Address code review feedback

- Fix redundant check for empty files
- Don't re-add already staged index changes
- Fix race condition by reading stash flag after checkout

Co-authored-by: alexr00 <38270282+alexr00@users.noreply.github.com>

Author: Copilot

src/github/activityBarViewProvider.ts

@@ -131,8 +131,9 @@ export class PullRequestViewProvider extends WebviewViewBase implements vscode.W
 		try {
 			const defaultBranch = await this._folderRepositoryManager.getPullRequestRepositoryDefaultBranch(this._item);
 			const prBranch = this._folderRepositoryManager.repository.state.HEAD?.name;
-			const shouldPopStash = this._folderRepositoryManager.stashedOnCheckout;
 			await this._folderRepositoryManager.checkoutDefaultBranch(defaultBranch);
+			// Check if we should pop the stash after successful checkout
+			const shouldPopStash = this._folderRepositoryManager.stashedOnCheckout;
 			if (shouldPopStash) {
 				try {
 					Logger.appendLine('Popping stash after returning to default branch', 'ActivityBarViewProvider');

src/github/pullRequestOverview.ts

@@ -652,8 +652,9 @@ export class PullRequestOverviewPanel extends IssueOverviewPanel<PullRequestMode
 	private async checkoutDefaultBranch(message: IRequestMessage<string>): Promise<void> {
 		try {
 			const prBranch = this._folderRepositoryManager.repository.state.HEAD?.name;
-			const shouldPopStash = this._folderRepositoryManager.stashedOnCheckout;
 			await this._folderRepositoryManager.checkoutDefaultBranch(message.args);
+			// Check if we should pop the stash after successful checkout
+			const shouldPopStash = this._folderRepositoryManager.stashedOnCheckout;
 			if (shouldPopStash) {
 				try {
 					Logger.appendLine('Popping stash after returning to default branch', PullRequestOverviewPanel.ID);

src/view/reviewManager.ts

@@ -1100,13 +1100,10 @@ export class ReviewManager extends Disposable {
 			if (hasChanges) {
 				try {
 					Logger.appendLine('Auto-stashing changes before PR checkout', this.id);
-					// Add all tracked changes to staging area
-					const allChangedFiles = [
-						...workingTreeChanges.map(change => change.uri.fsPath),
-						...indexChanges.map(change => change.uri.fsPath),
-					];
-					if (allChangedFiles.length > 0) {
-						await this._repository.add(allChangedFiles);
+					// Add only working tree changes to staging area (indexChanges are already staged)
+					if (workingTreeChanges.length > 0) {
+						const workingTreeFiles = workingTreeChanges.map(change => change.uri.fsPath);
+						await this._repository.add(workingTreeFiles);
 					}
 					// Stash the changes
 					await vscode.commands.executeCommand('git.stash', this._repository);