You can clone with
Anything in the --input section of a plist is taken as relative to the plist's location, using something like
[self combineBasePath:plistPath withRelativePath:inputPath];
However, this doesn't appear to be applied to things passed in via --index-desc and --include. I think it should be.
Will leave this open as a reminder - will probably deal with it once I'll start working on global/project settings on the new update.