251277: making asmmanager non-singleton

5 files changed, 927 insertions, 951 deletions

diff --git a/ajdoc/src/org/aspectj/tools/ajdoc/CompilerWrapper.java b/ajdoc/src/org/aspectj/tools/ajdoc/CompilerWrapper.java
index cf8c15edf..f27d3b166 100644
--- a/ajdoc/src/org/aspectj/tools/ajdoc/CompilerWrapper.java
+++ b/ajdoc/src/org/aspectj/tools/ajdoc/CompilerWrapper.java
@@ -9,8 +9,9 @@
  * Contributors: 
  *     Mik Kersten     initial implementation 
  * ******************************************************************/
- package org.aspectj.tools.ajdoc;
+package org.aspectj.tools.ajdoc;
 
+import org.aspectj.asm.AsmManager;
 import org.aspectj.bridge.IMessage;
 
 /**
@@ -21,17 +22,17 @@ import org.aspectj.bridge.IMessage;
 public class CompilerWrapper extends org.aspectj.tools.ajc.Main {
 
 	private static CompilerWrapper INSTANCE = null;
-	
-    public static void main(String[] args) {
-    	INSTANCE = new CompilerWrapper();
+
+	public static AsmManager executeMain(String[] args) {
+		INSTANCE = new CompilerWrapper();
 		INSTANCE.runMain(args, true);
+		return AsmManager.lastActiveStructureModel;
+	}
 
-    }
-    
 	public static boolean hasErrors() {
 		return INSTANCE.ourHandler.getErrors().length > 0;
 	}
-	
+
 	public static IMessage[] getErrors() {
 		return INSTANCE.ourHandler.getErrors();
 	}
diff --git a/ajdoc/src/org/aspectj/tools/ajdoc/HtmlDecorator.java b/ajdoc/src/org/aspectj/tools/ajdoc/HtmlDecorator.java
index 12c994bcd..bad35529f 100644
--- a/ajdoc/src/org/aspectj/tools/ajdoc/HtmlDecorator.java
+++ b/ajdoc/src/org/aspectj/tools/ajdoc/HtmlDecorator.java
@@ -53,13 +53,13 @@ class HtmlDecorator {
 	static File rootDir = null;
 	static String docVisibilityModifier;
 
-	static void decorateHTMLFromInputFiles(Hashtable table, File newRootDir, File[] inputFiles, String docModifier)
+	static void decorateHTMLFromInputFiles(AsmManager model, Hashtable table, File newRootDir, File[] inputFiles, String docModifier)
 			throws IOException {
 		rootDir = newRootDir;
 		declIDTable = table;
 		docVisibilityModifier = docModifier;
 		for (int i = 0; i < inputFiles.length; i++) {
-			decorateHTMLFromIPEs(getProgramElements(inputFiles[i].getCanonicalPath()), rootDir.getCanonicalPath()
+			decorateHTMLFromIPEs(getProgramElements(model, inputFiles[i].getCanonicalPath()), rootDir.getCanonicalPath()
 					+ Config.DIR_SEP_CHAR, docModifier, false);
 		}
 	}
@@ -516,7 +516,7 @@ class HtmlDecorator {
 				IProgramElement currDecl = null;
 				if (o instanceof String) {
 					String currHandle = (String) o;
-					currDecl = AsmManager.getDefault().getHierarchy().findElementForHandle(currHandle);
+					currDecl = node.getModel().getHierarchy().findElementForHandle(currHandle);
 				} else if (o instanceof IProgramElement) {
 					currDecl = (IProgramElement) o;
 				} else {
@@ -668,7 +668,7 @@ class HtmlDecorator {
 		List addedNames = new ArrayList(); // for ensuring that we don't add duplciates
 		for (Iterator it = targets.iterator(); it.hasNext();) {
 			String currHandle = (String) it.next();
-			IProgramElement currDecl = AsmManager.getDefault().getHierarchy().findElementForHandle(currHandle);
+			IProgramElement currDecl = decl.getModel().getHierarchy().findElementForHandle(currHandle);
 			if (currDecl.getKind().equals(IProgramElement.Kind.CODE)) {
 				currDecl = currDecl.getParent(); // promote to enclosing
 			}
@@ -850,9 +850,9 @@ class HtmlDecorator {
 		return formattedComment;
 	}
 
