consolidate collapseClones, to avoid multiple functions

The original function collapseCloneshas been renamed to collapseClonesL. Now, collapseClones is a switch to decide if the collapse function to be used should be the original one (collapseClonesL) or the new function that uses extended region definitions (collapseOneClone). We should refactor and have a unique collapseClones, to simplify maintenance.