tools: encode empty sets too

Most data compilers expect them to exist even if empty.

Follow-up to: 42226faf4

tools/core/database.vala

@@ -801,9 +801,6 @@ public class Database
 			// Since null-key is equivalent to non-existent key, skip serialization.
 			if (db[key] == null)
 				continue;
-			// Skip empty sets.
-			if (db[key].holds(typeof(Gee.HashSet)) && ((Gee.HashSet)db[key]).size == 0)
-				continue;
 
 			string[] foo = key.split(".");
 			Hashtable x = obj;