-	static public IProgramElement[] getProgramElements(String filename) {
+	static public IProgramElement[] getProgramElements(AsmManager model, String filename) {
 
-		IProgramElement file = (IProgramElement) AsmManager.getDefault().getHierarchy().findElementForSourceFile(filename);
+		IProgramElement file = (IProgramElement) model.getHierarchy().findElementForSourceFile(filename);
 		final List nodes = new ArrayList();
 		HierarchyWalker walker = new HierarchyWalker() {
 			public void preProcess(IProgramElement node) {
diff --git a/ajdoc/src/org/aspectj/tools/ajdoc/Main.java b/ajdoc/src/org/aspectj/tools/ajdoc/Main.java
index a69dbc1d5..15c4301e1 100644
--- a/ajdoc/src/org/aspectj/tools/ajdoc/Main.java
+++ b/ajdoc/src/org/aspectj/tools/ajdoc/Main.java
@@ -14,400 +14,405 @@
 
 package org.aspectj.tools.ajdoc;
 
-import java.io.*;
-import java.util.*;
-
+import java.io.BufferedReader;
+import java.io.File;
 import java.io.FileFilter;
-
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.FilenameFilter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import org.aspectj.asm.AsmManager;
 import org.aspectj.bridge.IMessage;
 import org.aspectj.bridge.Version;
 import org.aspectj.util.FileUtil;
 
 /**
- * This is an old implementation of ajdoc that does not use an OO style.  However, it 
- * does the job, and should serve to evolve a lightweight ajdoc implementation until
- * we can make a properly extended javadoc implementation.
+ * This is an old implementation of ajdoc that does not use an OO style. However, it does the job, and should serve to evolve a
+ * lightweight ajdoc implementation until we can make a properly extended javadoc implementation.
  * 
  * @author Mik Kersten
  */
 public class Main implements Config {
 
-	private static final String FAIL_MESSAGE =  "> compile failed, exiting ajdoc";
+	private static final String FAIL_MESSAGE = "> compile failed, exiting ajdoc";
+
+	/** Command line options. */
+	static Vector options;
 
-    /** Command line options. */
-    static Vector options;
+	/** Options to pass to ajc. */
+	static Vector ajcOptions;
 
-    /** Options to pass to ajc. */
-    static Vector ajcOptions;
+	/** All of the files to be processed by ajdoc. */
+	static Vector filenames;
 
-    /** All of the files to be processed by ajdoc. */
-    static Vector filenames;
+	/** List of files to pass to javadoc. */
+	static Vector fileList;
 
-    /** List of files to pass to javadoc. */
-    static Vector fileList;
+	/** List of packages to pass to javadoc. */
+	static Vector packageList;
 
-    /** List of packages to pass to javadoc. */
-    static Vector packageList;
+	/** Default to package visiblity. */
+	static String docModifier = "package";
 
-    /** Default to package visiblity. */
-    static String docModifier = "package";
+	static Vector sourcepath;
 
-    static Vector sourcepath;
+	static boolean verboseMode = false;
+	static boolean packageMode = false;
+	static boolean authorStandardDocletSwitch = false;
+	static boolean versionStandardDocletSwitch = false;
+	static File rootDir = null;
+	static Hashtable declIDTable = new Hashtable();
+	static String docDir = ".";
+
+	private static boolean deleteTempFilesOnExit = true;
 
