improve a link in the Transition Guide
document effects of agent death
imports cleanup in nvm.Instruction
fix ancient oops in create-link-with syntax

probably dates way back to when we were considering allowing links to
patches
change some "protected"s to "public"

they were interfering with my refactoring of the link creation
primitives, and besides protected is generally a smell anyway
DRY the link creation prims into one source file
convert agent.LinkManager to Scala
network extension: keep up with changes on master
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
bring network extension up to date with recent LinkManager changes