You know, I think it would be cool if there were file systems that would implement a form of a 'link' as part of a content-based-storage mechanism like Git itself. Meaning if I ran the above git-clone/jar command twice in two different directories it would only store the result once (assuming idempotence). Hard and soft links are not it because they need a canonical version that the duplicates point to. What you want is the thing stored once, and regardless of the order of deletion, the last deletion means it is truly gone. The Mac's 'alias' feature is closer because it allows you to at least move the original/canonical.
Kind of like String.intern(..) in Java. People are, of course, pushing the file system science in the direction of content-based (with dire/filenames a logical overlay). https://dev.arvados.org/projects/arvados/wiki/Keep https://github.com/ipfs/ipfs https://en.wikipedia.org/wiki/Content-addressable_storage - paul