This isn't the only place this pops up - commit hooks are another example, since they live in .git they don't travel with the repo when it is cloned (or maybe when it is updated, don't remember the specifics).
I really feel there needs to be like a git --pull-config option or something to pull all project configs (including submodules, commit hooks, etc). Or perhaps move those things into the top-level folder and allow them to be git-add'd.
You can easily make a `.githooks` directory and have your docs suggest running `git config --local core.hooksPath .githooks`.
This could have security concerns in open source though as users should rightfully be skeptical of running arbitrary code if malicious code is in there (similar to the security issue of your shell hooking into git info in directories and an untarred archive containing `.git` with malicious code in it). However, at least if it's in the docs, it's consensual unlike tools like Husky that inject scripts at runtime as well as creating yet another NPM module to audit.