The following Garrison-affecting changes occur when patch 7.0.3 is released. Be prepared!
Vendor value of Follower equipment upgrades is reduced significantly. You may wish to sell them prior to the patch.
Current Follower and Shipyard missions with gold rewards will get alternative rewards (garrison resources, oil, apexis, draenor elemental mats etc). Some rare missions will still award minor amounts of gold, but:
Treasure Hunter trait becomes Extreme Scavenger, increasing garrison resource rewards by 200%. Extreme Scavenger and Scavenger stack, and you can have both traits on one follower. Dwarven Crew/Goblin Crew will provide a chance to receive ship equipment instead of increasing the gold rewards.
You will need to enable the "Load out of date AddOns" checkbox in the AddOn List window after the patch to load Master Plan, which should mostly work the same as it did prior to the patch. There may be some cosmetic issues.