Ok, I have finally finished the first stage of tidying up the package repository. It's now as it all should be. The old repos, though, are now empty except for one package: the repositories package (System / Repositories / UECIDE Master Repository). You need to ensure that you have updated that to the latest version before you will see the repository content properly.
The second stage is just getting all the libraries categorised right, but that's not important - it won't really impact you at all.