To merge/refactor both ISIS_processor.py and ISIS_processor2.py

What is the difference between `ISIS_processor.py` and `ISIS_processor2.py`? Is that for batch 1 & 2 or stage 1 & 2?
They both have the same functions. I suggest to merge functions and to add parameters whether is to run 1 or 2.

**Note:** I (Émiline) can give a hand for this task.

Compare ISIS_processor.py and ISIS_processor2.py first to determine how their functions differ and whether the split represents batches or stages. Trace how each file is used, then consolidate the shared processing while preserving both execution paths through an explicit parameter. Done means one processor supports the required cases without losing existing functions.

Written by the indexing model from the issue text.