b/tests/test_data/duplicate_names/src/utils.py
new file mode 100644
index 0000000..02d0db6
--- /dev/null
+++ b/tests/test_data/duplicate_names/src/utils.py
@@ -0,0 +1,8 @@
+# Source utils module
+def src_helper():
+    """Helper function in src/utils.py"""
+    return "src helper"
+
+def common_function():
+    """Common function name in src"""
+    return "src common"
diff --git a/tests/test_data/duplicate_names/tests/__pycache__/test_main.cpython-311-pytest-8.3.3.pyc b/tests/test_data/duplicate_names/tests/__pycache__/test_main.cpython-311-pytest-8.3.3.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..3f90f87f7d7715abc653aef2c16c1a0235cc2c35
GIT binary patch
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zxbr`7F#aKF9SFfJqzWn09bD%svwM#s@ksh+W@k0uw>w{gppU@V*M0T_{4blV%v%QY
zClH*V9Obw~F?QbLt<1xS`|$?06|ZdbPTb+$xC?pf6N-B|euIYoAKPT-%rgT`l}-y<
z)>N8Xnc!Sh>4&DuG!s>}q;k&kw&0tO08Ws`Zq>ml;Q2cJh_v0ew0~;&5FO$JsDTQ6
z@aQeDhby{J7et4RqAIkiRM==%DruVyJ=2y{HKjJ~g-B)fgyEIgdYZgbRH{T5A}VPz
z5?RA(rByN(Qqxho&Gc(pi)2gWbX$_TNHU1_T;zBXcLzDqB*~k)WEs&ktq7;k)9P5%
zIbl^)Ps~lXTM15e!KyuJCuJq75MYXa2X~KlKkrV*KZA$gg3a&2=5%~HxP3f6dU4_3
zpTizB?3?cUhLxIC%G`KaPttXEFRdrGe?%0V$<82>bYC(}O>ezqI;*ul{OsfqxtOGi
z7I)?Yjoh$c<((lpuyGIIs{4$Kyea8(c?VKEMfD0`*1{NH+7n#=T%gC-zBAv)4`%3p
HaFl-mzoo_d

literal 0
HcmV?d00001

diff --git a/tests/test_data/duplicate_names/tests/sample_test.py b/tests/test_data/duplicate_names/tests/sample_test.py
new file mode 100644
index 0000000..e6605f5
--- /dev/null
+++ b/tests/test_data/duplicate_names/tests/sample_test.py
@@ -0,0 +1,7 @@
+from tests.utils import test_helper, common_function
+
+def test_something():
+    """Test function that uses tests utils"""
+    result = test_helper()
+    common = common_function()
+    return result + common
diff --git a/tests/test_data/duplicate_names/tests/utils.py b/tests/test_data/duplicate_names/tests/utils.py
new file mode 100644
index 0000000..f7dced5
--- /dev/null
+++ b/tests/test_data/duplicate_names/tests/utils.py
@@ -0,0 +1,8 @@
+# Test utils module
+def test_helper():
+    """Helper function in tests/utils.py"""
+    return "test helper"
+
+def common_function():
+    """Common function name in tests"""
+    return "test common"
diff --git a/tests/test_graph_generation.py b/tests/test_graph_generation.py
index 7c917c5..3154438 100644
--- a/tests/test_graph_generation.py
+++ b/tests/test_graph_generation.py
@@ -173,11 +173,11 @@ def test_convert_simple_graph(self):
         assert "nodes" in result
         assert "links" in result
 
-        # Check nodes - entity IDs use format module.py:entity_name
+        # Check nodes - module IDs now use format 'module' (no .py), entity IDs use 'module:entity_name'
         node_ids = [n["id"] for n in result["nodes"]]
-        assert "module.py" in node_ids
-        assert "module.py:func_a" in node_ids
-        assert "module.py:func_b" in node_ids
+        assert "module" in node_ids
+        assert "module:func_a" in node_ids
+        assert "module:func_b" in node_ids
 
         # Check links
         links = result["links"]
@@ -196,8 +196,9 @@ def test_convert_multi_module_graph(self):
         result = convert_to_d3_format(usage_graph)
 
         node_ids = [n["id"] for n in result["nodes"]]
-        assert "a.py" in node_ids
-        assert "b.py" in node_ids
+        # Module IDs are now without .py extension
+        assert "a" in node_ids
+        assert "b" in node_ids
 
