Love lefthook!! I just dove in a day or so ago. This was the only real pain point for me. We have a CRA app in client directory and server node code in the root level folders. Below is the run command I came up with to fix the paths by removing the root level of the path. If someone needs this but deeper into the directory structure adjust the cut -d'/' -f2- part to make the number be +1 of how many directories to lop off.

run: fixedFiles=$(for staged_file in ${staged_files}; do echo $(echo $staged_file | cut -d'/' -f2-); done;); cd client; prettier --ignore-unknown --write $fixedFiles && eslint --max-warnings 0 $fixedFiles && git add $fixedFiles

Unrelated but thought I'd share this idea while I'm here. I made a post-merge action that globs on lefthook.yml to trigger lefthook install. This way new developers work out of the box after npm i from a fresh clone and existing developers will be kept up to date as the config evolves.

post-merge:
  commands: 
    lefthook:
      glob: "lefthook.yml"
      run: npm exec lefthook install

only other minor feedback is occasionally it spits characters out into my terminal after running npm exec lefthook run pre-commit. Not very consistent so repro is difficult of course. Anyways, thanks for this contribution and plus one to this feature request.