Scaffolding options are now commandline options.   If you want to override the defaults, you have to set the values explicitly like so:

-scaffold_removeOtherOutgoing true -scaffold_removeOtherIncoming true -scaffold_candidatesScoreWalk true -scaffold_delayPrune true -scaffold_earlyStop false -scaffold_expandCandidateBranchMaxDistance 20
Merge pull request #145 from uci-cbcl/wbiesing/scaffold-options-are-cmdline-options

Scaffolding options are now commandline options.