Implement SSatoms

* Moves proc/initialize() from being on /atom/movable, /are and /turf/simulated to being on /atom - Now turfs can initialize too
* Added the SSatoms subsystem which controls initialization of atoms at roundstart and during normal conditions.
* Disabled the old auto_init = 0 behavior, ALL atoms should get initialized() called on them now.
* Refactored the way initialize() is called during /New() to utilize SSatoms instead of SScreation
* Removed SScreation, as it was only a stop-gap until SSatoms could be ported.
* Updated the maploader to inform SSatoms when it is loading maps instead of SScreation.
* Updated the template map loader to use SSatoms to perform initTemplateBounds
* Renamed 'initialized' var in seed_storage to deconflict.
* Removed usage of auto_init = 0, replaced with a no-op initialize() proc for atoms that don't need initialization.

code/controllers/master_controller.dm

@@ -36,7 +36,7 @@ datum/controller/game_controller/New()
 datum/controller/game_controller/proc/setup()
 
 	setup_objects()
-	setupgenetics()
+	// setupgenetics() Moved to SSatoms
 	SetupXenoarch()
 
 	transfer_controller = new
@@ -59,6 +59,7 @@ datum/controller/game_controller/proc/setup_objects()
 	//Set up spawn points.
 	populate_spawn_points()
 
+/*
 	admin_notice("<span class='danger'>Initializing Floor Decals</span>", R_DEBUG)
 	var/list/turfs_with_decals = list()
 	for(var/obj/effect/floor_decal/D in world)
@@ -111,3 +112,4 @@ datum/controller/game_controller/proc/setup_objects()
 		if(!QDELETED(lift))
 			lift.initialize()
 			CHECK_SLEEP_MASTER
+	*/

code/controllers/subsystems/atoms.dm

@@ -0,0 +1,145 @@
+#define BAD_INIT_QDEL_BEFORE 1
+#define BAD_INIT_DIDNT_INIT 2
+#define BAD_INIT_SLEPT 4
+#define BAD_INIT_NO_HINT 8
+
+SUBSYSTEM_DEF(atoms)
+	name = "Atoms"
+	init_order = INIT_ORDER_ATOMS
+	flags = SS_NO_FIRE
+
+	var/initialized = INITIALIZATION_INSSATOMS
+	// var/list/created_atoms // This is never used, so don't bother. ~Leshana
+	var/old_initialized
+
+	var/list/late_loaders
+	var/list/created_atoms
+
+	var/list/BadInitializeCalls = list()
+
+/datum/controller/subsystem/atoms/Initialize(timeofday)
+	setupgenetics() //to set the mutations' place in structural enzymes, so initializers know where to put mutations.
+	initialized = INITIALIZATION_INNEW_MAPLOAD
+	to_world_log("Initializing objects")
+	admin_notice("<span class='danger'>Initializing objects</span>", R_DEBUG)
+	InitializeAtoms()
+	return ..()
+
+/datum/controller/subsystem/atoms/proc/InitializeAtoms(list/atoms)
+	if(initialized == INITIALIZATION_INSSATOMS)
+		return
+
+	initialized = INITIALIZATION_INNEW_MAPLOAD
+
+	LAZYINITLIST(late_loaders)
+
+	var/count
+	var/list/mapload_arg = list(TRUE)
+	if(atoms)
+		created_atoms = list()
+		count = atoms.len
+		for(var/I in atoms)
+			var/atom/A = I
+			if(!A.initialized)
+				if(InitAtom(I, mapload_arg))
+					atoms -= I
+				CHECK_TICK
+	else
+		count = 0
+		for(var/atom/A in world)
+			if(!A.initialized)
+				InitAtom(A, mapload_arg)
+				++count
+				CHECK_TICK
+
+	log_world("Initialized [count] atoms")
+
+	initialized = INITIALIZATION_INNEW_REGULAR
+
+	if(late_loaders.len)
+		for(var/I in late_loaders)
+			var/atom/A = I
+			A.LateInitialize()
+			CHECK_TICK
+		testing("Late initialized [late_loaders.len] atoms")
+		late_loaders.Cut()
+
+	// Nothing ever checks return value of this proc, so don't bother.  If this ever changes fix code in /atom/New() ~Leshana
+	// if(atoms)
+	// 	. = created_atoms + atoms
+	// 	created_atoms = null
+
+/datum/controller/subsystem/atoms/proc/InitAtom(atom/A, list/arguments)
+	var/the_type = A.type
+	if(QDELING(A))
+		BadInitializeCalls[the_type] |= BAD_INIT_QDEL_BEFORE
+		return TRUE
+
+	var/start_tick = world.time
+
+	var/result = A.initialize(arglist(arguments))
+
+	if(start_tick != world.time)
+		BadInitializeCalls[the_type] |= BAD_INIT_SLEPT
+
+	var/qdeleted = FALSE
+
+	if(result != INITIALIZE_HINT_NORMAL)
+		switch(result)
+			if(INITIALIZE_HINT_LATELOAD)
+				if(arguments[1])	//mapload
+					late_loaders += A
+				else
+					A.LateInitialize()
+			if(INITIALIZE_HINT_QDEL)
+				qdel(A)
+				qdeleted = TRUE
+			else
+				BadInitializeCalls[the_type] |= BAD_INIT_NO_HINT
+
+	if(!A)	//possible harddel
+		qdeleted = TRUE
+	else if(!A.initialized)
+		BadInitializeCalls[the_type] |= BAD_INIT_DIDNT_INIT
+
+	return qdeleted || QDELING(A)
+
+/datum/controller/subsystem/atoms/proc/map_loader_begin()
+	old_initialized = initialized
+	initialized = INITIALIZATION_INSSATOMS
+
+/datum/controller/subsystem/atoms/proc/map_loader_stop()
+	initialized = old_initialized
+
+/datum/controller/subsystem/atoms/Recover()
+	initialized = SSatoms.initialized
+	if(initialized == INITIALIZATION_INNEW_MAPLOAD)
+		InitializeAtoms()
+	old_initialized = SSatoms.old_initialized
+	BadInitializeCalls = SSatoms.BadInitializeCalls
+
+/datum/controller/subsystem/atoms/proc/InitLog()
+	. = ""
+	for(var/path in BadInitializeCalls)
+		. += "Path : [path] \n"
+		var/fails = BadInitializeCalls[path]
+		if(fails & BAD_INIT_DIDNT_INIT)
+			. += "- Didn't call atom/Initialize()\n"
+		if(fails & BAD_INIT_NO_HINT)
+			. += "- Didn't return an Initialize hint\n"
+		if(fails & BAD_INIT_QDEL_BEFORE)
+			. += "- Qdel'd in New()\n"
+		if(fails & BAD_INIT_SLEPT)
+			. += "- Slept during Initialize()\n"
+
+/datum/controller/subsystem/atoms/Shutdown()
+	var/initlog = InitLog()
+	if(initlog)
+		//text2file(initlog, "[GLOB.log_directory]/initialize.log")
+		var/date_string = time2text(world.realtime, "YYYY/MM-Month/DD-Day")
+		text2file(initlog, "data/logs/[date_string]-initialize.log")
+
+#undef BAD_INIT_QDEL_BEFORE
+#undef BAD_INIT_DIDNT_INIT
+#undef BAD_INIT_SLEPT
+#undef BAD_INIT_NO_HINT

