Bay Merge 05NOV2014

Known errors:

* A set of errors tied to updating the fire overlays.
* A single error related to a dischephency between new and old slime
code
* A set of errors related to the recharging of stun batons
* A single error due to old machinery code coming from your grav
generator file
* A single error error from your space cooler code, due to old
atmopsherics code
* A playerpanel warning
* An error tied to extinguishing and old atmos code.

code/modules/organs/blood.dm

@@ -63,7 +63,7 @@ var/const/BLOOD_VOLUME_SURVIVE = 122
 
 		// Damaged heart virtually reduces the blood volume, as the blood isn't
 		// being pumped properly anymore.
-		var/datum/organ/internal/heart/heart = internal_organs["heart"]
+		var/datum/organ/internal/heart/heart = internal_organs_by_name["heart"]
 
 		if(heart.damage > 1 && heart.damage < heart.min_bruised_damage)
 			blood_volume *= 0.8
@@ -127,14 +127,12 @@ var/const/BLOOD_VOLUME_SURVIVE = 122
 			if(!(temp.status & ORGAN_BLEEDING) || temp.status & ORGAN_ROBOT)
 				continue
 			for(var/datum/wound/W in temp.wounds) if(W.bleeding())
-				blood_max += W.damage / 4
-			if(temp.status & ORGAN_DESTROYED && !(temp.status & ORGAN_GAUZED) && !temp.amputated)
-				blood_max += 20 //Yer missing a fucking limb.
+				blood_max += W.damage / 40
 			if (temp.open)
 				blood_max += 2  //Yer stomach is cut open
 		drip(blood_max)
 
-//Makes a blood drop, leaking certain amount of blood from the mob
+//Makes a blood drop, leaking amt units of blood from the mob
 /mob/living/carbon/human/proc/drip(var/amt as num)
 
 	if(species && species.flags & NO_BLOOD) //TODO: Make drips come from the reagents instead.
@@ -143,12 +141,11 @@ var/const/BLOOD_VOLUME_SURVIVE = 122
 	if(!amt)
 		return
 
-	var/amm = 0.1 * amt
 	var/turf/T = get_turf(src)
 	var/list/obj/effect/decal/cleanable/blood/drip/nums = list()
 	var/list/iconL = list("1","2","3","4","5")
 
-	vessel.remove_reagent("blood",amm)
+	vessel.remove_reagent("blood",amt)
 
 	for(var/obj/effect/decal/cleanable/blood/drip/G in T)
 		nums += G

code/modules/organs/organ.dm

@@ -5,6 +5,9 @@
 	var/list/datum/autopsy_data/autopsy_data = list()
 	var/list/trace_chemicals = list() // traces of chemicals in the organ,
 									  // links chemical IDs to number of ticks for which they'll stay in the blood
+
+	var/germ_level = 0		// INTERNAL germs inside the organ, this is BAD if it's greater than INFECTION_LEVEL_ONE
+
 	proc/process()
 		return 0
 
@@ -14,6 +17,20 @@
 /datum/organ/proc/get_icon(var/icon/race_icon, var/icon/deform_icon)
 	return icon('icons/mob/human.dmi',"blank")
 
+//Germs
+/datum/organ/proc/handle_antibiotics()
+	var/antibiotics = owner.reagents.get_reagent_amount("spaceacillin")
+
+	if (!germ_level || antibiotics < 5)
+		return
+
+	if (germ_level < INFECTION_LEVEL_ONE)
+		germ_level = 0	//cure instantly
+	else if (germ_level < INFECTION_LEVEL_TWO)
+		germ_level -= 6	//at germ_level == 500, this should cure the infection in a minute
+	else
+		germ_level -= 2 //at germ_level == 1000, this will cure the infection in 5 minutes
+
 //Handles chem traces
 /mob/living/carbon/human/proc/handle_trace_chems()
 	//New are added for reagents to random organs.
@@ -46,13 +63,18 @@
 	if(damage_this_tick > last_dam)
 		force_process = 1
 	last_dam = damage_this_tick
-	if(!force_process && !bad_external_organs.len)
-		return
 	if(force_process)
 		bad_external_organs.Cut()
 		for(var/datum/organ/external/Ex in organs)
 			bad_external_organs += Ex
 
+	//processing internal organs is pretty cheap, do that first.
+	for(var/datum/organ/internal/I in internal_organs)
+		I.process()
+
+	if(!force_process && !bad_external_organs.len)
+		return
+
 	for(var/datum/organ/external/E in bad_external_organs)
 		if(!E)
 			continue
@@ -62,63 +84,22 @@
 		else
 			E.process()
 			number_wounds += E.number_wounds
-			//Robotic limb malfunctions
-			var/malfunction = 0
-			if (E.status & ORGAN_ROBOT && prob(E.brute_dam + E.burn_dam))
-				malfunction = 1
-
-			//Broken limbs hurt too
-			var/broken = 0
-			if(E.status & ORGAN_BROKEN && !(E.status & ORGAN_SPLINTED) )
-				broken = 1
 
+			if (!lying && world.time - l_move_time < 15)
 			//Moving around with fractured ribs won't do you any good
-			if (broken && E.internal_organs && prob(15))
-				if (!lying && world.timeofday - l_move_time < 15)
+				if (E.is_broken() && E.internal_organs && prob(15))
 					var/datum/organ/internal/I = pick(E.internal_organs)
 					custom_pain("You feel broken bones moving in your [E.display_name]!", 1)
 					I.take_damage(rand(3,5))
 
-			//Special effects for limbs.
-			if(E.name in list("l_hand","l_arm","r_hand","r_arm"))
-				var/obj/item/c_hand		//Getting what's in this hand
-				var/hand
-				if(E.name == "l_hand" || E.name == "l_arm")
-					c_hand = l_hand
-					hand = "left hand"
-				if(E.name == "r_hand" || E.name == "r_arm")
-					c_hand = r_hand
-					hand = "right hand"
-				if (c_hand)
+				//Moving makes open wounds get infected much faster
+				if (E.wounds.len)
+					for(var/datum/wound/W in E.wounds)
+						if (W.infection_check())
+							W.germ_level += 1
 
