ATR-21589: Automate the merging strategy

Automatically parse the merging strategy from the alignment dictionary.

Set the default merging to 'auto'.

Remove merging='parallel'/'serial' from all chains in the menu. Changed newJO menu to include 'parallel'.

Auto-merging strategy is setup to allow for chains needing a hybrid strategy, though the serial merging explicitly disallows this case: opened ATR-22206 to follow up.