Split up and rename var/flags (#17794)

* Split up and rename `var/flags`

* Various fixes

* CL

* Don't rename Phoron Guard phoron preset

---------

Co-authored-by: Cody Brittain <cbrittain10@live.com>

code/controllers/subsystems/initialization/holomap.dm

@@ -63,7 +63,7 @@ SUBSYSTEM_DEF(holomap)
 		A = T.loc
 		Ttype = T.type
 
-		if (A.flags & HIDE_FROM_HOLOMAP)
+		if (A.area_flags & AREA_FLAG_HIDE_FROM_HOLOMAP)
 			continue
 		if (rock_tcache[Ttype])
 			continue

code/controllers/subsystems/initialization/misc_late.dm

@@ -8,7 +8,7 @@ SUBSYSTEM_DEF(misc_late)
 /datum/controller/subsystem/misc_late/Initialize(timeofday)
 	// Setup the teleport locs.
 	for(var/area/AR as anything in the_station_areas)
-		if(AR.flags & NO_GHOST_TELEPORT_ACCESS)
+		if(AR.area_flags & AREA_FLAG_NO_GHOST_TELEPORT_ACCESS)
 			continue
 		var/list/area_turfs = AR.contents
 		if (area_turfs.len) // Check the area is mapped

code/controllers/subsystems/radiation.dm

@@ -71,7 +71,7 @@ SUBSYSTEM_DEF(radiation)
 			continue // Radiation is not multi-z
 		if(source.respect_maint)
 			var/area/A = T.loc
-			if(A.flags & RAD_SHIELDED)
+			if(A.area_flags & AREA_FLAG_RAD_SHIELDED)
 				continue // In shielded area
 
 		var/dist = get_dist(source.source_turf, T)