Your reaction_standard.txt has most definitely been modified if there are no REAGENT entries. Hell, you even have new 2 reactions at the end that both
create 20 gold bars out of nothing (even though one of them was apparently supposed to create iron), something which certainly does not exist in the vanilla version. Either you edited your reactions to cheat a long time ago and forgot about it, or you downloaded a modded version that added the cheats for you.
The proper contents of reaction_standard.txt are as follows. Note that you will have to regenerate your world afterwards, since the "make precious gold" and "make iron" reactions won't be there anymore.
reaction_standard
[OBJECT:REACTION]
[REACTION:BITUMINOUS_COAL_TO_COKE]
[NAME:make coke from bituminous coal]
[SMELTER]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:COAL_BITUMINOUS]
[PRODUCT:100:3:BAR:NO_SUBTYPE:COAL:COKE]
[FUEL]
[REACTION:LIGNITE_TO_COKE]
[NAME:make coke from lignite]
[SMELTER]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:LIGNITE]
[PRODUCT:100:2:BAR:NO_SUBTYPE:COAL:COKE]
[FUEL]
[REACTION:BRASS_MAKING]
[NAME:make brass bars (use ore)]
[SMELTER]
[REAGENT:1:METAL_ORE:ZINC]
[REAGENT:1:METAL_ORE:COPPER]
[PRODUCT:100:2:BAR:NO_SUBTYPE:METAL:BRASS]
[FUEL]
[REACTION:BRASS_MAKING2]
[NAME:make brass bars (use bars)]
[SMELTER]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:ZINC]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:COPPER]
[PRODUCT:100:2:BAR:NO_SUBTYPE:METAL:BRASS]
[FUEL]
[REACTION:BRONZE_MAKING]
[NAME:make bronze bars (use ore)]
[SMELTER]
[REAGENT:1:METAL_ORE:TIN]
[REAGENT:1:METAL_ORE:COPPER]
[PRODUCT:100:2:BAR:NO_SUBTYPE:METAL:BRONZE]
[FUEL]
[REACTION:BRONZE_MAKING2]
[NAME:make bronze bars (use bars)]
[SMELTER]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:TIN]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:COPPER]
[PRODUCT:100:2:BAR:NO_SUBTYPE:METAL:BRONZE]
[FUEL]
[REACTION:ELECTRUM_MAKING]
[NAME:make electrum bars (use ore)]
[SMELTER]
[REAGENT:1:METAL_ORE:SILVER]
[REAGENT:1:METAL_ORE:GOLD]
[PRODUCT:100:2:BAR:NO_SUBTYPE:METAL:ELECTRUM]
[FUEL]
[REACTION:ELECTRUM_MAKING2]
[NAME:make electrum bars (use bars)]
[SMELTER]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:SILVER]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:GOLD]
[PRODUCT:100:2:BAR:NO_SUBTYPE:METAL:ELECTRUM]
[FUEL]
[REACTION:BILLON_MAKING]
[NAME:make billon bars (use ore)]
[SMELTER]
[REAGENT:1:METAL_ORE:SILVER]
[REAGENT:1:METAL_ORE:COPPER]
[PRODUCT:100:2:BAR:NO_SUBTYPE:METAL:BILLON]
[FUEL]
[REACTION:BILLON_MAKING2]
[NAME:make billon bars (use bars)]
[SMELTER]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:SILVER]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:COPPER]
[PRODUCT:100:2:BAR:NO_SUBTYPE:METAL:BILLON]
[FUEL]
[REACTION:PEWTER_FINE_MAKING]
[NAME:make fine pewter bars (use ore)]
[SMELTER]
[REAGENT:3:METAL_ORE:TIN]
[REAGENT:1:METAL_ORE:COPPER]
[PRODUCT:100:4:BAR:NO_SUBTYPE:METAL:PEWTER_FINE]
[FUEL]
[REACTION:PEWTER_FINE_MAKING2]
[NAME:make fine pewter bars (use bars)]
[SMELTER]
[REAGENT:3:BAR:NO_SUBTYPE:METAL:TIN]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:COPPER]
