The parse_irods_collection function filters out md5 files

[Nicolai-vKuegelgen]

Describe the bug
Currently all or most cubi-tk download functionality uses iRODSRetrieveCollection.retrieve_irods_data_objects (from irods_common), to gather a list of file in an irods project / collection.
However, the parse_irods_collection function from that parses the lists of all irods_data_objects created by the _irods_query output removes specifically excludes md5 files from its output in the current implementation, so md5 files can not be downloaded with cubi-tk.

To Reproduce
Steps to reproduce the behavior:
A. Try any cubi-tk donwload function that uses iRODSRetrieveCollection, md5 files will not be found/downloaded.

Expected behavior
Md5 files should - at least optionally - be included in the output, so they can be downloaded.