Click and drag on the background to use the rectangle select. You can also click and drag a single circle. The item you click is moved to the top. Press A to select all. Press space to change the backdrop (mostly because the rectangle select fill is transparent).
When clones are on top of each other, the bottom one can sometimes not realize it's being selected because of the way scripts are run. This could be nice in an OS. It can be a bit laggy while selecting as all the clones are sensing to see if they're being selected, and my rectangle filler isn't exactly the fastest. I started work on this a month or so ago, and never quite finished. I finally found the solution to the problem I was facing and decided to finish and share it. It's pretty bad code I think, but it works. All code by me. The mouse cursor in the thumbnail is from pngitem.
