Use the attached Aqua Project & import into ADServer.

Execute ExecuteScriptFiles.xjs and you'll get an NPE on line #45 in the AquaScript:

aqua.console.println("File Contents: " + userFiles[j].read());

The problem occurs in AFUserFileAQProjectFileAdapter line #77:

byte[] bytes = IOUtils.toByteArray(userFile.getFileContents().getBinaryStream());