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git-boot.sh silently proceeds if any library in the Arduino/libraries folder conflicts with a library specified in git-repos.dat. It will appear to succeed, but it will leave the old library unchanged. This causes no end of user confusion.
It's not clear what the tool should do, other than failing. The Arduino environment doesn't support side-by-side installs of different library versions for different sketches. Perhaps the suggestion would be similar to what I tell people when helping them get started: move any conflicting library to a new directory Arduino/libraries.hide. It feels like there's something too-clever-by-half that we could do with symbolic links on Linux and macOS. But that's still not a first-class Windows feature.