The comments for Command.output_files state that an output file cannot be the parent of another output file, but there is not a corresponding comment for directories.
Please add a comment to clarify which, if any, of these output layouts are valid:
Output directory is child of another output directory:
output_directories: "upper"
output_directories: "upper/lower"
Output file is child of output directory:
output_directories: "upper"
output_files: "upper/lower"
Output directory is child of output file (possible if file is a symlink)
output_files: "upper"
output_directories: "upper/lower"