No.  Instead of folders Pebble+ uses tags to organise work.  The benefit of tags is that you can add multiple tags to any asset or resource.  If you had folders you would have to choose which folder to put each asset into and you could only put an asset in multiple folders by copying it.  Tags can be used to search for and collate work. You can create collections based on tags and these can even be made 'dynamic' which means that any new assets given the particular tag are automatically added to the existing collection. To learn more about organising assets in PebblePad go to the Learning Centre in Pebble+ and choose Organising.

Your Store does contain a Deleted folder.  Any assets or resources that you delete go automatically into the Deleted folder.  From here you can restore them or purge them.  Purging removes them from the system completely and they cannot be retrieved.  The Deleted folder can contain 50 items - if more are added the earliest items are automatically purged.