I figured it out, it's a bug in DF. It seems that any plant lacking one or more of the following properties is not harvestable:
* An edible main material
* A mill result material
* An extract material (vial or barrel)
* A thread material
* I may be forgetting/missing one
Surprisingly the presence of a drink material is not enough.
Once I added a "dummy" extract it worked fine. Apparently this was broken when all the plant changes were made in .40? (I think it was .40) Anyway, I'll go report this on the bug tracker in a minute.
It doesn't need to be an extract or mill product, I think just about any reaction product works fine. Plants like this one:
[PLANT:TESB_VINE_EMERALD]
[NAME:emerald vine][NAME_PLURAL:emerald vines][ADJ:emerald vine]
[USE_MATERIAL_TEMPLATE:STRUCTURAL:STRUCTURAL_PLANT_TEMPLATE]
[MATERIAL_VALUE:3]
[EDIBLE_VERMIN]
[BASIC_MAT:LOCAL_PLANT_MAT:STRUCTURAL]
[USE_MATERIAL_TEMPLATE:FRUIT:FRUIT_TEMPLATE] Not edible, but will stockpile with other plant growths.
[MATERIAL_REACTION_PRODUCT:SPIRIT_MAT:LOCAL_PLANT_MAT:DRINK] Note the non-standard _MAT
[MATERIAL_REACTION_PRODUCT:SEEDS_MAT:LOCAL_PLANT_MAT:SEED] Note the non-standard _MAT
[MATERIAL_REACTION_PRODUCT:GEM_MAT:INORGANIC:HIDDEN EMERALD]
[STOCKPILE_PLANT_GROWTH]
[MATERIAL_VALUE:333]
[PICKED_TILE:37][PICKED_COLOR:2:6:0][DEAD_PICKED_TILE:182]
[WET][DRY][BIOME:SUBTERRANEAN_WATER][UNDERGROUND_DEPTH:4:4]
[VALUE:3]
[USE_MATERIAL_TEMPLATE:DRINK:PLANT_ALCOHOL_TEMPLATE]
[STATE_NAME_ADJ:ALL_SOLID:frozen emerald spirits]
[STATE_NAME_ADJ:LIQUID:emerald spirits]
[STATE_NAME_ADJ:GAS:boiling emerald spirits]
[STATE_COLOR:ALL:EMERALD]
[MATERIAL_VALUE:2]
[DISPLAY_COLOR:2:0:1]
[EDIBLE_RAW]
[EDIBLE_COOKED]
[PREFIX:NONE]
[DRINK:LOCAL_PLANT_MAT:DRINK] May want to remove this, to avoid the still's standard reactions.
[SPRING][SUMMER][AUTUMN][WINTER] Underground plant, so seasons should be irrelevant.
[USE_MATERIAL_TEMPLATE:SEED:SEED_TEMPLATE]
[MATERIAL_VALUE:333]
[EDIBLE_VERMIN]
[EDIBLE_COOKED]
[SEED:emerald seed:emerald seeds:2:0:1:LOCAL_PLANT_MAT:SEED]
[FREQUENCY:50]
[CLUSTERSIZE:5]
[PREFSTRING:emerald clusters]
[SHRUB_TILE:18]
[DEAD_SHRUB_TILE:18]
[SHRUB_COLOR:2:2:1]
[DEAD_SHRUB_COLOR:6:0:0]
[GROWTH:FRUIT]
[GROWTH_NAME:emerald cluster:emerald clusters]
[GROWTH_ITEM:PLANT_GROWTH:NONE:LOCAL_PLANT_MAT:FRUIT]
[GROWTH_DENSITY:1000]
[GROWTH_HOST_TILE:BRANCHES_AND_TWIGS]
[GROWTH_TIMING:120000:200000]
[GROWTH_DROPS_OFF_NO_CLOUD]
[GROWTH_PRINT:18:37:2:14:1:120000:200000:3]
Drop their fruit upon maturing, and the plant itself seems to vanish. Maybe add a dummy reaction product to the structural material to see if that lets it stick around. Without a specific reaction to use that reaction product, you don't run the risk of messing up vanilla reactions.