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/controllers/subsystems/atoms.dm

@@ -45,14 +45,14 @@ SUBSYSTEM_DEF(atoms)
 	var/list/arguments
 	for (var/i = 1 to length(created_atoms))
 		created = created_atoms[i]
-		if (!created.initialized)
+		if (!(created.atom_flags & ATOM_INITIALIZED))
 			arguments = created_atoms[created] ? mapload_arg + created_atoms[created] : mapload_arg
 			InitAtom(created, arguments)
 			CHECK_TICK
 	created_atoms.Cut()
 	if (!subsystem_initialized)
 		for (var/atom/atom in world)
-			if (!atom.initialized)
+			if (!(atom.atom_flags & ATOM_INITIALIZED))
 				InitAtom(atom, mapload_arg)
 				++count
 				CHECK_TICK
@@ -90,7 +90,7 @@ SUBSYSTEM_DEF(atoms)
 				bad_init_calls[atom_type] |= DID_NOT_RETURN_HINT
 	if (!atom)
 		qdeleted = TRUE
-	else if (!atom.initialized)
+	else if (!(atom.atom_flags & ATOM_INITIALIZED))
 		bad_init_calls[atom_type] |= DID_NOT_SET_INITIALIZED
 	return qdeleted || QDELING(atom)
 

code/controllers/subsystems/overlays.dm

@@ -24,7 +24,7 @@ SUBSYSTEM_DEF(overlays)
 	icon_cache.Cut()
 	cache_size = 0
 	for (var/atom/atom)
-		atom.flags &= ~OVERLAY_QUEUED
+		atom.atom_flags &= ~OVERLAY_QUEUED
 		CHECK_TICK
 
 
@@ -85,7 +85,7 @@ SUBSYSTEM_DEF(overlays)
 			result += GetIconAppearance(entry)
 		else
 			if (isloc(entry))
-				if (entry.flags & OVERLAY_QUEUED)
+				if (entry.atom_flags & OVERLAY_QUEUED)
 					entry.ImmediateOverlayUpdate()
 			if (!ispath(entry))
 				result += entry.appearance
@@ -97,10 +97,10 @@ SUBSYSTEM_DEF(overlays)
 
 /// Enqueues the atom for an overlay update if not already queued
 /atom/proc/QueueOverlayUpdate()
-	if (flags & OVERLAY_QUEUED)
+	if (atom_flags & OVERLAY_QUEUED)
 		return
 	SSoverlays.queue += src
-	flags |= OVERLAY_QUEUED
+	atom_flags |= OVERLAY_QUEUED
 
 
 /// Builds the atom's overlay state from caches
@@ -109,7 +109,7 @@ SUBSYSTEM_DEF(overlays)
 		if (length(overlays))
 			overlays.Cut()
 		return
-	flags &= ~OVERLAY_QUEUED
+	atom_flags &= ~OVERLAY_QUEUED
 	if (length(priority_overlays))
 		if (length(our_overlays))
 			overlays = priority_overlays + our_overlays

code/controllers/subsystems/persistence.dm

@@ -28,7 +28,7 @@ SUBSYSTEM_DEF(persistence)
 		return
 
 	var/area/A = get_area(T)
-	if(!A || (A.flags & AREA_FLAG_IS_NOT_PERSISTENT))
+	if(!A || (A.atom_flags & AREA_FLAG_IS_NOT_PERSISTENT))
 		return
 
 //	if((!T.z in GLOB.using_map.station_levels) || !initialized)

code/controllers/subsystems/radiation.dm

@@ -73,7 +73,7 @@ SUBSYSTEM_DEF(radiation)
 
 		if(source.respect_maint)
 			var/area/A = T.loc
-			if(A.flags & RAD_SHIELDED)
+			if(A.atom_flags & RAD_SHIELDED)
 				continue // In shielded area
 
 		var/dist = get_dist(source.source_turf, T)
@@ -145,4 +145,4 @@ SUBSYSTEM_DEF(radiation)
 	if(!(power && source))
 		return
 	var/turf/epicentre = locate(round(world.maxx / 2), round(world.maxy / 2), source.z)
-	flat_radiate(epicentre, power, world.maxx, respect_maint)
+	flat_radiate(epicentre, power, world.maxx, respect_maint)