Make sure multi-chain support works in patch_output_cif_files, which will require modifications to protenix structure processing

[k-chrispens]

The structure processing utilities for protenix currently assign a chain ID that may not match the reference CIF, which limits our evaluations downstream in the patching of the CIF. If we fix this upstream (possibly when bumping to protenix 1.0 or 2.0) we can undo the commenting out of the message in https://github.com/diff-use/sampleworks/pull/237/changes#diff-5c307432dbc6cd78fbf08459457c34a867551fd4314815dc1476f98ac8fb011eR163.

[marcuscollins]

@michael-diffuse Can you take a look at this one? It isn't trivial, but I'd like to consolidate the various things we have to do to fix our CIF outputs, and this is one of the big headaches. We probably need to come up with a design doc to catalog and start addressing all the issues in how structures are processed differently across the different models (RF3, Boltz, Protenix).

[michael-diffuse]

i work at a different diffuse 🙃