-					if(broken)
-						if(istype(c_hand, /obj/item/weapon/gun/offhand))
-							var/obj/item/weapon/gun/O = get_inactive_hand()
-							var/obj/item/weapon/gun/offhand/OH = c_hand
-							O.unwield()
-							OH.unwield()
-						else
-							u_equip(c_hand)
-						var/emote_scream = pick("screams in pain and", "let's out a sharp hiss and", "cries out and")
-						emote("me", 1, "[(species && species.flags & NO_PAIN) ? "" : emote_scream ] drops what they were holding in their [hand]!")
-					if(malfunction)
-						if(istype(c_hand, /obj/item/weapon/gun/offhand))
-							var/obj/item/weapon/gun/O = get_inactive_hand()
-							var/obj/item/weapon/gun/offhand/OH = c_hand
-							O.unwield()
-							OH.unwield()
-						else
-							u_equip(c_hand)
-						emote("me", 1, "drops what they were holding, their [hand] malfunctioning!")
-						var/datum/effect/effect/system/spark_spread/spark_system = new /datum/effect/effect/system/spark_spread()
-						spark_system.set_up(5, 0, src)
-						spark_system.attach(src)
-						spark_system.start()
-						spawn(10)
-							del(spark_system)
-
-			else if(E.name in list("l_leg","l_foot","r_leg","r_foot") && !lying)
-				if (!E.is_usable() || malfunction || (broken && !(E.status & ORGAN_SPLINTED)))
+			if(E.name in list("l_leg","l_foot","r_leg","r_foot") && !lying)
+				if (!E.is_usable() || E.is_malfunctioning() || (E.is_broken() && !(E.status & ORGAN_SPLINTED)))
 					leg_tally--			// let it fail even if just foot&leg
 
 	// standing is poor

code/modules/organs/organ_external.dm

@@ -32,6 +32,7 @@
 	var/damage_msg = "\red You feel an intense pain"
 	var/broken_description
 
+	var/vital //Lose a vital limb, die immediately.
 	var/status = 0
 	var/open = 0
 	var/stage = 0
@@ -40,8 +41,6 @@
 
 	var/obj/item/hidden = null
 	var/list/implants = list()
-	// INTERNAL germs inside the organ, this is BAD if it's greater 0
-	var/germ_level = 0
 
 	// how often wounds should be updated, a higher number means less often
 	var/wound_update_accuracy = 1
@@ -92,15 +91,8 @@
 		brute *= brmod //~2/3 damage for ROBOLIMBS
 		burn *= bumod //~2/3 damage for ROBOLIMBS
 
-	//If limb took enough damage, try to cut or tear it off
-	if(body_part != UPPER_TORSO && body_part != LOWER_TORSO) //as hilarious as it is, getting hit on the chest too much shouldn't effectively gib you.
-		if(config.limbs_can_break && brute_dam >= max_damage * config.organ_health_multiplier)
-			if( (edge && prob(5 * brute)) || (brute > 20 && prob(2 * brute)) )
-				droplimb(1)
-				return
-
 	// High brute damage or sharp objects may damage internal organs
-	if(internal_organs != null) if( (sharp && brute >= 5) || brute >= 10) if(prob(5))
+	if(internal_organs && ( (sharp && brute >= 5) || brute >= 10) && prob(5))
 		// Damage an internal organ
 		var/datum/organ/internal/I = pick(internal_organs)
 		I.take_damage(brute / 2)
@@ -163,6 +155,14 @@
 
 	// sync the organ's damage with its wounds
 	src.update_damages()
+
+	//If limb took enough damage, try to cut or tear it off
+	if(body_part != UPPER_TORSO && body_part != LOWER_TORSO) //as hilarious as it is, getting hit on the chest too much shouldn't effectively gib you.
+		if(config.limbs_can_break && brute_dam >= max_damage * config.organ_health_multiplier)
+			if( (edge && prob(5 * brute)) || (brute > 20 && prob(2 * brute)) )
+				droplimb(1)
+				return
+
 	owner.updatehealth()
 
 	var/result = update_icon()
@@ -194,18 +194,6 @@
 	var/result = update_icon()
 	return result
 
-
-/datum/organ/external/proc/embed(var/obj/item/weapon/W, var/silent = 0)
-	if(!silent)
-		owner.visible_message("<span class='danger'>\The [W] sticks in the wound!</span>")
-	implants += W
-	owner.embedded_flag = 1
-	owner.verbs += /mob/proc/yank_out_object
-	W.add_blood(owner)
-	if(ismob(W.loc))
-		var/mob/living/H = W.loc
-		H.drop_item()
-	W.loc = owner
 /*
 This function completely restores a damaged organ to perfect condition.
 */
@@ -218,6 +206,9 @@ This function completely restores a damaged organ to perfect condition.
 	perma_injury = 0
 	brute_dam = 0
 	burn_dam = 0
+	germ_level = 0
+	wounds.Cut()
+	number_wounds = 0
 
 	// handle internal organs
 	for(var/datum/organ/internal/current_organ in internal_organs)
@@ -235,11 +226,11 @@ This function completely restores a damaged organ to perfect condition.
 /datum/organ/external/proc/createwound(var/type = CUT, var/damage)
 	if(damage == 0) return
 
-	//moved this before the open_wound check so that having many small wounds for example doesn't somehow protect you from taking internal damage
+	//moved this before the open_wound check so that having many small wounds for example doesn't somehow protect you from taking internal damage (because of the return)
 	//Possibly trigger an internal wound, too.
 	var/local_damage = brute_dam + burn_dam + damage
 	if(damage > 15 && type != BURN && local_damage > 30 && prob(damage) && !(status & ORGAN_ROBOT))
-		var/datum/wound/internal_bleeding/I = new (15)
+		var/datum/wound/internal_bleeding/I = new (min(damage - 15, 15))
 		wounds += I
 		owner.custom_pain("You feel something rip in your [display_name]!", 1)
 
@@ -277,25 +268,6 @@ This function completely restores a damaged organ to perfect condition.
 		if(W)
 			wounds += W
 
-/datum/organ/external/proc/get_wound_type(var/type = CUT, var/damage)
-	//if you look a the names in the wound's stages list for each wound type you will see the logic behind these values
-	switch(type)
-		if(CUT)
-			if (damage <= 5) return /datum/wound/cut/small
-			if (damage <= 15) return /datum/wound/cut/deep
-			if (damage <= 25) return /datum/wound/cut/flesh
-			if (damage <= 50) return /datum/wound/cut/gaping
-			if (damage <= 60) return /datum/wound/cut/gaping_big
-			return /datum/wound/cut/massive
-		if(BRUISE)
-			return /datum/wound/bruise
-		if(BURN)
-			if (damage <= 5) return /datum/wound/burn/moderate
-			if (damage <= 15) return /datum/wound/burn/large
-			if (damage <= 30) return /datum/wound/burn/severe
-			if (damage <= 40) return /datum/wound/burn/deep
-			return /datum/wound/burn/carbonised
-
 /****************************************************
 			   PROCESSING & UPDATING
 ****************************************************/
@@ -303,6 +275,8 @@ This function completely restores a damaged organ to perfect condition.
 //Determines if we even need to process this organ.
 
