Well it compiles; just synthtissue and TongueLoss now.

code/modules/antagonists/changeling/changeling.dm

@@ -340,7 +340,7 @@
 	if(istype(C))
 		var/obj/item/organ/brain/B = C.getorganslot(ORGAN_SLOT_BRAIN)
 		if(B)
-			B.vital = FALSE
+			B.organ_flags &= ~ORGAN_VITAL
 			B.decoy_override = TRUE
 	update_changeling_icons_added()
 	return

code/modules/antagonists/changeling/powers/regenerate.dm

@@ -35,7 +35,7 @@
 				B = new C.dna.species.mutant_brain()
 			else
 				B = new()
-			B.vital = FALSE
+			B.organ_flags &= ~ORGAN_VITAL
 			B.decoy_override = TRUE
 			B.Insert(C)
 	if(ishuman(user))

code/modules/mob/living/brain/brain_item.dm

@@ -7,7 +7,7 @@
 	layer = ABOVE_MOB_LAYER
 	zone = BODY_ZONE_HEAD
 	slot = ORGAN_SLOT_BRAIN
-	organ_flags |= ORGAN_VITAL
+	organ_flags = ORGAN_VITAL
 	attack_verb = list("attacked", "slapped", "whacked")
 	///The brain's organ variables are significantly more different than the other organs, with half the decay rate for balance reasons, and twice the maxHealth
 	decay_factor = STANDARD_ORGAN_DECAY	/ 2		//30 minutes of decaying to result in a fully damaged brain, since a fast decay rate would be unfun gameplay-wise
@@ -16,7 +16,7 @@
 	low_threshold = 45
 	high_threshold = 120
 	var/mob/living/brain/brainmob = null
-	var/organ_flags & ORGAN_FAILING = FALSE //whether the brain organ is damaged.
+	var/brain_death = FALSE //if the brainmob was intentionally killed by attacking the brain after removal, or by severe braindamage
 	var/decoy_override = FALSE	//I apologize to the security players, and myself, who abused this, but this is going to go.
 	//two variables necessary for calculating whether we get a brain trauma or not
 	var/damage_delta = 0
@@ -103,16 +103,16 @@
 
 	if((organ_flags & ORGAN_FAILING) && O.is_drainable() && O.reagents.has_reagent("neurine")) //Neurine fixes dead brains
 		. = TRUE //don't do attack animation.
-		var/cached_Bdamage = brainmob?.health 
+		var/cached_Bdamage = brainmob?.health
 		var/datum/reagent/medicine/neurine/N = reagents.has_reagent("neurine")
 
-		if(O.reagents.has_reagent("mannitol")//Just a quick way to bolster the effects if someone mixes up a batch.
+		if(O.reagents.has_reagent("mannitol"))//Just a quick way to bolster the effects if someone mixes up a batch.
 			N.volume *= 1.5
 
 		if(!O.reagents.has_reagent("neurine", 10))
 			to_chat(user, "<span class='warning'>There's not enough neurine in [O] to restore [src]!</span>")
 			return
-		
+
 		user.visible_message("<span class='notice'>[user] starts to pour the contents of [O] onto [src].</span>", "<span class='notice'>You start to slowly pour the contents of [O] onto [src].</span>")
 		if(!do_after(user, 60, TRUE, src))
 			to_chat(user, "<span class='warning'>You failed to pour [O] onto [src]!</span>")
@@ -123,10 +123,10 @@
 		O.reagents.clear_reagents()
 
 		if(cached_Bdamage) //Fixing dead brains yeilds a trauma
-			if(cached_Bdamage <= HEALTH_THRESHOLD_DEAD && brainmob.health > HEALTH_THRESHOLD_DEAD)
+			if((cached_Bdamage <= HEALTH_THRESHOLD_DEAD) && (brainmob.health > HEALTH_THRESHOLD_DEAD))
 				if(prob(90))
 					gain_trauma_type(BRAIN_TRAUMA_MILD)
-				if else(prob(50))
+				else if(prob(50))
 					gain_trauma_type(BRAIN_TRAUMA_SEVERE)
 				else
 					gain_trauma_type(BRAIN_TRAUMA_SPECIAL)
@@ -136,8 +136,8 @@
 		. = TRUE //don't do attack animation.
 		var/datum/reagent/medicine/mannitol/M = reagents.has_reagent("mannitol")
 		if(brain_death || brainmob?.health <= HEALTH_THRESHOLD_DEAD) //if the brain is fucked anyway, do nothing
-				to_chat(user, "<span class='warning'>[src] is far too damaged, you'll have to use neurine on it!</span>")
-				return
+			to_chat(user, "<span class='warning'>[src] is far too damaged, you'll have to use neurine on it!</span>")
+			return
 
