Harvest festival is another townbuilding mod, but it's more. It disables vanilla crops, so seeds what farmers plants, won't grow. HF crops are also different, because they use 9 soil for one click, they only grows at 6:00 am, and need to be watered, irrigating doesn't work.
Minecolonies' farmer acceps HF crops, but when he/she plants it, the crop became a "NULL seed" without texture. And it's only one crop.
By the way, this last thing doesn't need to be changed, because you can get your seeds only by buying from the store, so if you want an automatic farming with Minecolonies, you have to use much more money.

There is a $5 open bounty on this issue. Add to the bounty at Bountysource.

It can be cheaper in work if the farmer found a HF seed in the scarecrow, he doesn't want to do anything, except harvest when crops are ready.
Anyways, if you want to make better tools, you have to use them. You should hoe the field, place sprinklers, plant the seeds and that's it. The farmer will collect them. It's enough.

Seeds name is harvesfestival:crops_seed, and the type of them should be in NBT tag. I'll find out.

Yup, NBTExplorer says:
id: harvesfestival:crops_seed
tag: 1 entry
Crop: harvestfestival:cabbage

You can just check the item for its registry name.

This seems like a thing we need a fake player for. And in that respect a Harvest Festival worker for these special crops. Because planting in 3x3 messes up all the normal farmer calculations.

Will be added to a new joint mod compat issue.