-    static boolean verboseMode = false;
-    static boolean packageMode = false;
-    static boolean authorStandardDocletSwitch = false;
-    static boolean versionStandardDocletSwitch = false;
-    static File    rootDir       = null;
-    static Hashtable declIDTable   = new Hashtable();
-    static String  docDir          = ".";
-    
-    private static boolean deleteTempFilesOnExit = true;
-    
 	private static boolean aborted = false;
 	private static IMessage[] errors;
 	private static boolean shownAjdocUsageMessage = false;
-	
+
 	// creating a local variable to enable us to create the ajdocworkingdir
 	// in a local sandbox during testing
 	private static String outputWorkingDir = Config.WORKING_DIR;
 
-    public static void clearState() {
-        options = new Vector();
-        ajcOptions = new Vector();
-        filenames = new Vector();
-        fileList= new Vector();
-        packageList = new Vector();
-        docModifier = "package";
-        sourcepath = new Vector();
-        verboseMode = false;
-        packageMode = false;
-        rootDir       = null;
-        declIDTable   = new Hashtable();
-        docDir          = ".";
-    	aborted = false;
-    	deleteTempFilesOnExit = true;
-    }
-
-    public static void main(String[] args) {
-    	clearState();
-    	if (!JavadocRunner.has14ToolsAvailable()) {
-    		System.err.println("ajdoc requires a JDK 1.4 or later tools jar - exiting");
-    		aborted = true;
-    		return;
-    	}
-    	  
-        // STEP 1: parse the command line and do other global setup
-        sourcepath.addElement("."); // add the current directory to the classapth
-        parseCommandLine(args);  
-        rootDir = getRootDir();
-        File[] inputFiles      = new File[filenames.size()];
-        File[] signatureFiles  = new File[filenames.size()];
-        try {
-            // create the workingdir if it doesn't exist
-            if ( !(new File( outputWorkingDir ).isDirectory()) ) {
-                File dir = new File( outputWorkingDir );
-                dir.mkdir();
-                if (deleteTempFilesOnExit) dir.deleteOnExit();
-            }
-
-            for (int i = 0; i < filenames.size(); i++) {
-                inputFiles[i]     = new File((String)filenames.elementAt(i));
-            }
-
-            // PHASE 0: call ajc
-            callAjc(inputFiles);
-            if (CompilerWrapper.hasErrors()) {
-            	System.out.println(FAIL_MESSAGE);
-            	aborted = true;
-            	errors = CompilerWrapper.getErrors();
-            	return;
-            }    
-
-            for (int ii = 0; ii < filenames.size(); ii++) {
-                signatureFiles[ii] = createSignatureFile(inputFiles[ii]);
-            }
-
-            // PHASE 1: generate Signature files (Java with DeclIDs and no bodies).
-            System.out.println( "> Building signature files..." );
-			try{
-				StubFileGenerator.doFiles(declIDTable, inputFiles, signatureFiles);
-			} catch (DocException d){
+	public static void clearState() {
+		options = new Vector();
+		ajcOptions = new Vector();
+		filenames = new Vector();
+		fileList = new Vector();
+		packageList = new Vector();
+		docModifier = "package";
+		sourcepath = new Vector();
+		verboseMode = false;
+		packageMode = false;
+		rootDir = null;
+		declIDTable = new Hashtable();
+		docDir = ".";
+		aborted = false;
+		deleteTempFilesOnExit = true;
+	}
+
+	public static void main(String[] args) {
+		clearState();
+		if (!JavadocRunner.has14ToolsAvailable()) {
+			System.err.println("ajdoc requires a JDK 1.4 or later tools jar - exiting");
+			aborted = true;
+			return;
+		}
+
+		// STEP 1: parse the command line and do other global setup
+		sourcepath.addElement("."); // add the current directory to the classapth
+		parseCommandLine(args);
+		rootDir = getRootDir();
+		File[] inputFiles = new File[filenames.size()];
+		File[] signatureFiles = new File[filenames.size()];
+		try {
+			// create the workingdir if it doesn't exist
+			if (!(new File(outputWorkingDir).isDirectory())) {
+				File dir = new File(outputWorkingDir);
+				dir.mkdir();
+				if (deleteTempFilesOnExit)
+					dir.deleteOnExit();
+			}
+
+			for (int i = 0; i < filenames.size(); i++) {
+				inputFiles[i] = new File((String) filenames.elementAt(i));
+			}
+
+			// PHASE 0: call ajc
+			AsmManager model = callAjc(inputFiles);
+			if (CompilerWrapper.hasErrors()) {
+				System.out.println(FAIL_MESSAGE);
+				aborted = true;
+				errors = CompilerWrapper.getErrors();
+				return;
+			}
+
+			for (int ii = 0; ii < filenames.size(); ii++) {
+				signatureFiles[ii] = createSignatureFile(model, inputFiles[ii]);
+			}
+
+			// PHASE 1: generate Signature files (Java with DeclIDs and no bodies).
+			System.out.println("> Building signature files...");
+			try {
+				StubFileGenerator.doFiles(model, declIDTable, inputFiles, signatureFiles);
+			} catch (DocException d) {
 				System.err.println(d.getMessage());
 				return;
 			}
 