 		if(!O.reagents.has_reagent("mannitol", 10))
 			to_chat(user, "<span class='warning'>There's not enough mannitol in [O] to restore [src]!</span>")
@@ -152,13 +152,13 @@
 		setOrganDamage((damage - (0.05 * maxHealth)*M.volume))	//heals a small amount, and by using "setorgandamage", we clear the failing variable if that was up
 		O.reagents.clear_reagents()
 		return
-	
 
 
-/obj/item/organ/brain/examine(mob/user)//BUG_PROBABLE_CAUSE to_chats changed to . += 
+
+/obj/item/organ/brain/examine(mob/user)//BUG_PROBABLE_CAUSE to_chats changed to . +=
 	. = ..()
 
-	if(suicided)
+	if(user.suiciding)
 		. += "<span class='info'>It's started turning slightly grey. They must not have been able to handle the stress of it all.</span>"
 	else if(brainmob)
 		if(brainmob.get_ghost(FALSE, TRUE))
@@ -247,6 +247,10 @@
 		owner.death()
 		brain_death = TRUE
 
+/obj/item/organ/brain/on_death()
+	if(damage <= BRAIN_DAMAGE_DEATH) //rip
+		brain_death = FALSE
+
 /obj/item/organ/brain/process()	//needs to run in life AND death
 	..()
 	//if we're not more injured than before, return without gambling for a trauma

code/modules/mob/living/brain/life.dm

@@ -20,7 +20,7 @@
 		else if(istype(loc, /obj/item/organ/brain))
 			BR = loc
 		if(BR)
-			BR.organ_flags & ORGAN_FAILING = 1 //beaten to a pulp
+			BR.brain_death = TRUE
 
 /mob/living/brain/proc/handle_emp_damage()
 	if(emp_damage)

code/modules/mob/living/carbon/carbon.dm

@@ -814,7 +814,6 @@
 		reagents.clear_reagents()
 	var/obj/item/organ/brain/B = getorgan(/obj/item/organ/brain)
 	if(B)
-		B.organ_flags & ORGAN_FAILING = FALSE
 		B.brain_death = FALSE
 	for(var/thing in diseases)
 		var/datum/disease/D = thing

code/modules/mob/living/carbon/carbon_defense.dm

@@ -405,16 +405,16 @@
 
 		if(istype(ears) && (deafen_pwr || damage_pwr))
 			var/ear_damage = damage_pwr * effect_amount
-			var/deaf = max(ears.deaf, deafen_pwr * effect_amount)
+			var/deaf = deafen_pwr * effect_amount
 			adjustEarDamage(ear_damage,deaf)
 
-			if(ears.ear_damage >= 15)
+			if(ears.damage >= 15)
 				to_chat(src, "<span class='warning'>Your ears start to ring badly!</span>")
-				if(prob(ears.ear_damage - 5))
+				if(prob(ears.damage - 5))
 					to_chat(src, "<span class='userdanger'>You can't hear anything!</span>")
-					ears.ear_damage = min(ears.ear_damage, UNHEALING_EAR_DAMAGE)
+					ears.damage = min(ears.damage, ears.maxHealth)
 					// you need earmuffs, inacusiate, or replacement
-			else if(ears.ear_damage >= 5)
+			else if(ears.damage >= 5)
 				to_chat(src, "<span class='warning'>Your ears start to ring!</span>")
 			SEND_SOUND(src, sound('sound/weapons/flash_ring.ogg',0,1,0,250))
 		return effect_amount //how soundbanged we are

code/modules/mob/living/carbon/damage_procs.dm

@@ -147,15 +147,15 @@
 	if(O)
 		return O.damage
 
-/mob/living/carbon/adjustAllOrganLoss(amount, maximum)
-	for(var/o in internal_organs)
+/mob/living/carbon/proc/adjustAllOrganLoss(amount, maximum)
+	for(var/obj/item/organ/O in internal_organs)
 		if(O && !(status_flags & GODMODE))
 			continue
 		if(!maximum)
 			maximum = O.maxHealth
 		O.applyOrganDamage(amount, maximum)
 		O.onDamage(amount, maximum)
-		
+
 
