Is an SSL cert applied to a specific folder or also all subfolders of that folder?
If the SSL is applied to the root, will it be applied to all sub-folders?
If so why would I not always apply to root?
SSL certificates are applied to an IP Address (optionally with associated hostname). All paths on that host are then available via encryption.
A separate issue which you may be confusing SSL with is certificate-based authentication, which can be applied at the level of any URL path unit, e.g.