I am not seeing a way to manage the store or perform a clean up of the store location via command line. If I find a way I will post it. I did test the store clean up feature. It will delete any files that are not in a repository list. It will also delete all catalog files, so you will need to export the repository again after performing a clean up to recreate the catalog file. I was testing with a single repository. The only difference with two repository would be the catalog files. The files that are downloaded should be put in the same folder structure regardless of the repository. The folder structure is determined by the catalog, the folders are not procedural. The catalog file is based on the repository name, so you would have two catalog files if you use two repositories. I tested with three repositories that all contained the same update, I exported all three of them and it only created one file folder and three catalog files. If you set the store location to the location of your repositories and perform a clean up it should remove unused files.
I created a repository from command line. The repository I just created has no subfolders, just a list of firmware. So in /dell_repo/repositoryname I have the catalog and firmware files. Previously when I made the repository though the GUI, it downloaded all firmware to the repository folder and created unique subfolders underneath. In exploring the folders I have found the same files exist in the root folder. So in /dell_repo/repository1 I have the repository1_catalog.xml, the firmware files, and subfolders with unique numbers that also contain firmware files already in the root directory. (This duplication is making the repository larger than I'd like) Can anyone give an example as to what a repository is supposed to look like? Does DRM do anything to clean up a repo and make sure it only has one copy of each unique firmware update?   Any guidance is much appreciated!
Repository folder structure