diff --git a/web/js/script.js b/web/js/script.js
index 716ffdf..283f265 100644
--- a/web/js/script.js
+++ b/web/js/script.js
@@ -45,45 +45,56 @@ function transformNode(node) {
 
     const hasIssueArrays = Object.prototype.hasOwnProperty.call(node, 'addressed') ||
         Object.prototype.hasOwnProperty.call(node, 'known');
+    const childKeys = Object.keys(node).filter(key => key !== 'addressed' && key !== 'known');
 
-    if (hasIssueArrays) {
-        const addressed = Array.isArray(node.addressed) ? node.addressed : [];
-        const known = Array.isArray(node.known) ? node.known : [];
-        const allFiles = [...addressed, ...known];
+    const transformedChildren = {};
+    childKeys.forEach(key => {
+        transformedChildren[key] = transformNode(node[key]);
+    });
 
-        if (allFiles.length === 0) {
-            return {
-                addressed: [],
-                known: []
-            };
-        }
-
-        const groupedByPrefix = {};
-
-        addressed.forEach(fileName => {
-            const prefix = getFilePrefix(fileName);
-            if (!groupedByPrefix[prefix]) {
-                groupedByPrefix[prefix] = { addressed: [], known: [] };
-            }
-            groupedByPrefix[prefix].addressed.push(fileName);
-        });
-
-        known.forEach(fileName => {
-            const prefix = getFilePrefix(fileName);
-            if (!groupedByPrefix[prefix]) {
-                groupedByPrefix[prefix] = { addressed: [], known: [] };
-            }
-            groupedByPrefix[prefix].known.push(fileName);
-        });
-
-        return groupHotfixPrefixes(groupedByPrefix);
+    if (!hasIssueArrays) {
+        return transformedChildren;
     }
 
-    const transformed = {};
-    Object.keys(node).forEach(key => {
-        transformed[key] = transformNode(node[key]);
+    const addressed = Array.isArray(node.addressed) ? node.addressed : [];
+    const known = Array.isArray(node.known) ? node.known : [];
+    const allFiles = [...addressed, ...known];
+
+    if (allFiles.length === 0) {
+        if (childKeys.length > 0) {
+            return transformedChildren;
+        }
+
+        return {
+            addressed: [],
+            known: []
+        };
+    }
+
+    const groupedByPrefix = {};
+
+    addressed.forEach(fileName => {
+        const prefix = getFilePrefix(fileName);
+        if (!groupedByPrefix[prefix]) {
+            groupedByPrefix[prefix] = { addressed: [], known: [] };
+        }
+        groupedByPrefix[prefix].addressed.push(fileName);
     });
-    return transformed;
+
+    known.forEach(fileName => {
+        const prefix = getFilePrefix(fileName);
+        if (!groupedByPrefix[prefix]) {
+            groupedByPrefix[prefix] = { addressed: [], known: [] };
+        }
+        groupedByPrefix[prefix].known.push(fileName);
+    });
+
+    const transformedIssueFiles = groupHotfixPrefixes(groupedByPrefix);
+    if (childKeys.length === 0) {
+        return transformedIssueFiles;
+    }
+
+    return mergeTreeNodes(transformedChildren, transformedIssueFiles);
 }
 
