Propagate cluster related properties in caprieval

[rvhonorato]

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This PR adds the extraction and combination of cluster-related information from the models into the extract_data_from_capri_class method. I've also updated the test to cover this behaviour and added a deprecation notice to the soon-to-be-removed branch with less_io=false - see #970

Also keep in mind that this retrieval of clustering information should not be done via the model object - by doing this we are breaking the modular design by using the PDBFile object as means to transport information instead of the ontology object. Should be addressed in a separate PR tho

[VGPReys]

Should fix the bug

[mgiulini]

does not solve the code duplication problem but solves the bug

[rvhonorato]

does not solve the code duplication problem but solves the bug

You probably mean feature duplication, since the code is different. Again see #970, I've expanded the list to also include this sort of branching that causes feature duplication in relation to running modes