replaces atom.initialized with ATOM_INITIALIZED

refactors atom/var/flags to atom_flags and area_flags
moves NOBLOODY, NOBLUDGEON, and PHORONGUARD to item_flags instead of atom_flags
corrects various misapplied flags

code/modules/mob/living/bot/bot.dm

@@ -415,7 +415,7 @@
 		return 1
 
 	for(var/obj/O in B)
-		if(O.density && !istype(O, /obj/machinery/door) && !(O.flags & ON_BORDER))
+		if(O.density && !istype(O, /obj/machinery/door) && !(O.atom_flags & ON_BORDER))
 			return 1
 
 	return 0

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

@@ -308,7 +308,7 @@ emp_act
 		if(!((I.damtype == BRUTE) || (I.damtype == HALLOSS)))
 			return
 
-		if(!(I.flags & NOBLOODY))
+		if(!(I.item_flags & NOBLOODY))
 			I.add_blood(src)
 
 		var/bloody = 0

code/modules/mob/living/silicon/ai/multicam.dm

@@ -145,7 +145,7 @@ Whatever you did that made the last camera window disappear-- don't do that agai
 	name = ""
 	icon = 'icons/misc/pic_in_pic.dmi'
 	icon_state = "room_background"
-	flags = NOJAUNT
+	atom_flags = NOJAUNT
 	plane = SPACE_PLANE
 	layer = AREA_LAYER + 0.1
 

code/modules/mob/living/silicon/robot/drone/drone_items.dm

@@ -10,7 +10,7 @@
 	drop_sound = 'sound/items/drop/device.ogg'
 	icon_state = "gripper"
 
-	flags = NOBLUDGEON
+	item_flags = NOBLUDGEON
 
 	//Has a list of items that it can hold.
 	var/list/can_hold = list(

code/modules/mob/mob_grab.dm

@@ -19,7 +19,7 @@
 	name = "grab"
 	icon = 'icons/mob/screen1.dmi'
 	icon_state = "reinforce"
-	flags = 0
+	atom_flags = 0
 	var/obj/screen/grab/hud = null
 	var/mob/living/affecting = null
 	var/mob/living/carbon/human/assailant = null