-            // PHASE 2: let Javadoc generate HTML (with DeclIDs)
+			// PHASE 2: let Javadoc generate HTML (with DeclIDs)
 			callJavadoc(signatureFiles);
 
-            // PHASE 3: add AspectDoc specific stuff to the HTML (and remove the DeclIDS).
-			decorateHtmlFiles(inputFiles);
-            System.out.println( "> Finished." );
-        } catch (Throwable e) {
-            handleInternalError(e);
-            exit(-2);
-        }
-    }
-    
-    private static void callAjc(File[] inputFiles) {
-        ajcOptions.addElement("-noExit");
-		ajcOptions.addElement("-XjavadocsInModel");  	// TODO: wrong option to force model gen
-        ajcOptions.addElement("-d"); 
-        ajcOptions.addElement(rootDir.getAbsolutePath());
+			// PHASE 3: add AspectDoc specific stuff to the HTML (and remove the DeclIDS).
+			decorateHtmlFiles(model, inputFiles);
+			System.out.println("> Finished.");
+		} catch (Throwable e) {
+			handleInternalError(e);
+			exit(-2);
+		}
+	}
+
+	private static AsmManager callAjc(File[] inputFiles) {
+		ajcOptions.addElement("-noExit");
+		ajcOptions.addElement("-XjavadocsInModel"); // TODO: wrong option to force model gen
+		ajcOptions.addElement("-d");
+		ajcOptions.addElement(rootDir.getAbsolutePath());
 		String[] argsToCompiler = new String[ajcOptions.size() + inputFiles.length];
-        int i = 0;
-        for ( ; i < ajcOptions.size(); i++ ) {
-            argsToCompiler[i] = (String)ajcOptions.elementAt(i);
-        }
-        for ( int j = 0; j < inputFiles.length; j++) {
-            argsToCompiler[i] = inputFiles[j].getAbsolutePath();
-            //System.out.println(">> file to ajc: " + inputFiles[j].getAbsolutePath());
-            i++;
-        }
-        System.out.println( "> Calling ajc..." );
-        CompilerWrapper.main(argsToCompiler);
-    }
-    
-    private static void callJavadoc(File[] signatureFiles) throws IOException {
-        System.out.println( "> Calling javadoc..." );
-        String[] javadocargs = null;
-        if ( packageMode ) {
-            int numExtraArgs = 2;
-            if (authorStandardDocletSwitch) numExtraArgs++;
-            if (versionStandardDocletSwitch) numExtraArgs++;
-            javadocargs = new String[numExtraArgs + options.size() + packageList.size() +
-                                     fileList.size() ];
-            javadocargs[0] = "-sourcepath";
-            javadocargs[1] = outputWorkingDir;
-            int argIndex = 2;
-            if (authorStandardDocletSwitch) {
-                javadocargs[argIndex] = "-author";
-                argIndex++;
-            }
-            if (versionStandardDocletSwitch) {
-                javadocargs[argIndex] = "-version";
-            }
-            //javadocargs[1] = getSourcepathAsString();
-            for (int k = 0; k < options.size(); k++) {
-                javadocargs[numExtraArgs+k] = (String)options.elementAt(k);
-            }
-            for (int k = 0; k < packageList.size(); k++) {
-                javadocargs[numExtraArgs+options.size() + k] = (String)packageList.elementAt(k);
-            }
-            for (int k = 0; k < fileList.size(); k++) {
-                javadocargs[numExtraArgs+options.size() + packageList.size() + k] = (String)fileList.elementAt(k);
-            }
-        }
-        else {
-            javadocargs = new String[options.size() + signatureFiles.length];
-            for (int k = 0; k < options.size(); k++) {
-                javadocargs[k] = (String)options.elementAt(k);
-            }