         # Check module types
         module_nodes = [n for n in result["nodes"] if n["type"] == "module"]
@@ -511,3 +512,124 @@ def test_export_codegraph_on_itself(self):
         assert int(codegraph_row['lines']) > 0
 
         pathlib.Path(output_path).unlink()
+
+
+class TestDuplicateFilenames:
+    """Tests for handling duplicate filenames in different directories."""
+
+    def test_duplicate_filename_handling(self):
+        """Test that files with same basename in different directories are handled correctly."""
+        test_dir = TEST_DATA_DIR / "duplicate_names"
+        args = Namespace(paths=[str(test_dir)])
+        
+        code_graph = CodeGraph(args)
+        usage_graph = code_graph.usage_graph()
+        entity_metadata = code_graph.get_entity_metadata()
+        
+        # Get all module paths
+        module_paths = list(usage_graph.keys())
+        
+        # Should have both utils.py files
+        src_utils = [p for p in module_paths if p.endswith('src\\utils.py') or p.endswith('src/utils.py')]
+        test_utils = [p for p in module_paths if p.endswith('tests\\utils.py') or p.endswith('tests/utils.py')]
+        
+        assert len(src_utils) == 1, "Should find src/utils.py"
+        assert len(test_utils) == 1, "Should find tests/utils.py"
+        
+        # Convert to D3 format to check node IDs
+        graph_data = convert_to_d3_format(usage_graph, entity_metadata, code_graph.base_paths)
+        nodes = graph_data["nodes"]
+        
+        # Extract module nodes
+        module_nodes = [n for n in nodes if n["type"] == "module"]
+        module_ids = [n["id"] for n in module_nodes]
+        
+        # Should have unique IDs for both utils modules
+        utils_nodes = [n for n in module_nodes if "utils" in n["id"]]
+        assert len(utils_nodes) == 2, f"Should have 2 utils module nodes, got {len(utils_nodes)}"
+        
+        # IDs should be different (path-based)
+        utils_ids = [n["id"] for n in utils_nodes]
+        assert utils_ids[0] != utils_ids[1], f"Utils module IDs should be different: {utils_ids}"
+        
+        # Both should have path information in their IDs
+        assert any("src" in uid for uid in utils_ids), "One utils should have 'src' in ID"
+        assert any("tests" in uid or "test" in uid for uid in utils_ids), "One utils should have 'tests' in ID"
+        
+        # Labels should show basename for readability
+        for utils_node in utils_nodes:
+            assert utils_node["label"] == "utils", f"Label should be 'utils', got {utils_node['label']}"
+        
+        # fullPath should be different
+        utils_paths = [n["fullPath"] for n in utils_nodes]
+        assert utils_paths[0] != utils_paths[1], f"Full paths should be different: {utils_paths}"
+
+    def test_duplicate_filename_dependencies(self):
+        """Test that dependencies are correctly attributed when filenames are duplicated."""
+        test_dir = TEST_DATA_DIR / "duplicate_names"
+        args = Namespace(paths=[str(test_dir)])
+        
+        code_graph = CodeGraph(args)
+        usage_graph = code_graph.usage_graph()
+        entity_metadata = code_graph.get_entity_metadata()
+        
+        # Convert to D3 format
+        graph_data = convert_to_d3_format(usage_graph, entity_metadata, code_graph.base_paths)
+        links = graph_data["links"]
+        
+        # Find links involving utils modules
+        # src/main.py should link to src/utils.py entities
+        # tests/test_main.py should link to tests/utils.py entities
+        
+        # Get all dependency links (exclude module-entity structural links)
+        dep_links = [l for l in links if l["type"] == "dependency"]
+        
+        # Should have some dependency links
+        assert len(dep_links) > 0, "Should have dependency links"
+        
+        # Check that src/main links to src/utils functions
+        src_main_links = [l for l in dep_links if "main" in str(l["source"]) and "src" in str(l["source"])]
+        if src_main_links:
+            # These should target src/utils entities, not tests/utils
+            for link in src_main_links:
+                target = link["target"]
+                if "utils" in str(target):
+                    assert "src" in str(target) or "test" not in str(target).lower(), \
+                        f"src/main should link to src/utils, not tests/utils: {target}"
+
+    def test_duplicate_filename_csv_export(self):
+        """Test that CSV export correctly handles duplicate filenames."""
+        test_dir = TEST_DATA_DIR / "duplicate_names"
+        args = Namespace(paths=[str(test_dir)])
+        
+        code_graph = CodeGraph(args)
+        usage_graph = code_graph.usage_graph()
+        entity_metadata = code_graph.get_entity_metadata()
+        
+        with tempfile.NamedTemporaryFile(mode='w', suffix='.csv', delete=False) as f:
+            output_path = f.name
+        
+        export_to_csv(usage_graph, entity_metadata=entity_metadata, 
+                     output_path=output_path, base_paths=code_graph.base_paths)
+        
+        # Read and verify CSV
+        with open(output_path, 'r', encoding='utf-8') as csvfile:
+            reader = csv.DictReader(csvfile)
+            rows = list(reader)
+        
+        # Find both utils modules in CSV
+        utils_modules = [r for r in rows if r['type'] == 'module' and 'utils' in r['name']]
+        
+        # Should have 2 utils module entries
+        assert len(utils_modules) >= 2, f"Should have at least 2 utils modules in CSV, got {len(utils_modules)}"
+        
+        # Their full paths should be different
+        utils_paths = [r['full_path'] for r in utils_modules]
+        assert len(set(utils_paths)) >= 2, f"Utils modules should have different full paths: {utils_paths}"
+        
+        # Verify one is in src and one is in tests
+        path_strs = ' '.join(utils_paths)
+        assert 'src' in path_strs.lower(), "Should have src/utils in paths"
+        assert 'test' in path_strs.lower(), "Should have tests/utils in paths"
+        
+        pathlib.Path(output_path).unlink()

