When you add new files to your project, modify existing ones, or delete existing files from your project or Git code base, they will be marked as modified since the last commit. You can see a list of your changes by navigating to Project | Changes under Team Explorer, as shown in the following screenshot:

Right click on the files/folders that you want to move to the staging area and, from the context menu, click Stage. Later, if you want to unmark any file/folder from the staging area, right click on those files/folders and click Unstage from the context menu, as shown in the following screenshot:

If you stage any files/folders after you staged them already, the delta will be added to the changes available in staging. When you are ready to save the changes to your repository, you need to commit those changes.