-            for (int k = 0; k < signatureFiles.length; k++) {
-                javadocargs[options.size() + k] = StructureUtil.translateAjPathName(signatureFiles[k].getCanonicalPath());
-            }
-        }
-     
-        JavadocRunner.callJavadoc(javadocargs);    	
-    }
-    
-    /** 
-     * We start with the known HTML files (the ones that correspond directly to the
-     * input files.)  As we go along, we may learn that Javadoc split one .java file
-     * into multiple .html files to handle inner classes or local classes.  The html
-     * file decorator picks that up.
-     */
-    private static void decorateHtmlFiles(File[] inputFiles) throws IOException {
-        System.out.println( "> Decorating html files..." );
-        HtmlDecorator.decorateHTMLFromInputFiles(declIDTable,
-                                          rootDir,
-                                          inputFiles,
-                                          docModifier); 
-        
-        System.out.println( "> Removing generated tags..." );
-        removeDeclIDsFromFile("index-all.html", true);
-        removeDeclIDsFromFile("serialized-form.html", true);
-        if (packageList.size() > 0) {
-            for (int p = 0; p < packageList.size(); p++) {
-                removeDeclIDsFromFile(((String)packageList.elementAt(p)).replace('.','/') +
-                                       Config.DIR_SEP_CHAR +
-                                       "package-summary.html", true);
-            }
-        } else {
+		int i = 0;
+		for (; i < ajcOptions.size(); i++) {
+			argsToCompiler[i] = (String) ajcOptions.elementAt(i);
+		}
+		for (int j = 0; j < inputFiles.length; j++) {
+			argsToCompiler[i] = inputFiles[j].getAbsolutePath();
+			// System.out.println(">> file to ajc: " + inputFiles[j].getAbsolutePath());
+			i++;
+		}
+		System.out.println("> Calling ajc...");
+		return CompilerWrapper.executeMain(argsToCompiler);
+	}
+
+	private static void callJavadoc(File[] signatureFiles) throws IOException {
+		System.out.println("> Calling javadoc...");
+		String[] javadocargs = null;
+		if (packageMode) {
+			int numExtraArgs = 2;
+			if (authorStandardDocletSwitch)
+				numExtraArgs++;
+			if (versionStandardDocletSwitch)
+				numExtraArgs++;
+			javadocargs = new String[numExtraArgs + options.size() + packageList.size() + fileList.size()];
+			javadocargs[0] = "-sourcepath";
+			javadocargs[1] = outputWorkingDir;
+			int argIndex = 2;
+			if (authorStandardDocletSwitch) {
+				javadocargs[argIndex] = "-author";
+				argIndex++;
+			}
+			if (versionStandardDocletSwitch) {
+				javadocargs[argIndex] = "-version";
+			}
+			// javadocargs[1] = getSourcepathAsString();
+			for (int k = 0; k < options.size(); k++) {
+				javadocargs[numExtraArgs + k] = (String) options.elementAt(k);
+			}
+			for (int k = 0; k < packageList.size(); k++) {
+				javadocargs[numExtraArgs + options.size() + k] = (String) packageList.elementAt(k);
+			}
+			for (int k = 0; k < fileList.size(); k++) {
+				javadocargs[numExtraArgs + options.size() + packageList.size() + k] = (String) fileList.elementAt(k);
+			}
+		} else {
+			javadocargs = new String[options.size() + signatureFiles.length];
+			for (int k = 0; k < options.size(); k++) {
+				javadocargs[k] = (String) options.elementAt(k);
+			}
+			for (int k = 0; k < signatureFiles.length; k++) {
+				javadocargs[options.size() + k] = StructureUtil.translateAjPathName(signatureFiles[k].getCanonicalPath());
+			}
+		}
+
+		JavadocRunner.callJavadoc(javadocargs);
+	}
+
+	/**