[PRODUCT:100:4:BAR:NO_SUBTYPE:METAL:PEWTER_FINE]
[FUEL]
[REACTION:PEWTER_TRIFLE_MAKING]
[NAME:make trifle pewter bars (use ore)]
[SMELTER]
[REAGENT:2:METAL_ORE:TIN]
[REAGENT:1:METAL_ORE:COPPER]
[PRODUCT:100:3:BAR:NO_SUBTYPE:METAL:PEWTER_TRIFLE]
[FUEL]
[REACTION:PEWTER_TRIFLE_MAKING2]
[NAME:make trifle pewter bars (use bars)]
[SMELTER]
[REAGENT:2:BAR:NO_SUBTYPE:METAL:TIN]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:COPPER]
[PRODUCT:100:3:BAR:NO_SUBTYPE:METAL:PEWTER_TRIFLE]
[FUEL]
[REACTION:PEWTER_LAY_MAKING]
[NAME:make lay pewter bars (use bars)]
[SMELTER]
[REAGENT:2:BAR:NO_SUBTYPE:METAL:TIN]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:COPPER]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:LEAD]
[PRODUCT:100:4:BAR:NO_SUBTYPE:METAL:PEWTER_LAY]
[FUEL]
[REACTION:PIG_IRON_MAKING]
[NAME:make pig iron bars]
[SMELTER]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:IRON]
[REAGENT:1:REACTION_CLASS:FLUX]
[REAGENT:1:BAR:NO_SUBTYPE:COAL:NO_MATGLOSS]
[PRODUCT:100:1:BAR:NO_SUBTYPE:METAL:PIG_IRON]
[FUEL]
[REACTION:STEEL_MAKING]
[NAME:make steel bars]
[SMELTER]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:IRON]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:PIG_IRON]
[REAGENT:1:REACTION_CLASS:FLUX]
[REAGENT:1:BAR:NO_SUBTYPE:COAL:NO_MATGLOSS]
[PRODUCT:100:2:BAR:NO_SUBTYPE:METAL:STEEL]
[FUEL]
[REACTION:NICKEL_SILVER_MAKING]
[NAME:make nickel silver bars]
[SMELTER]
[REAGENT:2:BAR:NO_SUBTYPE:METAL:NICKEL]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:COPPER]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:ZINC]
[PRODUCT:100:4:BAR:NO_SUBTYPE:METAL:NICKEL_SILVER]
[FUEL]
[REACTION:BLACK_BRONZE_MAKING]
[NAME:make black bronze bars]
[SMELTER]
[REAGENT:2:BAR:NO_SUBTYPE:METAL:COPPER]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:SILVER]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:GOLD]
[PRODUCT:100:4:BAR:NO_SUBTYPE:METAL:BLACK_BRONZE]
[FUEL]
[REACTION:STERLING_SILVER_MAKING]
[NAME:make sterling silver bars]
[SMELTER]
[REAGENT:3:BAR:NO_SUBTYPE:METAL:SILVER]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:COPPER]
[PRODUCT:100:4:BAR:NO_SUBTYPE:METAL:STERLING_SILVER]
[FUEL]
[REACTION:ROSE_GOLD_MAKING]
[NAME:make rose gold bars]
[SMELTER]
[REAGENT:3:BAR:NO_SUBTYPE:METAL:GOLD]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:COPPER]
[PRODUCT:100:4:BAR:NO_SUBTYPE:METAL:ROSE_GOLD]
[FUEL]
[REACTION:BISMUTH_BRONZE_MAKING]
[NAME:make bismuth bronze bars]
[SMELTER]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:TIN]
[REAGENT:2:BAR:NO_SUBTYPE:METAL:COPPER]
[REAGENT:1:BAR:NO_SUBTYPE:METAL:BISMUTH]
[PRODUCT:100:4:BAR:NO_SUBTYPE:METAL:BISMUTH_BRONZE]
[FUEL]
[REACTION:ADAMANTINE_WAFERS]
[NAME:make adamantine wafers]
[SMELTER]
[REAGENT:1:THREAD:NO_SUBTYPE:METAL:ADAMANTINE]
[PRODUCT:100:1:BAR:NO_SUBTYPE:METAL:ADAMANTINE]
[FUEL]
Incidentally, while the 2D version explicitly hid all adamantine-related jobs from all workshops and the job manager until you actually found it, the 3D version starts with it all available but effectively unusable.