 /datum/organ/external/proc/need_process()
+	if(destspawn)	//Missing limb is missing
+		return 0
 	if(status && status != ORGAN_ROBOT) // If it's robotic, that's fine it will have a status.
 		return 1
 	if(brute_dam || burn_dam)
@@ -310,21 +284,13 @@ This function completely restores a damaged organ to perfect condition.
 	if(last_dam != brute_dam + burn_dam) // Process when we are fully healed up.
 		last_dam = brute_dam + burn_dam
 		return 1
-	last_dam = brute_dam + burn_dam
+	else
+		last_dam = brute_dam + burn_dam
+	if(germ_level)
+		return 1
 	return 0
 
 /datum/organ/external/process()
-	// Process wounds, doing healing etc. Only do this every few ticks to save processing power
-	if(owner.life_tick % wound_update_accuracy == 0)
-		update_wounds()
-
-	//Chem traces slowly vanish
-	if(owner.life_tick % 10 == 0)
-		for(var/chemID in trace_chemicals)
-			trace_chemicals[chemID] = trace_chemicals[chemID] - 1
-			if(trace_chemicals[chemID] <= 0)
-				trace_chemicals.Remove(chemID)
-
 	//Dismemberment
 	if(status & ORGAN_DESTROYED)
 		if(!destspawn && config.limbs_can_break)
@@ -336,56 +302,134 @@ This function completely restores a damaged organ to perfect condition.
 			owner.update_body(1)
 			return
 
+	// Process wounds, doing healing etc. Only do this every few ticks to save processing power
+	if(owner.life_tick % wound_update_accuracy == 0)
+		update_wounds()
+
+	//Chem traces slowly vanish
+	if(owner.life_tick % 10 == 0)
+		for(var/chemID in trace_chemicals)
+			trace_chemicals[chemID] = trace_chemicals[chemID] - 1
+			if(trace_chemicals[chemID] <= 0)
+				trace_chemicals.Remove(chemID)
+
 	//Bone fracurtes
 	if(config.bones_can_break && brute_dam > min_broken_damage * config.organ_health_multiplier && !(status & ORGAN_ROBOT))
 		src.fracture()
 	if(!(status & ORGAN_BROKEN))
 		perma_injury = 0
 
+	//Infections
 	update_germs()
-	return
 
 //Updating germ levels. Handles organ germ levels and necrosis.
-#define GANGREN_LEVEL_ONE		100
-#define GANGREN_LEVEL_TWO		1000
-#define GANGREN_LEVEL_TERMINAL	2500
-#define GERM_TRANSFER_AMOUNT	germ_level/500
+/*
+The INFECTION_LEVEL values defined in setup.dm control the time it takes to reach the different
+infection levels. Since infection growth is exponential, you can adjust the time it takes to get
+from one germ_level to another using the rough formula:
+
+desired_germ_level = initial_germ_level*e^(desired_time_in_seconds/1000)
+
+So if I wanted it to take an average of 15 minutes to get from level one (100) to level two
+I would set INFECTION_LEVEL_TWO to 100*e^(15*60/1000) = 245. Note that this is the average time,
+the actual time is dependent on RNG.
+
+INFECTION_LEVEL_ONE		below this germ level nothing happens, and the infection doesn't grow
+INFECTION_LEVEL_TWO		above this germ level the infection will start to spread to internal and adjacent organs
+INFECTION_LEVEL_THREE	above this germ level the player will take additional toxin damage per second, and will die in minutes without
+						antitox. also, above this germ level you will need to overdose on spaceacillin to reduce the germ_level.
+
+Note that amputating the affected organ does in fact remove the infection from the player's body.
+*/
 /datum/organ/external/proc/update_germs()
 
-	if(status & ORGAN_ROBOT|ORGAN_DESTROYED) //Robotic limbs shouldn't be infected, nor should nonexistant limbs.
+	if(status & (ORGAN_ROBOT|ORGAN_DESTROYED) || (owner.species && owner.species.flags & IS_PLANT)) //Robotic limbs shouldn't be infected, nor should nonexistant limbs.
 		germ_level = 0
 		return
 
-	if(germ_level > 0 && owner.bodytemperature >= 170)	//cryo stops germs from moving and doing their bad stuffs
-		//Syncing germ levels with external wounds
+	if(owner.bodytemperature >= 170)	//cryo stops germs from moving and doing their bad stuffs
+		//** Syncing germ levels with external wounds
+		handle_germ_sync()
+
+		//** Handle antibiotics and curing infections
+		handle_antibiotics()
+
+		//** Handle the effects of infections
+		handle_germ_effects()
+
+/datum/organ/external/proc/handle_germ_sync()
+	var/antibiotics = owner.reagents.get_reagent_amount("spaceacillin")
+	for(var/datum/wound/W in wounds)
+		//Open wounds can become infected
+		if (owner.germ_level > W.germ_level && W.infection_check())
+			W.germ_level++
+
+	if (antibiotics < 5)
 		for(var/datum/wound/W in wounds)
-			if(!W.bandaged && !W.salved)
-				W.germ_level = max(W.germ_level, germ_level)	//Wounds get all the germs
-				if (W.germ_level > germ_level)	//Badly infected wounds raise internal germ levels
-					germ_level++
+			//Infected wounds raise the organ's germ level
+			if (W.germ_level > germ_level)
+				germ_level++
+				break	//limit increase to a maximum of one per second
 
-		if(germ_level > GANGREN_LEVEL_ONE && prob(round(germ_level/100)))
-			germ_level++
-			owner.adjustToxLoss(1)
+/datum/organ/external/proc/handle_germ_effects()
+	var/antibiotics = owner.reagents.get_reagent_amount("spaceacillin")
 
