/atom New() => Initialize() [MDB IGNORE] (#8298)

* Find and replace argless atom New() to Initialize().

* Manual replacement of no-arg New() to Initialize().

* Manually replacing remaining New() overrides.

* Fixing linter issues with now-removed New() args.

* Tidying area init overrides.

* Porting Neb's atom subsystem.

* Trying to isolate init problems.

* Adjusting Init code post-test.

* Merging duplicate Initialize() procs.

* Merge resolution.

code/modules/mining/abandonedcrates.dm

@@ -8,8 +8,8 @@
 	var/codelen = 4
 	locked = 1
 
-/obj/structure/closet/crate/secure/loot/New()
-	..()
+/obj/structure/closet/crate/secure/loot/Initialize()
+	. = ..()
 	var/list/digits = list("1", "2", "3", "4", "5", "6", "7", "8", "9", "0")
 
 	for(var/i in 1 to codelen)

code/modules/mining/drilling/drill.dm

@@ -328,8 +328,8 @@
 	circuit = /obj/item/weapon/circuitboard/miningdrillbrace
 	var/obj/machinery/mining/drill/connected
 
-/obj/machinery/mining/brace/New()
-	..()
+/obj/machinery/mining/brace/Initialize()
+	. = ..()
 
 	component_parts = list()
 

code/modules/mining/machinery/machine_input_output_plates.dm

@@ -7,8 +7,9 @@
 	density = 0
 	anchored = 1.0
 
-/obj/machinery/mineral/input/New()
+/obj/machinery/mineral/input/Initialize()
 	icon_state = "blank"
+	. = ..()
 
 /obj/machinery/mineral/output
 	icon = 'icons/mob/screen1.dmi'
@@ -17,5 +18,6 @@
 	density = 0
 	anchored = 1.0
 
-/obj/machinery/mineral/output/New()
-	icon_state = "blank"
+/obj/machinery/mineral/output/Initialize()
+	icon_state = "blank"
+	. = ..()

code/modules/mining/machinery/machine_stacking.dm

@@ -10,9 +10,9 @@
 	var/obj/machinery/mineral/stacking_machine/machine = null
 	//var/machinedir = SOUTHEAST //This is really dumb, so lets burn it with fire.
 
-/obj/machinery/mineral/stacking_unit_console/New()
+/obj/machinery/mineral/stacking_unit_console/Initialize()
 
-	..()
+	. = ..()
 
 	spawn(7)
 		//src.machine = locate(/obj/machinery/mineral/stacking_machine, get_step(src, machinedir)) //No.
@@ -83,8 +83,8 @@
 	var/list/stack_paths[0]
 	var/stack_amt = 50; // Amount to stack before releassing
 
-/obj/machinery/mineral/stacking_machine/New()
-	..()
+/obj/machinery/mineral/stacking_machine/Initialize()
+	. = ..()
 
 	for(var/stacktype in (subtypesof(/obj/item/stack/material) - typesof(/obj/item/stack/material/cyborg)))
 		var/obj/item/stack/material/S = stacktype

code/modules/mining/mine_turfs.dm

@@ -340,7 +340,7 @@ var/list/mining_overlay_cache = list()
 
 /turf/simulated/mineral/proc/UpdateMineral()
 	clear_ore_effects()
-	if(mineral)
+	if(initialized && istype(mineral))
 		new /obj/effect/mineral(src, mineral)
 	update_icon()
 
@@ -637,9 +637,9 @@ var/list/mining_overlay_cache = list()
 	//otherwise, they come out inside a chunk of rock
 	var/obj/item/weapon/X
 	if(is_clean)
-		X = new /obj/item/weapon/archaeological_find(src, new_item_type = F.find_type)
+		X = new /obj/item/weapon/archaeological_find(src, F.find_type)
 	else
-		X = new /obj/item/weapon/strangerock(src, inside_item_type = F.find_type)
+		X = new /obj/item/weapon/strangerock(src, F.find_type)
 		geologic_data.UpdateNearbyArtifactInfo(src)
 		var/obj/item/weapon/strangerock/SR = X
 		SR.geologic_data = geologic_data
@@ -699,5 +699,6 @@ var/list/mining_overlay_cache = list()
 
 	if(mineral_name && (mineral_name in GLOB.ore_data))
 		mineral = GLOB.ore_data[mineral_name]
-		UpdateMineral()
+		if(initialized)
+			UpdateMineral()
 	update_icon()

code/modules/mining/mineral_effect.dm

@@ -9,8 +9,8 @@
 	var/image/scanner_image
 	var/ore_reagent	// Reagent from pumping water near this ore.
 
-/obj/effect/mineral/New(var/newloc, var/ore/M)
-	..(newloc)
+/obj/effect/mineral/Initialize(var/ml, var/ore/M)
+	. = ..(ml)
 	name = "[M.display_name] deposit"
 	ore_key = M.name
 	if(M.reagent)