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/projectiles/projectile.dm

@@ -135,7 +135,7 @@
 	var/impact_effect_type = null
 
 	var/list/impacted_mobs = list()
-	
+
 	// TGMC Ammo HUD Port
 	var/hud_state = "unknown" // What HUD state we use when we have ammunition.
 	var/hud_state_empty = "unknown" // The empty state. DON'T USE _FLASH IN THE NAME OF THE EMPTY STATE STRING, THAT IS ADDED BY THE CODE.
@@ -636,7 +636,7 @@
 	return 1
 
 /obj/item/projectile/proc/check_fire(atom/target as mob, mob/living/user as mob)  //Checks if you can hit them or not.
-	check_trajectory(target, user, pass_flags, flags)
+	check_trajectory(target, user, pass_flags, atom_flags)
 
 /obj/item/projectile/CanPass()
 	return TRUE

code/modules/projectiles/projectile/trace.dm

@@ -1,6 +1,6 @@
 // Helper proc to check if you can hit them or not.
 // Will return a list of hit mobs/objects.
-/proc/check_trajectory(atom/target as mob|obj, atom/firer as mob|obj, var/pass_flags=PASSTABLE|PASSGLASS|PASSGRILLE, flags=null)
+/proc/check_trajectory(atom/target as mob|obj, atom/firer as mob|obj, var/pass_flags=PASSTABLE|PASSGLASS|PASSGRILLE, flags=0)
 	if(!istype(target) || !istype(firer))
 		return 0
 
@@ -8,13 +8,13 @@
 
 	//Set the flags and pass flags to that of the real projectile...
 	if(!isnull(flags))
-		trace.flags = flags
+		trace.atom_flags = flags
 	trace.pass_flags = pass_flags
 
 	return trace.launch_projectile(target) //Test it!
 
 /obj/item/projectile/proc/_check_fire(atom/target as mob, var/mob/living/user as mob)  //Checks if you can hit them or not.
-	check_trajectory(target, user, pass_flags, flags)
+	check_trajectory(target, user, pass_flags, atom_flags)
 
 //"Tracing" projectile
 /obj/item/projectile/test //Used to see if you can hit them.