-		if(germ_level > GANGREN_LEVEL_TWO)
-			germ_level++
-			owner.adjustToxLoss(1)
-/*
-		if(germ_level > GANGREN_LEVEL_TERMINAL)
-			if (!(status & ORGAN_DEAD))
-				status |= ORGAN_DEAD
-				owner << "<span class='notice'>You can't feel your [display_name] anymore...</span>"
-				owner.update_body(1)
-			if (prob(10))	//Spreading the fun
-				if (children)	//To child organs
-					for (var/datum/organ/external/child in children)
-						if (!(child.status & (ORGAN_DEAD|ORGAN_DESTROYED|ORGAN_ROBOT)))
-							child.germ_level += round(GERM_TRANSFER_AMOUNT)
-				if (parent)
-					if (!(parent.status & (ORGAN_DEAD|ORGAN_DESTROYED|ORGAN_ROBOT)))
-						parent.germ_level += round(GERM_TRANSFER_AMOUNT)
-*/
+	if (germ_level > 0 && germ_level < INFECTION_LEVEL_ONE && prob(60))	//this could be an else clause, but it looks cleaner this way
+		germ_level--	//since germ_level increases at a rate of 1 per second with dirty wounds, prob(60) should give us about 5 minutes before level one.
+
+	if(germ_level >= INFECTION_LEVEL_ONE)
+		//having an infection raises your body temperature
+		var/fever_temperature = (owner.species.heat_level_1 - owner.species.body_temperature - 5)* min(germ_level/INFECTION_LEVEL_TWO, 1) + owner.species.body_temperature
+		//need to make sure we raise temperature fast enough to get around environmental cooling preventing us from reaching fever_temperature
+		owner.bodytemperature += between(0, (fever_temperature - T20C)/BODYTEMP_COLD_DIVISOR + 1, fever_temperature - owner.bodytemperature)
+
+		if(prob(round(germ_level/10)))
+			if (antibiotics < 5)
+				germ_level++
+
+			if (prob(10))	//adjust this to tweak how fast people take toxin damage from infections
+				owner.adjustToxLoss(1)
+
+	if(germ_level >= INFECTION_LEVEL_TWO && antibiotics < 5)
+		//spread the infection to internal organs
+		var/datum/organ/internal/target_organ = null	//make internal organs become infected one at a time instead of all at once
+		for (var/datum/organ/internal/I in internal_organs)
+			if (I.germ_level > 0 && I.germ_level < min(germ_level, INFECTION_LEVEL_TWO))	//once the organ reaches whatever we can give it, or level two, switch to a different one
+				if (!target_organ || I.germ_level > target_organ.germ_level)	//choose the organ with the highest germ_level
+					target_organ = I
+
+		if (!target_organ)
+			//figure out which organs we can spread germs to and pick one at random
+			var/list/candidate_organs = list()
+			for (var/datum/organ/internal/I in internal_organs)
+				if (I.germ_level < germ_level)
+					candidate_organs += I
+			if (candidate_organs.len)
+				target_organ = pick(candidate_organs)
+
+		if (target_organ)
+			target_organ.germ_level++
+
+		//spread the infection to child and parent organs
+		if (children)
+			for (var/datum/organ/external/child in children)
+				if (child.germ_level < germ_level && !(child.status & ORGAN_ROBOT))
+					if (child.germ_level < INFECTION_LEVEL_ONE*2 || prob(30))
+						child.germ_level++
+
+		if (parent)
+			if (parent.germ_level < germ_level && !(parent.status & ORGAN_ROBOT))
+				if (parent.germ_level < INFECTION_LEVEL_ONE*2 || prob(30))
+					parent.germ_level++
+
+	if(germ_level >= INFECTION_LEVEL_THREE && antibiotics < 30)	//overdosing is necessary to stop severe infections
+		if (!(status & ORGAN_DEAD))
+			status |= ORGAN_DEAD
+			owner << "<span class='notice'>You can't feel your [display_name] anymore...</span>"
+			owner.update_body(1)
+
+		germ_level++
+		owner.adjustToxLoss(1)
 
 //Updating wounds. Handles wound natural I had some free spachealing, internal bleedings and infections
 /datum/organ/external/proc/update_wounds()
@@ -401,16 +445,15 @@ This function completely restores a damaged organ to perfect condition.
 			// let the GC handle the deletion of the wound
 
 		// Internal wounds get worse over time. Low temperatures (cryo) stop them.
-		if(W.internal && !W.is_treated() && owner.bodytemperature >= 170)
+		if(W.internal && owner.bodytemperature >= 170)
 			var/bicardose = owner.reagents.get_reagent_amount("bicaridine")
 			var/inaprovaline = owner.reagents.get_reagent_amount("inaprovaline")
-			if(!bicardose || !inaprovaline)	//bicaridine and inaprovaline stop internal wounds from growing bigger with time, and also stop bleeding
+			if(!(W.can_autoheal() || (bicardose && inaprovaline)))	//bicaridine and inaprovaline stop internal wounds from growing bigger with time, unless it is so small that it is already healing
 				W.open_wound(0.1 * wound_update_accuracy)
-				owner.vessel.remove_reagent("blood",0.05 * W.damage * wound_update_accuracy)
 			if(bicardose >= 30)	//overdose of bicaridine begins healing IB
 				W.damage = max(0, W.damage - 0.2)
 
-			owner.vessel.remove_reagent("blood",0.02 * W.damage * wound_update_accuracy)
+			owner.vessel.remove_reagent("blood", wound_update_accuracy * W.damage/40) //line should possibly be moved to handle_blood, so all the bleeding stuff is in one place.
 			if(prob(1 * wound_update_accuracy))
 				owner.custom_pain("You feel a stabbing pain in your [display_name]!",1)
 
@@ -418,7 +461,7 @@ This function completely restores a damaged organ to perfect condition.
 		var/heal_amt = 0
 
 		// if damage >= 50 AFTER treatment then it's probably too severe to heal within the timeframe of a round.
-		if (W.is_treated() && W.wound_damage() < 50)
+		if (W.can_autoheal() && W.wound_damage() < 50)
 			heal_amt += 0.5
 
 		//we only update wounds once in [wound_update_accuracy] ticks so have to emulate realtime
@@ -433,8 +476,8 @@ This function completely restores a damaged organ to perfect condition.
 
