Farmers (and other brown-coated villagers) who were happily farming in 15w40 now stand around staring at ripe crops. They very occasionally remember how to break them, and then usually leave the drops on the ground to despawn and fail to replant.
The only time they seem to successfully do anything is when they "switch tasks" between farming and breeding attempts, farming and wandering, or farming and running for home at sunset. After one successful operation they get stuck again.
EDIT: Villagers who are pushed into the farm block can harvest/re-plant, so it appears to be an issue with the distance for walking to/from a crop and the distance for working on a crop/farmland block not matching up anymore.
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Confirmed for me. Both my automatic wheat and beetroot farms have stopped working. Every 2-3 minutes the villager finally decides to harvest/replant a patch or two. More often than not, he harvests and doesn't replant at all. He's just constantly looking down, doing nothing, as if totally depressed!
Farmer villagers still harvest, but they don't pick up the items or replant. It seems that most of the mobs AI's are broken.
Maybe you should try putting pressure plates to detect when they harvest to trigger water that flows the crops into hoppers.
I think that it is just a universal pathfinding issue, hence my link to the bug with zombies path finding.
It appears that farmers are not "close enough" to the block of farmland they are targeting. If nudged forward a little bit, they will harvest/plant the block.