+	 * We start with the known HTML files (the ones that correspond directly to the input files.) As we go along, we may learn that
+	 * Javadoc split one .java file into multiple .html files to handle inner classes or local classes. The html file decorator
+	 * picks that up.
+	 */
+	private static void decorateHtmlFiles(AsmManager model, File[] inputFiles) throws IOException {
+		System.out.println("> Decorating html files...");
+		HtmlDecorator.decorateHTMLFromInputFiles(model, declIDTable, rootDir, inputFiles, docModifier);
+
+		System.out.println("> Removing generated tags...");
+		removeDeclIDsFromFile("index-all.html", true);
+		removeDeclIDsFromFile("serialized-form.html", true);
+		if (packageList.size() > 0) {
+			for (int p = 0; p < packageList.size(); p++) {
+				removeDeclIDsFromFile(((String) packageList.elementAt(p)).replace('.', '/') + Config.DIR_SEP_CHAR
+						+ "package-summary.html", true);
+			}
+		} else {
 			File[] files = rootDir.listFiles();
-			if (files == null){
+			if (files == null) {
 				System.err.println("Destination directory is not a directory: " + rootDir.toString());
 				return;
 			}
-        	files = FileUtil.listFiles(rootDir, new FileFilter() {
-        		public boolean accept(File f) {
+			files = FileUtil.listFiles(rootDir, new FileFilter() {
+				public boolean accept(File f) {
 					return f.getName().equals("package-summary.html");
 				}
-        	});
-        	for (int j = 0; j < files.length; j++) {
-        		removeDeclIDsFromFile(files[j].getAbsolutePath(), false);
-        	}
-        }    	
-    }
-    
-    private static void removeDeclIDsFromFile(String filename, boolean relativePath) {
-        // Remove the decl ids from "index-all.html"
-        File indexFile;
-        if (relativePath) {
-        	indexFile = new File(docDir + Config.DIR_SEP_CHAR + filename);
-        } else {
-        	indexFile = new File(filename);
-        }
-        try {
-        if ( indexFile.exists() ) {
-            BufferedReader indexFileReader = new BufferedReader( new FileReader( indexFile ) );
-            // StringBuffer greatly reduces the time it takes to remove generated tags
-            StringBuffer indexFileBuffer = new StringBuffer((int)indexFile.length());
-            String line = indexFileReader.readLine();
-            while ( line != null ) {
-              int indexStart = line.indexOf( Config.DECL_ID_STRING );
-              int indexEnd   = line.indexOf( Config.DECL_ID_TERMINATOR );
-              if ( indexStart != -1 && indexEnd != -1 ) {
-                line = line.substring( 0, indexStart ) +
-                       line.substring( indexEnd+Config.DECL_ID_TERMINATOR.length() );
-              }
-              indexFileBuffer.append(line);
-              line = indexFileReader.readLine();
-            }
-            FileOutputStream fos = new FileOutputStream( indexFile );
-            fos.write( indexFileBuffer.toString().getBytes() );
-            
-            indexFileReader.close();
-            fos.close();
-        }
-        }
-        catch (IOException ioe) {
-              // be siltent
-        }
-    }
-
-    static Vector getSourcePath() {
-        Vector  sourcePath = new Vector();
-        boolean found      = false;
-        for ( int i = 0; i < options.size(); i++ ) {
-            String currOption = (String)options.elementAt(i);
-            if (found && !currOption.startsWith("-")) {
-                sourcePath.add(currOption);
-            }
-            if (currOption.equals("-sourcepath")) {