 		// Salving also helps against infection
 		if(W.germ_level > 0 && W.salved && prob(2))
-			W.germ_level = 0
 			W.disinfected = 1
+			W.germ_level = 0
 
 	// sync the organ's damage with its wounds
 	src.update_damages()
@@ -525,13 +568,27 @@ This function completely restores a damaged organ to perfect condition.
 		src.status &= ~ORGAN_BROKEN
 		src.status &= ~ORGAN_BLEEDING
 		src.status &= ~ORGAN_SPLINTED
+		src.status &= ~ORGAN_DEAD
 		for(var/implant in implants)
 			del(implant)
 
+		germ_level = 0
+
+		//Replace all wounds on that arm with one wound on parent organ.
+		wounds.Cut()
+		if (parent)
+			var/datum/wound/W
+			if(max_damage < 50)
+				W = new/datum/wound/lost_limb/small(max_damage)
+			else
+				W = new/datum/wound/lost_limb(max_damage)
+			parent.wounds += W
+			parent.update_damages()
+		update_damages()
+
 		// If any organs are attached to this, destroy them
-		for(var/datum/organ/external/O in owner.organs)
-			if(O.parent == src)
-				O.droplimb(1)
+		for(var/datum/organ/external/O in children)
+			O.droplimb(1)
 
 		var/obj/organ	//Dropped limb object
 		switch(body_part)
@@ -581,33 +638,37 @@ This function completely restores a damaged organ to perfect condition.
 				if(!(status & ORGAN_ROBOT))
 					organ = new /obj/item/weapon/organ/l_foot(owner.loc, owner)
 				owner.u_equip(owner.shoes)
+
+		destspawn = 1
+		//Robotic limbs explode if sabotaged.
+		if(status & ORGAN_ROBOT && !no_explode && sabotaged)
+			owner.visible_message("\red \The [owner]'s [display_name] explodes violently!",\
+			"\red <b>Your [display_name] explodes!</b>",\
+			"You hear an explosion followed by a scream!")
+			explosion(get_turf(owner),-1,-1,2,3)
+			var/datum/effect/effect/system/spark_spread/spark_system = new /datum/effect/effect/system/spark_spread()
+			spark_system.set_up(5, 0, owner)
+			spark_system.attach(owner)
+			spark_system.start()
+			spawn(10)
+				del(spark_system)
+
+		owner.visible_message("\red [owner.name]'s [display_name] flies off in an arc.",\
+		"<span class='moderate'><b>Your [display_name] goes flying off!</b></span>",\
+		"You hear a terrible sound of ripping tendons and flesh.")
+
 		if(organ)
-			destspawn = 1
-			//Robotic limbs explode if sabotaged.
-			if(status & ORGAN_ROBOT && !no_explode && sabotaged)
-				owner.visible_message("\red \The [owner]'s [display_name] explodes violently!",\
-				"\red <b>Your [display_name] explodes!</b>",\
-				"You hear an explosion followed by a scream!")
-				explosion(get_turf(owner),-1,-1,2,3)
-				var/datum/effect/effect/system/spark_spread/spark_system = new /datum/effect/effect/system/spark_spread()
-				spark_system.set_up(5, 0, owner)
-				spark_system.attach(owner)
-				spark_system.start()
-				spawn(10)
-					del(spark_system)
-
-			owner.visible_message("\red [owner.name]'s [display_name] flies off in an arc.",\
-			"<span class='moderate'><b>Your [display_name] goes flying off!</b></span>",\
-			"You hear a terrible sound of ripping tendons and flesh.")
-
 			//Throw organs around
 			var/lol = pick(cardinal)
 			step(organ,lol)
 
-			owner.update_body(1)
+		owner.update_body(1)
 
-			// OK so maybe your limb just flew off, but if it was attached to a pair of cuffs then hooray! Freedom!
-			release_restraints()
+		// OK so maybe your limb just flew off, but if it was attached to a pair of cuffs then hooray! Freedom!
+		release_restraints()
+
+		if(vital)
+			owner.death()
 
 /****************************************************
 			   HELPERS
@@ -637,6 +698,15 @@ This function completely restores a damaged organ to perfect condition.
 		W.bandaged = 1
 	return rval
 
+/datum/organ/external/proc/disinfect()
+	var/rval = 0
+	for(var/datum/wound/W in wounds)
+		if(W.internal) continue
+		rval |= !W.disinfected
+		W.disinfected = 1
+		W.germ_level = 0
+	return rval
+
 /datum/organ/external/proc/clamp()
 	var/rval = 0
 	src.status &= ~ORGAN_BLEEDING
@@ -654,8 +724,10 @@ This function completely restores a damaged organ to perfect condition.
 	return rval
 
 /datum/organ/external/proc/fracture()
+
 	if(status & ORGAN_BROKEN)
 		return
+
 	owner.visible_message(\
 		"\red You hear a loud cracking sound coming from \the [owner].",\
 		"\red <b>Something feels like it shattered in your [display_name]!</b>",\
@@ -672,6 +744,25 @@ This function completely restores a damaged organ to perfect condition.
 	if (prob(25))
 		release_restraints()
 
+	// This is mostly for the ninja suit to stop ninja being so crippled by breaks.
+	// TODO: consider moving this to a suit proc or process() or something during
+	// hardsuit rewrite.
+	if(!(status & ORGAN_SPLINTED) && istype(owner,/mob/living/carbon/human))
+
+		var/mob/living/carbon/human/H = owner
+
+		if(H.wear_suit && istype(H.wear_suit,/obj/item/clothing/suit/space))
+
+			var/obj/item/clothing/suit/space/suit = H.wear_suit
+
+			if(isnull(suit.supporting_limbs))
+				return
+
+			owner << "You feel \the [suit] constrict about your [display_name], supporting it."
+			status |= ORGAN_SPLINTED
+			suit.supporting_limbs |= src
+	return
+
 /datum/organ/external/proc/robotize()
 	src.status &= ~ORGAN_BROKEN
 	src.status &= ~ORGAN_BLEEDING
@@ -696,9 +787,9 @@ This function completely restores a damaged organ to perfect condition.
 /datum/organ/external/proc/get_damage()	//returns total damage
 	return max(brute_dam + burn_dam - perma_injury, perma_injury)	//could use health?
 
