Round-tripping created OMEX files gives a warning

[luciansmith]

If I have a directory of files that I want to turn into an OMEX file, I do:

    sedml_filenames = glob.glob(os.path.join(project_path, '**', '*.sedml'), recursive=True)
    sedml_locations = [os.path.relpath(path, project_path) for path in sedml_filenames]
    archive = build_combine_archive(project_path, sedml_locations)
    combine_writer.run(archive, project_path, omex_dir + "/" + project_id + ".omex")

If I then read that file:

reader = CombineArchiveReader()
reader.run(omexfile, "temp/")

I get the warning:

COMBINE/OMEX archive has warnings.
  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.

I can't fix this directly, even if I include a manifest file in the original directory: the 'build_combine_archive' explicitly ignores any existing manifest file and creates a new one from scratch.