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.

Author: MaxDNG

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);