Add option to save traces during run_combos

Would it be possible to save the traces during run step? It can be useful to check the behaviour of different me-combos and to choose appropriate thresholds for model rejection. Maybe 'save_traces' can be specified as an option, with default as False (to avoid saving too many traces in case of large morphology releases).

Locate the run_combos entry point and inspect how the run step processes traces and options. Add an opt-in save_traces setting with a default of False, then verify that traces are saved only when enabled and that the existing run behavior remains unchanged.

Written by the indexing model from the issue text.