I have described my situation here. It seems clear that if the "shared folders" were submodules, subtrees, or subrepos, then Repo 1 and Repo 2 can both enjoy possession of them, but if I have 1000s of shared folders, I don't want to make each of them a Git repository, and neither do I want to make a third Git repository just for the common folders. Is there a way to do this in Git?
I also asked this question here: ingydotnet/git-subrepo#573