Create placeholders before checking in a new project to git or your versioning system of choice.

createplaceholders.groovy

#!/usr/bin/env groovy

assert args.size() == 1 : "Specify the path of the folder that needs placeholders."

def projectFolder = new File(args[0])
projectFolder.eachDirRecurse { dir ->
    if(dir.list().size() == 0) {
        def placeholder = new File(dir, '.PLACEHOLDER')
        println "Creating: $placeholder.absolutePath"
        placeholder.createNewFile()
    }
}