Add PermissionError handling to vault indexer and implement recursive descendant expansion in sidebar tree filter with auto-expand for matching directories

backend/indexer.py

@@ -218,6 +218,9 @@ def _scan_vault(vault_name: str, vault_path: str) -> Dict[str, Any]:
             for tag in tags:
                 tag_counts[tag] = tag_counts.get(tag, 0) + 1
 
+        except PermissionError as e:
+            logger.warning(f"Permission denied, skipping {fpath}: {e}")
+            continue
         except Exception as e:
             logger.error(f"Error indexing {fpath}: {e}")
             continue

frontend/app.js

@@ -758,23 +758,31 @@
   function filterSidebarTree(query) {
     const tree = document.getElementById("vault-tree");
     const items = tree.querySelectorAll(".tree-item");
+    const containers = tree.querySelectorAll(".tree-children");
 
     if (!query) {
       items.forEach((item) => item.classList.remove("filtered-out"));
-      tree.querySelectorAll(".tree-children").forEach((c) => c.classList.remove("filtered-out"));
+      containers.forEach((c) => {
+        c.classList.remove("filtered-out");
+        // Keep current collapsed state when clearing filter
+      });
       return;
     }
 
     // First pass: mark all as filtered out
     items.forEach((item) => item.classList.add("filtered-out"));
-    tree.querySelectorAll(".tree-children").forEach((c) => c.classList.add("filtered-out"));
+    containers.forEach((c) => c.classList.add("filtered-out"));
 
-    // Second pass: show matching items and their ancestors
+    // Second pass: find matching items and mark them + ancestors + descendants
+    const matchingItems = new Set();
+    
     items.forEach((item) => {
       const text = sidebarFilterCaseSensitive ? item.textContent : item.textContent.toLowerCase();
       const searchQuery = sidebarFilterCaseSensitive ? query : query.toLowerCase();
       if (text.includes(searchQuery)) {
+        matchingItems.add(item);
         item.classList.remove("filtered-out");
+        
         // Show all ancestor containers
         let parent = item.parentElement;
         while (parent && parent !== tree) {
@@ -784,8 +792,46 @@
           }
           parent = parent.parentElement;
         }
+        
+        // If this is a directory (has a children container after it), show all descendants
+        const nextEl = item.nextElementSibling;
+        if (nextEl && nextEl.classList.contains("tree-children")) {
+          nextEl.classList.remove("filtered-out");
+          nextEl.classList.remove("collapsed");
+          // Recursively show all children in this container
+          showAllDescendants(nextEl);
+        }
       }
     });
+    
+    // Third pass: show items that are descendants of matching directories
+    // and ensure their containers are visible
+    matchingItems.forEach((item) => {
+      const nextEl = item.nextElementSibling;
+      if (nextEl && nextEl.classList.contains("tree-children")) {
+        const children = nextEl.querySelectorAll(".tree-item");
+        children.forEach((child) => child.classList.remove("filtered-out"));
+      }
+    });
+  }
+  
+  function showAllDescendants(container) {
+    const items = container.querySelectorAll(".tree-item");
+    items.forEach((item) => {
+      item.classList.remove("filtered-out");
+      // If this item has children, also show them
+      const nextEl = item.nextElementSibling;
+      if (nextEl && nextEl.classList.contains("tree-children")) {
+        nextEl.classList.remove("filtered-out");
+        nextEl.classList.remove("collapsed");
+      }
+    });
+    // Also ensure all nested containers are visible
+    const nestedContainers = container.querySelectorAll(".tree-children");
+    nestedContainers.forEach((c) => {
+      c.classList.remove("filtered-out");
+      c.classList.remove("collapsed");
+    });
   }
 
   function filterTagCloud(query) {