Add --threshold_clashes and --plddt_threshold to the TrueMultimer quick mode

[jkosinski]

Currently, --threshold_clashes and --plddt_threshold are options for the default TrueMultimer mode with create_individual_features.py but it would be actually very useful to have it as arguments for run_multimer_jobs.py in --multimeric_template quick mode. A common application is to remove clashes of models from other methods or AlphaFold3 (which often leaves clashes).

[DimaMolod]

@jkosinski what are the advantages of using 'quick' mode? You can already use AF3&2 models with 'default' mode, don't have to do realignments for template sequence manually after removing overlapping residues and is not much slower actually.

[jkosinski]

Speed, ease of use, and no need for MSAs present, but quick_mode works only for cases where the template sequence is similar or identical. Let's discuss the truemultimer "enhancement" features later offline, for now just putting them to remember.