code/controllers/subsystems/floor_decals.dm

@@ -0,0 +1,28 @@
+//
+// Floor Decals Initialization Subsystem
+// This is part of the giant decal hack that works around a BYOND bug where DreamDaemon will crash if you
+// update overlays on turfs too much.
+// The master_controller on Polaris used to init decals prior to initializing areas (which initilized turfs)
+// Now that we switched to subsystems we still want to do the same thing, so this takes care of it.
+//
+SUBSYSTEM_DEF(floor_decals)
+	name = "Floor Decals"
+	init_order = INIT_ORDER_DECALS
+	flags = SS_NO_FIRE
+
+/datum/controller/subsystem/floor_decals/Initialize(timeofday)
+	if(floor_decals_initialized)
+		return ..()
+	to_world_log("Initializing Floor Decals")
+	admin_notice("<span class='danger'>Initializing Floor Decals</span>", R_DEBUG)
+	var/list/turfs_with_decals = list()
+	for(var/obj/effect/floor_decal/D in world)
+		var/T = D.add_to_turf_decals()
+		if(T) turfs_with_decals |= T
+		CHECK_TICK
+	for(var/item in turfs_with_decals)
+		var/turf/T = item
+		if(T.decals) T.apply_decals()
+		CHECK_TICK
+	floor_decals_initialized = TRUE
+	return ..()

code/controllers/subsystems/machines.dm

@@ -33,8 +33,9 @@ SUBSYSTEM_DEF(machines)
 	var/list/current_run = list()
 
 /datum/controller/subsystem/machines/Initialize(timeofday)
-	SSmachines.makepowernets()
-	// TODO - Move world-creation time setup of atmos machinery and pipenets to here
+	makepowernets()
+	admin_notice("<span class='danger'>Initializing atmos machinery.</span>", R_DEBUG)
+	setup_atmos_machinery(global.machines)
 	fire()
 	..()
 
@@ -53,13 +54,33 @@ SUBSYSTEM_DEF(machines)
 	for(var/datum/powernet/PN in powernets)
 		qdel(PN)
 	powernets.Cut()
+	setup_powernets_for_cables(cable_list)
 
-	for(var/obj/structure/cable/PC in cable_list)
+/datum/controller/subsystem/machines/proc/setup_powernets_for_cables(list/cables)
+	for(var/obj/structure/cable/PC in cables)
 		if(!PC.powernet)
 			var/datum/powernet/NewPN = new()
 			NewPN.add_cable(PC)
 			propagate_network(PC,PC.powernet)
 
+/datum/controller/subsystem/machines/proc/setup_atmos_machinery(list/atmos_machines)
+	for(var/obj/machinery/atmospherics/machine in atmos_machines)
+		machine.atmos_init()
+		CHECK_TICK
+
+	for(var/obj/machinery/atmospherics/machine in atmos_machines)
+		machine.build_network()
+		CHECK_TICK
+
+	for(var/obj/machinery/atmospherics/unary/U in atmos_machines)
+		if(istype(U, /obj/machinery/atmospherics/unary/vent_pump))
+			var/obj/machinery/atmospherics/unary/vent_pump/T = U
+			T.broadcast_status()
+		else if(istype(U, /obj/machinery/atmospherics/unary/vent_scrubber))
+			var/obj/machinery/atmospherics/unary/vent_scrubber/T = U
+			T.broadcast_status()
+		CHECK_TICK
+
 /datum/controller/subsystem/machines/stat_entry()
 	var/msg = list()
 	msg += "C:{"