If the number of (nested) files in a subfolder exceeds 64k, file.getFilteredFileList throws an error at https://github.com/requirejs/r.js/blob/master/build/jslib/node/file.js#L131

{ [Error: RangeError: Maximum call stack size exceeded]
  originalError: [RangeError: Maximum call stack size exceeded] }

We encountered this after adding several new libraries to node_modules, resulting in an attempt to push 140k dirFiles onto the files array.