TriggerMenuMT: pass flags explicitly in chain building

This if the first step in eliminating the use of the global ConfigFlags in TriggerMenuMT:

• Move the "flags" as the first argument in ChainConfigurationBase.getStep and pass them explicitly where needed.

There are a lot of changes but most of them have been done using grep/sed.

urgent to avoid merge conflicts.

cc @fpastore @tbold

Relates to ATR-24994.