def METHOD_NAME(root_dir):
    # Test the moose_dir is valid
    if not os.path.isdir(root_dir):
        print "ERROR: Supplied MOOSE root directory (" + root_dir + ") does not exist."
        sys.exit(1)
    # Open the Make file
    file = open(os.getcwd() + "/Makefile")
    # Storage for dependency directories, always include the moose directory
    if os.environ.get('MOOSE_DEV') == "true":
        dep_dirs = [os.path.join(root_dir, "devel", "moose")]
    else:
        dep_dirs = [os.path.join(root_dir, "moose")]
    # Loop through the file and look for include statements for .mk files
    for line in file:
        x = re.search('include .*\/(\w+)\.mk' , line)
        # Store all *.mk includes other than the moose.mk and build.mk
        if x and x.group(1) != "build" and x.group(1) != "moose":
            dep_dirs.append(os.path.join(root_dir, x.group(1)))
    # Close file, return the list of directories to clean
    file.close()
    return dep_dirs