-/datum/organ/external/proc/is_infected()
+/datum/organ/external/proc/has_infected_wound()
 	for(var/datum/wound/W in wounds)
-		if(W.germ_level > 100)
+		if(W.germ_level > INFECTION_LEVEL_ONE)
 			return 1
 	return 0
 
@@ -715,6 +806,43 @@ This function completely restores a damaged organ to perfect condition.
 /datum/organ/external/proc/is_usable()
 	return !(status & (ORGAN_DESTROYED|ORGAN_MUTATED|ORGAN_DEAD))
 
+/datum/organ/external/proc/is_broken()
+	return ((status & ORGAN_BROKEN) && !(status & ORGAN_SPLINTED))
+
+/datum/organ/external/proc/is_malfunctioning()
+	return ((status & ORGAN_ROBOT) && prob(brute_dam + burn_dam))
+
+//for arms and hands
+/datum/organ/external/proc/process_grasp(var/obj/item/c_hand, var/hand_name)
+	if (!c_hand)
+		return
+
+	if(is_broken())
+		owner.u_equip(c_hand)
+		var/emote_scream = pick("screams in pain and", "lets out a sharp cry and", "cries out and")
+		owner.emote("me", 1, "[(owner.species && owner.species.flags & NO_PAIN) ? "" : emote_scream ] drops what they were holding in their [hand_name]!")
+	if(is_malfunctioning())
+		owner.u_equip(c_hand)
+		owner.emote("me", 1, "drops what they were holding, their [hand_name] malfunctioning!")
+		var/datum/effect/effect/system/spark_spread/spark_system = new /datum/effect/effect/system/spark_spread()
+		spark_system.set_up(5, 0, owner)
+		spark_system.attach(owner)
+		spark_system.start()
+		spawn(10)
+			del(spark_system)
+
+/datum/organ/external/proc/embed(var/obj/item/weapon/W, var/silent = 0)
+	if(!silent)
+		owner.visible_message("<span class='danger'>\The [W] sticks in the wound!</span>")
+	implants += W
+	owner.embedded_flag = 1
+	owner.verbs += /mob/proc/yank_out_object
+	W.add_blood(owner)
+	if(ismob(W.loc))
+		var/mob/living/H = W.loc
+		H.drop_item()
+	W.loc = owner
+
 /****************************************************
 			   ORGAN DEFINES
 ****************************************************/
@@ -726,7 +854,7 @@ This function completely restores a damaged organ to perfect condition.
 	max_damage = 75
 	min_broken_damage = 40
 	body_part = UPPER_TORSO
-
+	vital = 1
 
 /datum/organ/external/groin
 	name = "groin"
@@ -735,6 +863,7 @@ This function completely restores a damaged organ to perfect condition.
 	max_damage = 50
 	min_broken_damage = 30
 	body_part = LOWER_TORSO
+	vital = 1
 
 /datum/organ/external/l_arm
 	name = "l_arm"
@@ -744,6 +873,10 @@ This function completely restores a damaged organ to perfect condition.
 	min_broken_damage = 20
 	body_part = ARM_LEFT
 
+	process()
+		..()
+		process_grasp(owner.l_hand, "left hand")
+
 /datum/organ/external/l_leg
 	name = "l_leg"
 	display_name = "left leg"
@@ -761,6 +894,10 @@ This function completely restores a damaged organ to perfect condition.
 	min_broken_damage = 20
 	body_part = ARM_RIGHT
 
+	process()
+		..()
+		process_grasp(owner.r_hand, "right hand")
+
 /datum/organ/external/r_leg
 	name = "r_leg"
 	display_name = "right leg"
@@ -796,6 +933,10 @@ This function completely restores a damaged organ to perfect condition.
 	min_broken_damage = 15
 	body_part = HAND_RIGHT
 
+	process()
+		..()
+		process_grasp(owner.r_hand, "right hand")
+
 /datum/organ/external/l_hand
 	name = "l_hand"
 	display_name = "left hand"
@@ -804,6 +945,10 @@ This function completely restores a damaged organ to perfect condition.
 	min_broken_damage = 15
 	body_part = HAND_LEFT
 
+	process()
+		..()
+		process_grasp(owner.l_hand, "left hand")
+
 /datum/organ/external/head
 	name = "head"
 	icon_name = "head"
@@ -812,6 +957,7 @@ This function completely restores a damaged organ to perfect condition.
 	min_broken_damage = 40
 	body_part = HEAD
 	var/disfigured = 0
+	vital = 1
 
 /datum/organ/external/head/get_icon(var/icon/race_icon, var/icon/deform_icon)
 	if (!owner)

code/modules/organs/organ_internal.dm

@@ -21,15 +21,47 @@
 	return damage >= min_broken_damage
 
 
+
 /datum/organ/internal/New(mob/living/carbon/human/H)
 	..()
 	var/datum/organ/external/E = H.organs_by_name[src.parent_organ]
 	if(E.internal_organs == null)
 		E.internal_organs = list()
-	E.internal_organs += src
-	H.internal_organs[src.name] = src
+	E.internal_organs |= src
+	H.internal_organs |= src
 	src.owner = H
 
+/datum/organ/internal/process()
+	//Process infections
+
+	if (robotic >= 2 || (owner.species && owner.species.flags & IS_PLANT))	//TODO make robotic internal and external organs separate types of organ instead of a flag
+		germ_level = 0
+		return
+
+	if(owner.bodytemperature >= 170)	//cryo stops germs from moving and doing their bad stuffs
+		//** Handle antibiotics and curing infections
+		handle_antibiotics()
+
+		//** Handle the effects of infections
+		var/antibiotics = owner.reagents.get_reagent_amount("spaceacillin")
+		
+		if (germ_level > 0 && germ_level < INFECTION_LEVEL_ONE/2 && prob(30))
+			germ_level--
+		
+		if (germ_level >= INFECTION_LEVEL_ONE/2)
+			//aiming for germ level to go from ambient to INFECTION_LEVEL_TWO in an average of 15 minutes
+			if(antibiotics < 5 && prob(round(germ_level/6)))
+				germ_level++
+
+		if (germ_level >= INFECTION_LEVEL_TWO)
+			var/datum/organ/external/parent = owner.get_organ(parent_organ)
+			//spread germs
+			if (antibiotics < 5 && parent.germ_level < germ_level && ( parent.germ_level < INFECTION_LEVEL_ONE*2 || prob(30) ))
+				parent.germ_level++
+			
+			if (prob(3))	//about once every 30 seconds
+				take_damage(1,silent=prob(30))
+
 /datum/organ/internal/proc/take_damage(amount, var/silent=0)
 	if(src.robotic == 2)
 		src.damage += (amount * 0.8)
@@ -40,7 +72,6 @@
 	if (!silent)
 		owner.custom_pain("Something inside your [parent.display_name] hurts a lot.", 1)
 
