Remove multiplicity as (input) parameter of the ChainStep (ATR-23928)

‘multiplicity' is removed as ChainStep parameter, and the ‘isEmpty' flag is used more extensively and in a clear way (empty steps have multiplicity = []). 'multiplicity' is still set internally in the ChainStep based on the array of sequences included in the step (and not from the chain dictionary). In the ChainStep indeed the number of sequences/legs is important, because used in the alignment.

Checked JobOptions.json with no changes