Are the directories really empty?
Yes, they are. See for example uspace/dist/app.
If the contents are generated, then creating the directory should be part of the generating script.
That is always one of the options how to solve it. However, if the purpose of the uspace/dist subtree is to capture the directory tree layout of the target root file system, having it as a physical directory subtree rather than a set of rules hidden somewhere is probably more intuitive (IMHO).
If the directory is really empty, then maybe there should be a README file explaining what the directory is for, just for the sake of reducing confusion.
Maybe. But I would rather put one README into uspace/dist than individual READMEs into uspace/dist/app, uspace/dist/srv, etc. Thus this still does not solve the Git issue.
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