Permanent bonuses are from the pro packs you can purchase in the oracle. When you purchase, you get an item that stays with you and doesn't take up an equipment slot. Some old accounts have reset bonuses (as indicated by certain permanent items) but those aren't available any longer.
Not just propack items anymore. Permanent items can be earned through doing mini legends now as well. At the end of those mini legends is usually a permanent item as a reward.