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/persistence/datum/persistence_datum.dm

@@ -77,7 +77,7 @@
 	if(!T || !(T.z in using_map.station_levels) )
 		return FALSE
 	var/area/A = get_area(T)
-	if(!A || (A.flags & AREA_FLAG_IS_NOT_PERSISTENT))
+	if(!A || (A.area_flags & AREA_FLAG_IS_NOT_PERSISTENT))
 		return FALSE
 	return TRUE
 
@@ -104,7 +104,7 @@
 /datum/persistent/proc/Shutdown()
 	if(fexists(filename))
 		fdel(filename)
-	
+
 	var/list/to_store = list()
 	for(var/thing in SSpersistence.tracking_values[type])
 		if(!IsValidEntry(thing))
@@ -121,10 +121,10 @@
 	var/list/my_tracks = SSpersistence.tracking_values[type]
 	if(!my_tracks?.len)
 		return
-	
+
 	. = list("<tr><td colspan = 4><b>[capitalize(name)]</b></td></tr>")
 	. += "<tr><td colspan = 4><hr></td></tr>"
-	
+
 	for(var/thing in my_tracks)
 		. += "<tr>[GetAdminDataStringFor(thing, can_modify, user)]</tr>"
 	. += "<tr><td colspan = 4><hr></td></tr>"
@@ -147,4 +147,4 @@
 		if(.)
 			var/mob/user = locate(href_list["caller"])
 			if(user)
-				SSpersistence.show_info(user)
+				SSpersistence.show_info(user)