Having problems with top-level classes no longer explicitly declaring themselves on top level

DumpClasses.java

@@ -10,7 +10,7 @@ import AST.Start;
 
 public class DumpClasses extends Parser {
 	public static void main(String args[]) {
-		Start ast = parse(args);
+		Start ast = parse(args[0]);
 
 		// Dump the AST
 // 		ast.dumpTree("  ", System.out);

GenCompiler.java

@@ -14,10 +14,14 @@ public class GenCompiler extends Parser {
 	public static void main(String args[]) {
 
 		String name = "default";
+		String dirName = "default";
 		String owlFile = "";
 		int i = 0;
 		while (i<args.length) {
 			if (args[i].equals("-d")) {
+				dirName = args[++i];
+				i++;
+			} else if (args[i].equals("-n")) {
 				name = args[++i];
 				i++;
 			} else {
@@ -27,7 +31,7 @@ public class GenCompiler extends Parser {
 
 		Start ast = parse(owlFile);
 
-		File siarasDir = new File(name);
+		File siarasDir = new File(dirName);
 		if (!siarasDir.isDirectory()) {
 			siarasDir.mkdir();
 		}
@@ -35,17 +39,17 @@ public class GenCompiler extends Parser {
 		String fileName = null;
 		try {
 			// Generate JastAdd abstract grammar
-			fileName = name+"/"+name+".ast";
+			fileName = dirName+"/"+name+".ast";
 			PrintStream pStream = new PrintStream(new File(fileName));
 			ast.genAbsGrammar(pStream);
 
 			// Generate Parser.java
-			fileName = name+"/Parser.java";
+			fileName = dirName+"/Parser.java";
 			pStream = new PrintStream(new File(fileName));
 			ast.genParser(pStream);
 
 			// Generate aspects
-			fileName = name+"/GeneratedAspects.jrag";
+			fileName = dirName+"/GeneratedAspects.jrag";
 			pStream = new PrintStream(new File(fileName));
 			ast.genAspects(pStream);
 

Types.jrag

@@ -31,6 +31,7 @@ aspect Types {
     eq OwlClassUse.decl() {
 		ComplexElement top = getTopElement();
 		for (int i=0; i<top.getNumElement(); i++) {
+// 			System.out.println(getId()+" == "+((ComplexElement) top.getElement(i)).getId());
 			if ((top.getElement(i) instanceof ComplexElement) &&
 				getId().equals(((ComplexElement) top.getElement(i)).getId())) {
 				return (OwlClassDecl) top.getElement(i);