 ////////////////////////////////////////////
 

code/modules/mob/living/carbon/life.dm

@@ -49,7 +49,6 @@
 
 //Start of a breath chain, calls breathe()
 /mob/living/carbon/handle_breathing(times_fired)
-	/mob/living/carbon/handle_breathing(times_fired)
 	var/next_breath = 4
 	var/obj/item/organ/lungs/L = getorganslot(ORGAN_SLOT_LUNGS)
 	var/obj/item/organ/heart/H = getorganslot(ORGAN_SLOT_HEART)

code/modules/mob/living/living.dm

@@ -500,10 +500,12 @@
 		mood.sanity = SANITY_GREAT
 		mood.update_mood()
 	//Heal all organs
-	if(internal_organs)
-		for(var/organ in internal_organs)
-			var/obj/item/organ/O = organ
-			O.setOrganDamage(0)
+	if(iscarbon(src))
+		var/mob/living/carbon/C = src
+		if(C.internal_organs)
+			for(var/organ in C.internal_organs)
+				var/obj/item/organ/O = organ
+				O.setOrganDamage(0)
 
 
 //proc called by revive(), to check if we can actually ressuscitate the mob (we don't want to revive him and have him instantly die again)

code/modules/mob/transform_procs.dm

@@ -75,7 +75,7 @@
 		O.setOxyLoss(getOxyLoss(), 0)
 		O.setCloneLoss(getCloneLoss(), 0)
 		O.adjustFireLoss(getFireLoss(), 0)
-		O.setBrainLoss(getOrganLoss(ORGAN_SLOT_BRAIN), 0)
+		O.setOrganLoss(ORGAN_SLOT_BRAIN, getOrganLoss(ORGAN_SLOT_BRAIN), 0)
 		O.adjustStaminaLoss(getStaminaLoss(), 0)//CIT CHANGE - makes monkey transformations inherit stamina
 		O.updatehealth()
 		O.radiation = radiation
@@ -236,7 +236,7 @@
 		O.setOxyLoss(getOxyLoss(), 0)
 		O.setCloneLoss(getCloneLoss(), 0)
 		O.adjustFireLoss(getFireLoss(), 0)
-		O.setBrainLoss(getOrganLoss(ORGAN_SLOT_BRAIN), 0)
+		O.setOrganLoss(ORGAN_SLOT_BRAIN, getOrganLoss(ORGAN_SLOT_BRAIN), 0)
 		O.adjustStaminaLoss(getStaminaLoss(), 0)//CIT CHANGE - makes monkey transformations inherit stamina
 		O.updatehealth()
 		O.radiation = radiation

code/modules/reagents/chemistry/reagents/medicine_reagents.dm

@@ -44,7 +44,7 @@
 	M.heal_bodypart_damage(5,5)
 	M.adjustToxLoss(-5, 0, TRUE)
 	M.hallucination = 0
-	M.setBrainLoss(0)
+	M.setOrganLoss(ORGAN_SLOT_BRAIN, 0)
 	REMOVE_TRAITS_NOT_IN(M, list(SPECIES_TRAIT, ROUNDSTART_TRAIT, ORGAN_TRAIT))
 	M.set_blurriness(0)
 	M.set_blindness(0)
@@ -856,16 +856,16 @@
 			if(M.notify_ghost_cloning(source = M))
 				spawn (100) //so the ghost has time to re-enter
 					return
-			
+
 			else
 				M.adjustOxyLoss(-20, 0)
 				M.adjustToxLoss(-20, 0)
 				var/mob/living/carbon/H = M
 				for(var/organ in H.internal_organs)
 					var/obj/item/organ/O = organ
-					O.setOrganDamage(0) 
+					O.setOrganDamage(0)
 				M.updatehealth()
-				
+
 				if(M.revive())
 					M.emote("gasp")
 					log_combat(M, M, "revived", src)

