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Hi,
I am not sure if you want this change in your project, but I needed this for my use case and thought you might find it useful.
It adds unique id to package directory name in packages directory, if "-unique_id" param is provided.
The implementation has a sideeffect that if the param is not provided it suffixes the name with ".", but I hope it will not be a problem.
Btw, this should solve issue #3, at least partially as the id is not based on a content hash thus is not deterministic.