 function groupHotfixPrefixes(groupedByPrefix) {
@@ -130,3 +141,39 @@ function getFilePrefix(fileName) {
     }
     return baseName.slice(0, underscoreIndex);
 }
+
+function mergeTreeNodes(left, right) {
+    if (!isObjectNode(left)) {
+        return right;
+    }
+    if (!isObjectNode(right)) {
+        return left;
+    }
+
+    const merged = { ...left };
+
+    Object.keys(right).forEach(key => {
+        const leftValue = merged[key];
+        const rightValue = right[key];
+
+        if (key === 'addressed' || key === 'known') {
+            const leftFiles = Array.isArray(leftValue) ? leftValue : [];
+            const rightFiles = Array.isArray(rightValue) ? rightValue : [];
+            merged[key] = Array.from(new Set([...leftFiles, ...rightFiles]));
+            return;
+        }
+
+        if (isObjectNode(leftValue) && isObjectNode(rightValue)) {
+            merged[key] = mergeTreeNodes(leftValue, rightValue);
+            return;
+        }
+
+        merged[key] = rightValue;
+    });
+
+    return merged;
+}
+
+function isObjectNode(value) {
+    return Boolean(value) && typeof value === 'object' && !Array.isArray(value);
+}
diff --git a/web/js/tree.js b/web/js/tree.js
index 7b60074..97d4fce 100644
--- a/web/js/tree.js
+++ b/web/js/tree.js
@@ -84,8 +84,8 @@ export function getCheckedFileRefs() {
     });
 
     return {
-        addressedFiles,
-        knownFiles
+        addressedFiles: dedupeFileRefs(addressedFiles),
+        knownFiles: dedupeFileRefs(knownFiles)
     };
 }
 
@@ -93,8 +93,12 @@ function createTreeNode(name, value, path) {
     const container = document.createElement('div');
     container.className = 'tree-item';
 
-    const isLeafWithFiles = value && typeof value === 'object' && ('addressed' in value || 'known' in value);
-    const hasChildren = value && typeof value === 'object' && !isLeafWithFiles && Object.keys(value).length > 0;
+    const isObjectValue = value && typeof value === 'object';
+    const hasFiles = isObjectValue && ('addressed' in value || 'known' in value);
+    const childKeys = isObjectValue
+        ? getSortedKeys(value).filter(key => key !== 'addressed' && key !== 'known')
+        : [];
+    const hasChildren = childKeys.length > 0;
 
     if (hasChildren) {
         container.classList.add('parent');
@@ -105,14 +109,14 @@ function createTreeNode(name, value, path) {
         toggle.style.cursor = 'pointer';
 
         const label = document.createElement('label');
-        const checkbox = createCheckbox(path);
+        const checkbox = createCheckbox(path, hasFiles ? value : undefined);
         label.appendChild(checkbox);
         label.appendChild(document.createTextNode(name));
 
         const childrenContainer = document.createElement('div');
         childrenContainer.className = 'tree-children';
 
-        getSortedKeys(value).forEach(childKey => {
+        childKeys.forEach(childKey => {
             const childNode = createTreeNode(childKey, value[childKey], [...path, childKey]);
             childrenContainer.appendChild(childNode);
         });
@@ -136,7 +140,7 @@ function createTreeNode(name, value, path) {
     }
 
     const label = document.createElement('label');
-    if (isLeafWithFiles) {
+    if (hasFiles) {
         const checkbox = createCheckbox(path, value);
         label.appendChild(checkbox);
     }
@@ -151,7 +155,7 @@ function shouldStartCollapsed(name, value) {
         return false;
     }
 
-    const childKeys = Object.keys(value);
+    const childKeys = Object.keys(value).filter(key => key !== 'addressed' && key !== 'known');
     if (childKeys.length === 0) {
         return false;
     }
@@ -164,6 +168,25 @@ function shouldStartCollapsed(name, value) {
     return hotfixChildren.length > 0;
 }
 
+function dedupeFileRefs(fileRefs) {
+    const seen = new Set();
+    return fileRefs.filter(ref => {
+        const productKey = String(ref && ref.productKey ? ref.productKey : '');
+        const fileName = String(ref && ref.fileName ? ref.fileName : '');
+        if (!productKey || !fileName) {
+            return false;
+        }
+
+        const key = `${productKey}::${fileName}`;
+        if (seen.has(key)) {
+            return false;
+        }
+
+        seen.add(key);
+        return true;
+    });
+}
+
 function createCheckbox(path, value) {
     const checkbox = document.createElement('input');
     checkbox.type = 'checkbox';