Improves comments in the GateHandler class and extracts some code into GateReader

Moves code for reading .gate files into the GateReader helper class
Improves all comments in GateHandler where possible
Adds more helper comments

src/main/java/net/knarcraft/stargate/Stargate.java

@@ -405,7 +405,7 @@ public class Stargate extends JavaPlugin {
 
         //If users have an outdated config, assume they also need to update their default gates
         if (isMigrating) {
-            GateHandler.populateDefaults(gateFolder);
+            GateHandler.writeDefaultGatesToFolder(gateFolder);
         }
 
         //Gates