code/modules/research/nanites/nanite_programs/healing.dm

@@ -198,7 +198,7 @@
 	if(host_mob.getOrganLoss(ORGAN_SLOT_BRAIN))
 		return ..()
 	return FALSE
-	
+
 /datum/nanite_program/brain_heal_advanced/active_effect()
 	host_mob.adjustOrganLoss(ORGAN_SLOT_BRAIN, -2, TRUE)
 	if(iscarbon(host_mob) && prob(10))
@@ -232,7 +232,7 @@
 	if(!C.getorgan(/obj/item/organ/heart)) //what are we even shocking
 		return FALSE
 	var/obj/item/organ/brain/BR = C.getorgan(/obj/item/organ/brain)
-	if(QDELETED(BR) || BR.brain_death || (BR.organ_flags & ORGAN_FAILING) || BR.suicided)
+	if(QDELETED(BR) || BR.brain_death || (BR.organ_flags & ORGAN_FAILING) || C.suiciding)
 		return FALSE
 	if(C.get_ghost())
 		return FALSE

code/modules/surgery/graft_synthtissue.dm

@@ -4,7 +4,7 @@
 
 /datum/surgery/graft_synthtissue
 	name = "Graft_synthtissue"
-	target_mobtypes = list(/mob/living/carbon/human, /mob/living/carbon/monkey)
+	species = list(/mob/living/carbon/human, /mob/living/carbon/monkey)
 	possible_locs = list(BODY_ZONE_CHEST)
 	steps = list(
 	/datum/surgery_step/incise,
@@ -16,8 +16,8 @@
 	/datum/surgery_step/close
 	)
 
-//repair lungs step
-/datum/surgery_step/repair_synthtissue
+//repair organs
+/datum/surgery_step/graft_synthtissue
 	name = "graft synthtissue"
 	implements = list(/obj/item/hemostat = 100, TOOL_SCREWDRIVER = 35, /obj/item/pen = 15)
 	repeatable = TRUE
@@ -25,10 +25,8 @@
 	chems_needed = list("synthtissue")
 	var/obj/item/organ/chosen_organ
 
-//Repair lungs
-/datum/surgery_step/repair_synthtissue/preop(mob/user, mob/living/carbon/human/target, target_zone, obj/item/tool, datum/surgery/surgery)
-	if(implement_type in implements_extract)
-		current_type = "insert"
+/datum/surgery_step/graft_synthtissue/preop(mob/user, mob/living/carbon/human/target, target_zone, obj/item/tool, datum/surgery/surgery)
+	if(implement_type in implements)
 		var/list/organs = target.getorganszone(target_zone)
 		if(!organs.len)
 			to_chat(user, "<span class='notice'>There are no targetable organs in [target]'s [parse_zone(target_zone)]!</span>")
@@ -39,24 +37,23 @@
 				organs -= O
 				organs[O.name] = O
 			chosen_organ = input("Remove which organ?", "Surgery", null, null) as null|anything in organs
-			if(chosen_organ.organ_flags & ORGAN_FAILING))
+			if(chosen_organ.organ_flags & ORGAN_FAILING)
 				to_chat(user, "<span class='notice'>[target]'s [chosen_organ] is too damaged to repair graft onto!</span>")
 				return -1
-			
+
 	user.visible_message("[user] begins to repair damaged portions of [target]'s [chosen_organ].</span>")
 
-/datum/surgery_step/repair_synthtissue/success(mob/user, mob/living/carbon/target, target_zone, obj/item/tool, datum/surgery/surgery)
+/datum/surgery_step/graft_synthtissue/success(mob/user, mob/living/carbon/target, target_zone, obj/item/tool, datum/surgery/surgery)
 	if((!chosen_organ)||(chosen_organ.organ_flags & ORGAN_FAILING))
 		to_chat(user, "[target] has no [chosen_organ] capable of repair!")
 	else
 		user.visible_message("[user] successfully repairs part of [target]'s [chosen_organ].", "<span class='notice'>You succeed in repairing parts of [target]'s [chosen_organ].</span>")
 		chosen_organ.applyOrganDamage(-10)
 
