Fix: Re-parent pulled-up directory children to ensure proper checkbox refresh (#8679)

* Fix: Re-parent pulled-up directory children to ensure proper checkbox refresh

When the tree has multiple top-level directories, a temporary DirectoryTreeNode
is created to build the tree, then its children are pulled up to the parent.
However, the children's parent pointers still referenced the phantom root,
causing processCheckboxUpdates to refresh an invisible node, so checkbox state
never updated visually.

Re-parent all pulled-up children to the actual container node (FilesCategoryNode,
PullRequestNode, or CommitNode) so ancestor walks target visible tree nodes.

* test: add regression tests for parent pointer invariant after tree building

Add tests to verify that pulled-up directory children are correctly re-parented
to the container node, not the phantom root. This ensures processCheckboxUpdates
can walk ancestors and find visible tree nodes for refresh() calls.

Tests cover:
- getParent() correctly returns undefined after re-parenting
- ancestor walk stops at topmost visible directory, not phantom root

Author: MaxDNG

src/test/view/treeNodes/directoryTreeNode.test.ts

@@ -206,4 +206,57 @@ describe('DirectoryTreeNode', function () {
 			assert.strictEqual(rootDir.checkboxState?.state, vscode.TreeItemCheckboxState.Unchecked);
 		});
 	});
+
+	describe('parent pointer after phantom-root pull-up', function () {
+		// When a tree has multiple top-level directories, a temporary DirectoryTreeNode
+		// with label='' (phantom root) is used to build the tree, then its children are
+		// pulled up to the actual container. If children are not re-parented, getParent()
+		// still returns the phantom DirectoryTreeNode and processCheckboxUpdates fires
+		// refresh() on an invisible node, so checkbox state never updates visually.
+
+		it('getParent() returns undefined after child is re-parented to the container', function () {
+			const container = createMockParent();
+			const phantomRoot = new DirectoryTreeNode(container, '');
+			const subDir = new DirectoryTreeNode(phantomRoot, 'src');
+
+			// Before re-parenting: parent is the phantom root DirectoryTreeNode
+			assert.ok(subDir.getParent() instanceof DirectoryTreeNode, 'sanity: should point to phantom root before re-parenting');
+
+			// Simulate the pull-up re-parenting fix applied in filesCategoryNode / pullRequestNode / commitNode
+			subDir.parent = container;
+
+			// After re-parenting: container is not a TreeNode, so getParent() returns undefined.
+			// This means the ancestor walk in processCheckboxUpdates stops here and refresh()
+			// is called on the visible subDir node, not the invisible phantom root.
+			assert.strictEqual(subDir.getParent(), undefined, 'after re-parenting, getParent() should not return the phantom root');
+		});
+
+		it('ancestor walk stops at the topmost visible directory after re-parenting', function () {
+			const container = createMockParent();
+			const phantomRoot = new DirectoryTreeNode(container, '');
+			const topDir = new DirectoryTreeNode(phantomRoot, 'cloud');
+			const subDir = new DirectoryTreeNode(topDir, 'helm');
+			const file = new MockFileNode(subDir);
+			file.checkboxState = { state: vscode.TreeItemCheckboxState.Checked };
+
+			(subDir._children as any[]).push(file);
+			topDir._children.push(subDir);
+
+			// Re-parent: simulate fix
+			topDir.parent = container;
+
+			// Walk ancestors from file, mimicking processCheckboxUpdates
+			const ancestors: TreeNode[] = [];
+			let current = file.getParent();
+			while (current instanceof DirectoryTreeNode) {
+				ancestors.push(current);
+				current = current.getParent();
+			}
+
+			// Should find subDir and topDir, but NOT the phantom root
+			assert.strictEqual(ancestors.length, 2);
+			assert.strictEqual(ancestors[0], subDir);
+			assert.strictEqual(ancestors[1], topDir);
+		});
+	});
 });

src/view/treeNodes/commitNode.ts

@@ -111,6 +111,7 @@ export class CommitNode extends TreeNode implements vscode.TreeItem {
 			dirNode.finalize();
 			if (dirNode.label === '') {
 				// nothing on the root changed, pull children to parent
+				dirNode._children.forEach(child => { child.parent = this; });
 				result.push(...dirNode._children);
 			} else {
 				result.push(dirNode);

src/view/treeNodes/filesCategoryNode.ts

@@ -93,6 +93,7 @@ export class FilesCategoryNode extends TreeNode implements vscode.TreeItem {
 		if (dirNode.label === '') {
 			// nothing on the root changed, pull children to parent
 			this.directories = dirNode._children;
+			this.directories.forEach(child => { child.parent = this; });
 		} else {
 			this.directories = [dirNode];
 		}

src/view/treeNodes/pullRequestNode.ts

@@ -105,6 +105,7 @@ export class PRNode extends TreeNode implements vscode.CommentingRangeProvider2
 				dirNode.finalize();
 				if (dirNode.label === '') {
 					// nothing on the root changed, pull children to parent
+					dirNode._children.forEach(child => { child.parent = this; });
 					result.push(...dirNode._children);
 				} else {
 					result.push(dirNode);