For example I have a project which installed a babel-cli locally, and added a script entry in the package.json to run babel by npm run, then I cd to a sub-folder(i.e. /foo/ folder) of my project and run npm run babel a.jsx -o a.js, the script will fail by not found the file a.jsx.

I should run the command npm run foo/a.jsx -o foo/a.js for the right behavior.

Which means npm run sets the cwd to the project root path but not the path which running the command, I think that is not an expected behavior, cause git(or most other command) will setting the correct cwd when you run git command in sub-folder of a repo:

/foo/ > git add a.js will work, not need to run git add foo/a.js(and in fact this command will fail)