rename collapseClonesL

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).I think the 'L' stands for list, but I am not sure. Maybe we could find a better name for the function?