-
 /datum/organ/internal/proc/emp_act(severity)
 	switch(robotic)
 		if(0)
@@ -90,13 +121,18 @@
 	parent_organ = "chest"
 
 	process()
+		..()
+		if (germ_level > INFECTION_LEVEL_ONE)
+			if(prob(5))
+				owner.emote("cough")		//respitory tract infection
+		
 		if(is_bruised())
 			if(prob(2))
 				spawn owner.emote("me", 1, "coughs up blood!")
 				owner.drip(10)
 			if(prob(4))
 				spawn owner.emote("me", 1, "gasps for air!")
-				owner.losebreath += 5
+				owner.losebreath += 15
 
 /datum/organ/internal/liver
 	name = "liver"
@@ -104,6 +140,14 @@
 	var/process_accuracy = 10
 
 	process()
+		..()
+		if (germ_level > INFECTION_LEVEL_ONE)
+			if(prob(1))
+				owner << "\red Your skin itches."
+		if (germ_level > INFECTION_LEVEL_TWO)
+			if(prob(1))
+				spawn owner.vomit()
+		
 		if(owner.life_tick % process_accuracy == 0)
 			if(src.damage < 0)
 				src.damage = 0
@@ -115,9 +159,9 @@
 					src.damage += 0.2 * process_accuracy
 				//Damaged one shares the fun
 				else
-					var/victim = pick(owner.internal_organs)
-					var/datum/organ/internal/O = owner.internal_organs[victim]
-					O.damage += 0.2  * process_accuracy
+					var/datum/organ/internal/O = pick(owner.internal_organs)
+					if(O)
+						O.damage += 0.2  * process_accuracy
 
 			//Detox can heal small amounts of damage
 			if (src.damage && src.damage < src.min_bruised_damage && owner.reagents.has_reagent("anti_toxin"))
@@ -146,6 +190,7 @@
 	parent_organ = "head"
 
 	process() //Eye damage replaces the old eye_stat var.
+		..()
 		if(is_bruised())
 			owner.eye_blurry = 20
 		if(is_broken())

code/modules/organs/pain.dm

@@ -102,8 +102,7 @@ mob/living/carbon/human/proc/handle_pain()
 		pain(damaged_organ.display_name, maxdam, 0)
 
 	// Damage to internal organs hurts a lot.
-	for(var/organ_name in internal_organs)
-		var/datum/organ/internal/I = internal_organs[organ_name]
+	for(var/datum/organ/internal/I in internal_organs)
 		if(I.damage > 2) if(prob(2))
 			var/datum/organ/external/parent = get_organ(I.parent_organ)
 			src.custom_pain("You feel a sharp pain in your [parent.display_name]", 1)

code/modules/organs/wound.dm

@@ -7,7 +7,7 @@
 	var/current_stage = 0
 
 	// description of the wound
-	var/desc = ""
+	var/desc = "wound" //default in case something borks
 
 	// amount of damage this wound causes
 	var/damage = 0
@@ -31,7 +31,7 @@
 	var/germ_level = 0
 
 	/*  These are defined by the wound type and should not be changed */
-	
+
 	// stages such as "cut", "deep cut", etc.
 	var/list/stages
 	// internal wounds can only be fixed through surgery
@@ -51,7 +51,7 @@
 	// helper lists
 	var/tmp/list/desc_list = list()
 	var/tmp/list/damage_list = list()
-	
+
 	New(var/damage)
 
 		created = world.time
@@ -65,7 +65,7 @@
 		src.damage = damage
 
 		max_bleeding_stage = src.desc_list.len - max_bleeding_stage
-		
+
 		// initialize with the appropriate stage
 		src.init_stage(damage)
 
@@ -74,7 +74,7 @@
 	// returns 1 if there's a next stage, 0 otherwise
 	proc/init_stage(var/initial_damage)
 		current_stage = stages.len
-		
+
 		while(src.current_stage > 1 && src.damage_list[current_stage-1] <= initial_damage / src.amount)
 			src.current_stage--
 
@@ -84,25 +84,26 @@
 	// the amount of damage per wound
 	proc/wound_damage()
 		return src.damage / src.amount
-	
-	// checks whether the wound has been appropriately treated
-	// always returns 1 for wounds that are too minor to need treatment
-	proc/is_treated()
+
+	proc/can_autoheal()
 		if(src.wound_damage() <= autoheal_cutoff)
 			return 1
 
+		return is_treated()
+
+	// checks whether the wound has been appropriately treated
+	proc/is_treated()
 		if(damage_type == BRUISE || damage_type == CUT)
 			return bandaged
 		else if(damage_type == BURN)
 			return salved
-	
-	
+
 	// Checks whether other other can be merged into src.
 	proc/can_merge(var/datum/wound/other)
 		if (other.type != src.type) return 0
 		if (other.current_stage != src.current_stage) return 0
 		if (other.damage_type != src.damage_type) return 0
-		if (!(other.is_treated()) != !(src.is_treated())) return 0
+		if (!(other.can_autoheal()) != !(src.can_autoheal())) return 0
 		if (!(other.bandaged) != !(src.bandaged)) return 0
 		if (!(other.clamped) != !(src.clamped)) return 0
 		if (!(other.salved) != !(src.salved)) return 0
@@ -119,21 +120,29 @@
 
