LinkManager cleanup: eliminate separate LinkManager3D class
LinkManager: use Scala collections not Java collections
LinkManager: avoid using AgentSetBuilder in LinkManagerImpl

let other code decide what data structure it wants out!
LinkManager: misc cleanup
LinkManager: relocate tie code to TieManager
LinkManager: might as well put LinkManagerImpl in same source file
LinkManager: get directedness checking out of nvm.Instruction

it was just gross having it there
relocate some misc code to api package
slim down Instruction (relocate getAgentsetMask)
minor cleanup
further DRY-ing of link creation prims