From d02260537d1cb0f037e0bb6432ee0a3fb95e9815 Mon Sep 17 00:00:00 2001
From: ForteD <57673412+ForteDexe@users.noreply.github.com>
Date: Wed, 28 Jan 2026 07:45:00 +0000
Subject: [PATCH 4/4] Delete HIDDENLOG.md

---
 HIDDENLOG.md | 44 --------------------------------------------
 1 file changed, 44 deletions(-)
 delete mode 100644 HIDDENLOG.md

diff --git a/HIDDENLOG.md b/HIDDENLOG.md
deleted file mode 100644
index 9cd1d9d..0000000
--- a/HIDDENLOG.md
+++ /dev/null
@@ -1,44 +0,0 @@
-1. Core Module (core.py)
-Updated parse_code_file() to pass full paths (instead of basename) to the parser
-Modified get_module_name() to return relative path-based keys (e.g., src/utils instead of utils)
-Changed get_code_objects() and CodeGraph.__init__() to track and pass base_paths
-Updated get_imports_and_entities_lines() to build module_names_set and names_map using relative paths
-2. Visualization Module (vizualyzer.py)
-Modified convert_to_d3_format() to generate unique node IDs from relative paths
-Module node IDs are now path-based (e.g., src/utils, tests/utils) without .py extension
-Entity node IDs use format path/module:entity_name (e.g., src/utils:helper)
-Updated entity_to_module mappings to use path-based identifiers
-Fixed dependency resolution loops to correctly attribute dependencies using relative paths
-Updated draw_graph(), draw_graph_matplotlib(), and export_to_csv() to accept and use base_paths
-CSV export now shows basenames with .py extension in the name column for backward compatibility
-3. Parser Module (parser.py)
-Updated create_objects_array() to accept full paths in the fname parameter
-Added base_paths parameter for future path-relative calculations
-4. Utilities Module (utils.py)
-Added get_relative_path() helper function to calculate relative paths from a list of base paths
-Normalizes path separators to forward slashes for cross-platform consistency
-5. Main Module (main.py)
-Updated to extract base_paths from CodeGraph instance
-Passes base_paths to all visualization functions
-6. Frontend (main.js)
-Already handles n.label || n.id pattern correctly
-Module nodes now display basename in labels while using path-based IDs internally
-fullPath attribute available in tooltips for disambiguation
-
-For modules: Shows the full file path (e.g., utils.py or utils.py)
-For entities: Shows the parent module (e.g., src/utils for src_helper function)
-
-Design Decisions Implemented:
-Clean relative paths for readability ✓
-
-Node IDs use sanitized relative paths: src/utils instead of utils.py
-Easy to read and understand in visualizations
-Basename for node labels + full path in tooltips ✓
-
-Module nodes show just the filename (e.g., utils) in the UI
-Full relative path available in the fullPath attribute for tooltips
-Users see familiar names while the system maintains unique identifiers
-Acceptable to break saved HTML files ✓
-
-Node ID format changed from module.py to module (relative path without extension)
-Existing visualizations will need to be regenerated
\ No newline at end of file