 	// checks if wound is considered open for external infections
 	// untreated cuts (and bleeding bruises) and burns are possibly infectable, chance higher if wound is bigger
-	proc/can_infect()
-		if (is_treated() && damage < 10)
+	proc/infection_check()
+		if (damage < 10)	//small cuts, tiny bruises, and moderate burns shouldn't be infectable.
+			return 0
+		if (is_treated() && damage < 25)	//anything less than a flesh wound (or equivalent) isn't infectable if treated properly
 			return 0
 		if (disinfected)
+			germ_level = 0	//reset this, just in case
 			return 0
+
+		if (damage_type == BRUISE && !bleeding()) //bruises only infectable if bleeding
+			return 0
+
 		var/dam_coef = round(damage/10)
 		switch (damage_type)
 			if (BRUISE)
-				return prob(dam_coef*5) && bleeding() //bruises only infectable if bleeding
+				return prob(dam_coef*5)
 			if (BURN)
 				return prob(dam_coef*10)
 			if (CUT)
 				return prob(dam_coef*20)
 
 		return 0
+
 	// heal the given amount of damage, and if the given amount of damage was more
 	// than what needed to be healed, return how much heal was left
 	// set @heals_internal to also heal internal organ damage
@@ -170,23 +179,71 @@
 	proc/can_worsen(damage_type, damage)
 		if (src.damage_type != damage_type)
 			return 0	//incompatible damage types
-		
+
 		if (src.amount > 1)
 			return 0
-		
+
 		//with 1.5*, a shallow cut will be able to carry at most 30 damage,
 		//37.5 for a deep cut
 		//52.5 for a flesh wound, etc.
 		var/max_wound_damage = 1.5*src.damage_list[1]
 		if (src.damage + damage > max_wound_damage)
 			return 0
-		
+
 		return 1
 
-	
 	proc/bleeding()
-		// internal wounds don't bleed in the sense of this function
-		return ((wound_damage() > 30 || bleed_timer > 0) && !(bandaged||clamped) && (damage_type == BRUISE && wound_damage() >= 20 || damage_type == CUT && wound_damage() >= 5) && current_stage <= max_bleeding_stage && !src.internal)
+		if (src.internal)
+			return 0	// internal wounds don't bleed in the sense of this function
+
+		if (current_stage > max_bleeding_stage)
+			return 0
+
+		if (bandaged||clamped)
+			return 0
+
+		if (wound_damage() <= 30 && bleed_timer <= 0)
+			return 0	//Bleed timer has run out. Wounds with more than 30 damage don't stop bleeding on their own.
+
+		return (damage_type == BRUISE && wound_damage() >= 20 || damage_type == CUT && wound_damage() >= 5)
+
+/** WOUND DEFINITIONS **/
+
+//Note that the MINIMUM damage before a wound can be applied should correspond to 
+//the damage amount for the stage with the same name as the wound.
+//e.g. /datum/wound/cut/deep should only be applied for 15 damage and up, 
+//because in it's stages list, "deep cut" = 15.
+/proc/get_wound_type(var/type = CUT, var/damage)
+	switch(type)
+		if(CUT)
+			switch(damage)
+				if(70 to INFINITY)
+					return /datum/wound/cut/massive
+				if(60 to 70)
+					return /datum/wound/cut/gaping_big
+				if(50 to 60)
+					return /datum/wound/cut/gaping
+				if(25 to 50)
+					return /datum/wound/cut/flesh
+				if(15 to 25)
+					return /datum/wound/cut/deep
+				if(0 to 15)
+					return /datum/wound/cut/small
+		if(BRUISE)
+			return /datum/wound/bruise
+		if(BURN)
+			switch(damage)
+				if(50 to INFINITY)
+					return /datum/wound/burn/carbonised
+				if(40 to 50)
+					return /datum/wound/burn/deep
+				if(30 to 40)
+					return /datum/wound/burn/severe
+				if(15 to 30)
+					return /datum/wound/burn/large
+				if(0 to 15)
+					return /datum/wound/burn/moderate
+	return null //no wound
 
 /** CUTS **/
 /datum/wound/cut/small
@@ -201,7 +258,7 @@
 	damage_type = CUT
 
 /datum/wound/cut/flesh
-	max_bleeding_stage = 3
+	max_bleeding_stage = 4
 	stages = list("ugly ripped flesh wound" = 35, "ugly flesh wound" = 30, "flesh wound" = 25, "blood soaked clot" = 15, "large scab" = 5, "fresh skin" = 0)
 	damage_type = CUT
 
@@ -230,27 +287,40 @@ datum/wound/cut/massive
 
 /** BURNS **/
 /datum/wound/burn/moderate
-	stages = list("ripped burn" = 10, "moderate burn" = 5, "moderate salved burn" = 2, "fresh skin" = 0)
+	stages = list("ripped burn" = 10, "moderate burn" = 5, "healing moderate burn" = 2, "fresh skin" = 0)
 	damage_type = BURN
 
 /datum/wound/burn/large
-	stages = list("ripped large burn" = 20, "large burn" = 15, "large salved burn" = 5, "fresh skin" = 0)
+	stages = list("ripped large burn" = 20, "large burn" = 15, "healing large burn" = 5, "fresh skin" = 0)
 	damage_type = BURN
 
 /datum/wound/burn/severe
-	stages = list("ripped severe burn" = 35, "severe burn" = 30, "severe salved burn" = 10, "burn scar" = 0)
+	stages = list("ripped severe burn" = 35, "severe burn" = 30, "healing severe burn" = 10, "burn scar" = 0)
 	damage_type = BURN
 
 /datum/wound/burn/deep
-	stages = list("ripped deep burn" = 45, "deep burn" = 40, "deep salved burn" = 15,  "large burn scar" = 0)
+	stages = list("ripped deep burn" = 45, "deep burn" = 40, "healing deep burn" = 15,  "large burn scar" = 0)
 	damage_type = BURN
 
 /datum/wound/burn/carbonised
-	stages = list("carbonised area" = 50, "treated carbonised area" = 20, "massive burn scar" = 0)
+	stages = list("carbonised area" = 50, "healing carbonised area" = 20, "massive burn scar" = 0)
 	damage_type = BURN
 
+/** INTERNAL BLEEDING **/
 /datum/wound/internal_bleeding
 	internal = 1
-	stages = list("severed vein" = 30, "cut vein" = 20, "damaged vein" = 10, "bruised vein" = 5)
+	stages = list("severed artery" = 30, "cut artery" = 20, "damaged artery" = 10, "bruised artery" = 5)
 	autoheal_cutoff = 5
 	max_bleeding_stage = 0	//all stages bleed. It's called internal bleeding after all.
+
+/** EXTERNAL ORGAN LOSS **/
+/datum/wound/lost_limb
+    damage_type = CUT
+    stages = list("ripped stump" = 65, "bloody stump" = 50, "clotted stump" = 25, "scarred stump" = 0)
+    max_bleeding_stage = 3
+
+    can_merge(var/datum/wound/other)
+        return 0 //cannot be merged
+
+/datum/wound/lost_limb/small
+    stages = list("ripped stump" = 40, "bloody stump" = 30, "clotted stump" = 15, "scarred stump" = 0)