I would be happy to code a patch for this if I knew how it should be configured. Obviously, no local setting for a config variable is meant to inherit the global or system value. We can go all "set of the null set" by making the empty string mean "revert to default". We could go fancy "I know what you really mean" by interpreting ".git/hooks" (or perhaps any path beginning with ".git") not literally in the case of worktrees, but as relative to GIT_DIR. Or there could be another setting set on a local repository to ignore global and system values of core.hooksPath. Thank you, Sam Newbold