Maybe you could provide possibility to use some kind of playfab config file that would be read from repository root and use it to configure paths for cloud script files.
I would like to keep my project in one repository and be able to use custom folder structure with some folders where i keep compiled/build versions of my files. I am working with webpack and typescript any other technologies have usually some kind of configuration file that enable configuration (like angular.json, karma.conf, tslint, tsconfig, .babelrc ect...).
If not configuration file maybe some CLI tool that could be used for pushing changes to cloud scripts.