I created this Minecraft server plugin using the Bukkit API to minimize the pain of inventory management. It automatically sorts player and chest inventories, intelligently deposits player loot into correct containers, and auto-refills hotbar slots when players use the last item in a stack (or break a tool!) but have more of the same in their backpacks.
I stopped working on this project after Minecraft 1.10. Anyone may use my source code to continue the project, but see the LICENSE file for restrictions.