Refactor commonly use functionality, esp. from `cubi-tk snappy`

[Nicolai-vKuegelgen]

Is your feature request related to a problem? Please describe. Several cubi-tk functions that are used/usable by all modules are currently part of the cubi-tk snappy subcollection, but would be better placed in general or common files. Specifically these are:

• itransfer_common.py which contains general functions for data upload to irods (but inherits some functionality from snappy specific sample sheet prasing)
• pull_data_common.py which contains general functions for data download and can probably be moved without many changes, except that it inherits from IrodsCheckCommand from the irods module, which should probably also be refactored
• retrieve_irods_collection.py which contains general functions for collecting information about files in irods and can probably be moved without many changes

Describe the solution you'd like All functionality that is commonly used by cubi-tk for interfacing with irods &/ Sodar should be refactored into files in the common space (i.e. irods_common / ... )

Describe alternatives you've considered NA / status quo

Additional context NA

[Nicolai-vKuegelgen]

227 only partially closed this.

In addition to points mentioned above we should ensure that CLI / argparse options for common sodar and irods functionality are properly inherited as well, instead of re-defined/overwritten in every final command.