There are some Major issues in Spigot for Minecraft 1.9.
1. PlayerInventory#getContents include crafting bench, while PlayerInventory#setContents does not. Makes saving harder.
2. No real way of setting armor.
PlayerInventory#setBoots, setLeggings, setChestplate, setHelmet
all places itself in the normal Inventory.
PlayerInventory#setArmorContents acts the same way.