-/datum/surgery_step/repair_synthtissue/failure(mob/user, mob/living/carbon/target, target_zone, obj/item/tool, datum/surgery/surgery)
+/datum/surgery_step/graft_synthtissue/failure(mob/user, mob/living/carbon/target, target_zone, obj/item/tool, datum/surgery/surgery)
 	if((!chosen_organ)||(chosen_organ.organ_flags & ORGAN_FAILING))
 		to_chat(user, "[target] has no [chosen_organ] capable of repair!")
 	else
 		user.visible_message("<span class='warning'>[user] accidentally damages part of [target]'s [chosen_organ]!</span>", "<span class='warning'>You damage [target]'s [chosen_organ]! Apply more synthtissue if it's run out.</span>")
 		chosen_organ.applyOrganDamage(10)
 	return FALSE
-

code/modules/surgery/organs/augments_internal.dm

@@ -103,7 +103,7 @@
 
 /obj/item/organ/cyberimp/brain/anti_stun/on_life()
 	..()
-	if((crit_fail || !(organ_flags & ORGAN_FAILING)) && amount > 0)
+	if(crit_fail || !(organ_flags & ORGAN_FAILING))
 		return
 	owner.adjustStaminaLoss(-3.5) //Citadel edit, makes it more useful in Stamina based combat
 	if(owner.AmountStun() > STUN_SET_AMOUNT)

code/modules/surgery/organs/liver.dm

@@ -15,10 +15,8 @@
 	healing_factor = STANDARD_ORGAN_HEALING
 	decay_factor = STANDARD_ORGAN_DECAY
 
-	var/damage = 0 //liver damage, 0 is no damage, damage=maxHealth causes liver failure
 	var/alcohol_tolerance = ALCOHOL_RATE//affects how much damage the liver takes from alcohol
 	var/failing //is this liver failing?
-	var/maxHealth = LIVER_DEFAULT_HEALTH
 	var/toxTolerance = LIVER_DEFAULT_TOX_TOLERANCE//maximum amount of toxins the liver can just shrug off
 	var/toxLethality = LIVER_DEFAULT_TOX_LETHALITY//affects how much damage toxins do to the liver
 	var/filterToxins = TRUE //whether to filter toxins

code/modules/surgery/organs/lungs.dm

@@ -416,13 +416,13 @@
 		var/cold_modifier = H.dna.species.coldmod
 		if(breath_temperature < cold_level_3_threshold)
 			H.apply_damage_type(cold_level_3_damage*cold_modifier, cold_damage_type)
-			adjustOrganLoss(ORGAN_SLOT_LUNG, (cold_level_3_damage*cold_modifier*2))
+			H.adjustOrganLoss(ORGAN_SLOT_LUNGS, (cold_level_3_damage*cold_modifier*2))
 		if(breath_temperature > cold_level_3_threshold && breath_temperature < cold_level_2_threshold)
 			H.apply_damage_type(cold_level_2_damage*cold_modifier, cold_damage_type)
-			adjustOrganLoss(ORGAN_SLOT_LUNG, (cold_level_2_damage*cold_modifier*2))
+			H.adjustOrganLoss(ORGAN_SLOT_LUNGS, (cold_level_2_damage*cold_modifier*2))
 		if(breath_temperature > cold_level_2_threshold && breath_temperature < cold_level_1_threshold)
 			H.apply_damage_type(cold_level_1_damage*cold_modifier, cold_damage_type)
-			adjustOrganLoss(ORGAN_SLOT_LUNG, (cold_level_1_damage*cold_modifier*2))
+			H.adjustOrganLoss(ORGAN_SLOT_LUNGS, (cold_level_1_damage*cold_modifier*2))
 		if(breath_temperature < cold_level_1_threshold)
 			if(prob(20))
 				to_chat(H, "<span class='warning'>You feel [cold_message] in your [name]!</span>")
@@ -431,13 +431,13 @@
 		var/heat_modifier = H.dna.species.heatmod
 		if(breath_temperature > heat_level_1_threshold && breath_temperature < heat_level_2_threshold)
 			H.apply_damage_type(heat_level_1_damage*heat_modifier, heat_damage_type)
-			adjustOrganLoss(ORGAN_SLOT_LUNG, (heat_level_1_damage*heat_modifier*2))
+			H.adjustOrganLoss(ORGAN_SLOT_LUNGS, (heat_level_1_damage*heat_modifier*2))
 		if(breath_temperature > heat_level_2_threshold && breath_temperature < heat_level_3_threshold)
 			H.apply_damage_type(heat_level_2_damage*heat_modifier, heat_damage_type)
-			adjustOrganLoss(ORGAN_SLOT_LUNG, (heat_level_2_damage*heat_modifier*2))
+			H.adjustOrganLoss(ORGAN_SLOT_LUNGS, (heat_level_2_damage*heat_modifier*2))
 		if(breath_temperature > heat_level_3_threshold)
 			H.apply_damage_type(heat_level_3_damage*heat_modifier, heat_damage_type)
-			adjustOrganLoss(ORGAN_SLOT_LUNG, (heat_level_3_damage*heat_modifier*2))
+			H.adjustOrganLoss(ORGAN_SLOT_LUNGS, (heat_level_3_damage*heat_modifier*2))
 		if(breath_temperature > heat_level_1_threshold)
 			if(prob(20))
 				to_chat(H, "<span class='warning'>You feel [hot_message] in your [name]!</span>")