-                found = true;
-            }
-        }
-        return sourcePath;
-    }
-
-    static File getRootDir() {
-        File rootDir = new File( "." );
-        for ( int i = 0; i < options.size(); i++ ) {
-            if ( ((String)options.elementAt(i)).equals( "-d" ) ) {
-                rootDir = new File((String)options.elementAt(i+1));
-                if ( !rootDir.exists() ) {
-                	rootDir.mkdir();
-//                    System.out.println( "Destination directory not found: " +
-//                                        (String)options.elementAt(i+1) );
-//                    System.exit( -1 );
-                }
-            }
-        }
-        return rootDir;
-    }
-
-    static File createSignatureFile(File inputFile) throws IOException {
-    	String packageName = StructureUtil.getPackageDeclarationFromFile(inputFile);
-    	
-        String filename    = "";
-        if ( packageName != null ) {
-            String pathName =  outputWorkingDir + '/' + packageName.replace('.', '/');
-            File packageDir = new File(pathName);
-            if ( !packageDir.exists() ) {
-                packageDir.mkdirs();
-                if (deleteTempFilesOnExit) packageDir.deleteOnExit();
-            }
-            //verifyPackageDirExists(packageName, null);
-            packageName = packageName.replace( '.','/' ); // !!!
-            filename = outputWorkingDir + Config.DIR_SEP_CHAR + packageName +
-                       Config.DIR_SEP_CHAR + inputFile.getName();
-        }
-        else {
-            filename = outputWorkingDir + Config.DIR_SEP_CHAR + inputFile.getName();
-        }
-        File signatureFile = new File( filename );
-        if (deleteTempFilesOnExit) signatureFile.deleteOnExit();
-        return signatureFile;
-    }
-
-
-//    static void verifyPackageDirExists( String packageName, String offset ) {
-//        System.err.println(">>> name: " + packageName + ", offset: " + offset);
-//        if ( packageName.indexOf( "." ) != -1 ) {
-//            File tempFile = new File("c:/aspectj-test/d1/d2/d3");
-//            tempFile.mkdirs();
-//            String currPkgDir = packageName.substring( 0, packageName.indexOf( "." ) );
-//            String remainingPkg = packageName.substring( packageName.indexOf( "." )+1 );
-//            String filePath = null;
-//            if ( offset != null ) {
-//                filePath = Config.WORKING_DIR + Config.DIR_SEP_CHAR +
-//                           offset + Config.DIR_SEP_CHAR + currPkgDir ;
-//            }
-//            else {
-//                filePath = Config.WORKING_DIR + Config.DIR_SEP_CHAR + currPkgDir;
-//            }
-//            File packageDir = new File( filePath );
-//            if ( !packageDir.exists() ) {
-//                packageDir.mkdir();
-//                if (deleteTempFilesOnExit) packageDir.deleteOnExit();
-//            }
-//            if ( remainingPkg != "" ) {
-//                verifyPackageDirExists( remainingPkg, currPkgDir );
-//            }
-//        }
-//        else {
-//            String filePath = null;
-//            if ( offset != null ) {
-//                filePath = Config.WORKING_DIR + Config.DIR_SEP_CHAR + offset + Config.DIR_SEP_CHAR + packageName;
-//            }
-//            else {
-//                filePath = Config.WORKING_DIR + Config.DIR_SEP_CHAR + packageName;
-//            }
-//            File packageDir = new File( filePath );
-//            if ( !packageDir.exists() ) {
-//                packageDir.mkdir();