code/modules/surgery/organs/organ_internal.dm

@@ -29,17 +29,6 @@
 	var/high_threshold_cleared
 	var/low_threshold_cleared
 
-/obj/item/organ/proc/Assemble_Failure_Message()	//need to assemble a failure message since we can't have variables be based off of the same object's variables
-	var/name_length
-	//if no unique failure message is set, output the generic one, otherwise give the one we have set
-	if(!Unique_Failure_Msg)
-		name_length = lentext(name)
-		if(name[name_length] == "s")	//plural case, done without much sanitization since I don't know any organ that ends with an "s" that isn't plural at the moment
-			Unique_Failure_Msg = "<span class='danger'>Subject's [name] are too damaged to function, and needs to be replaced or fixed!</span>"
-		else
-			Unique_Failure_Msg = "<span class='danger'>Subject's [name] is too damaged to function, and needs to be replaced or fixed!</span>"
-	return Unique_Failure_Msg
-
 /obj/item/organ/proc/Insert(mob/living/carbon/M, special = 0, drop_if_replaced = TRUE)
 	if(!iscarbon(M) || owner == M)
 		return
@@ -94,8 +83,8 @@
 	var/healing_amount = -(maxHealth * healing_factor)
 	///Damage decrements again by a percent of its maxhealth, up to a total of 4 extra times depending on the owner's health
 	healing_amount -= owner.satiety > 0 ? 4 * healing_factor * owner.satiety / MAX_SATIETY : 0
-	applyOrganDamage(healing_amount) //FERMI_TWEAK
-	
+	applyOrganDamage(healing_amount) //to FERMI_TWEAK
+
 /obj/item/organ/examine(mob/user)
 	. = ..()
 	if(organ_flags & ORGAN_FAILING)

code/modules/surgery/organs/stomach.dm

@@ -25,9 +25,6 @@
 		if(!(organ_flags & ORGAN_FAILING))
 			H.dna.species.handle_digestion(H)
 		handle_disgust(H)
-	
-	if(Nutri)
-
 
 	if(damage < low_threshold)
 		return
@@ -44,7 +41,7 @@
 			H.vomit(damage)
 			to_chat(H, "<span class='warning'>Your stomach reels in pain as you're incapable of holding down all that food!</span>")
 
-	
+
 
 /obj/item/organ/stomach/proc/handle_disgust(mob/living/carbon/human/H)
 	if(H.disgust)

code/modules/surgery/organs/tongue.dm

@@ -10,8 +10,7 @@
 	var/list/languages_possible
 	var/say_mod = null
 	var/taste_sensitivity = 15 // lower is more sensitive.
-	var/maxHealth = TONGUE_MAX_HEALTH
-	var/damage = 0
+	maxHealth = TONGUE_MAX_HEALTH
 	var/modifies_speech = FALSE
 	var/static/list/languages_possible_base = typecacheof(list(
 		/datum/language/common,