-//                if (deleteTempFilesOnExit) packageDir.deleteOnExit();
-//            }
-//        }
-//    }
-
-    /**
-     * Can read Eclipse-generated single-line arg
-     */
-    static void parseCommandLine(String[] args) {
-        if (args.length == 0) {
-            displayHelpAndExit( null );
-        } else if (args.length == 1 && args[0].startsWith("@")) {
-        	String argFile = args[0].substring(1);
-        	System.out.println("> Using arg file: " + argFile);  
-        	BufferedReader br;
+			});
+			for (int j = 0; j < files.length; j++) {
+				removeDeclIDsFromFile(files[j].getAbsolutePath(), false);
+			}
+		}
+	}
+
+	private static void removeDeclIDsFromFile(String filename, boolean relativePath) {
+		// Remove the decl ids from "index-all.html"
+		File indexFile;
+		if (relativePath) {
+			indexFile = new File(docDir + Config.DIR_SEP_CHAR + filename);
+		} else {
+			indexFile = new File(filename);
+		}
+		try {
+			if (indexFile.exists()) {
+				BufferedReader indexFileReader = new BufferedReader(new FileReader(indexFile));
+				// StringBuffer greatly reduces the time it takes to remove generated tags
+				StringBuffer indexFileBuffer = new StringBuffer((int) indexFile.length());
+				String line = indexFileReader.readLine();
+				while (line != null) {
+					int indexStart = line.indexOf(Config.DECL_ID_STRING);
+					int indexEnd = line.indexOf(Config.DECL_ID_TERMINATOR);
+					if (indexStart != -1 && indexEnd != -1) {
+						line = line.substring(0, indexStart) + line.substring(indexEnd + Config.DECL_ID_TERMINATOR.length());
+					}
+					indexFileBuffer.append(line);
+					line = indexFileReader.readLine();
+				}
+				FileOutputStream fos = new FileOutputStream(indexFile);
+				fos.write(indexFileBuffer.toString().getBytes());
+
+				indexFileReader.close();
+				fos.close();
+			}
+		} catch (IOException ioe) {
+			// be siltent
+		}
+	}
+
+	static Vector getSourcePath() {
+		Vector sourcePath = new Vector();
+		boolean found = false;
+		for (int i = 0; i < options.size(); i++) {
+			String currOption = (String) options.elementAt(i);
+			if (found && !currOption.startsWith("-")) {
+				sourcePath.add(currOption);
+			}
+			if (currOption.equals("-sourcepath")) {
+				found = true;
+			}
+		}
+		return sourcePath;
+	}
+
+	static File getRootDir() {
+		File rootDir = new File(".");
+		for (int i = 0; i < options.size(); i++) {
+			if (((String) options.elementAt(i)).equals("-d")) {
+				rootDir = new File((String) options.elementAt(i + 1));
+				if (!rootDir.exists()) {
+					rootDir.mkdir();
+					// System.out.println( "Destination directory not found: " +
+					// (String)options.elementAt(i+1) );
+					// System.exit( -1 );
+				}
+			}
+		}
+		return rootDir;
+	}
+
+	static File createSignatureFile(AsmManager model, File inputFile) throws IOException {
+		String packageName = StructureUtil.getPackageDeclarationFromFile(model, inputFile);
+
+		String filename = "";
+		if (packageName != null) {
+			String pathName = outputWorkingDir + '/' + packageName.replace('.', '/');
+			File packageDir = new File(pathName);
+			if (!packageDir.exists()) {
+				packageDir.mkdirs();
+				if (deleteTempFilesOnExit)
+					packageDir.deleteOnExit();
+			}
+			// verifyPackageDirExists(packageName, null);
+			packageName = packageName.replace('.', '/'); // !!!
+			filename = outputWorkingDir + Config.DIR_SEP_CHAR + packageName + Config.DIR_SEP_CHAR + inputFile.getName();
+		} else {
+			filename = outputWorkingDir + Config.DIR_SEP_CHAR + inputFile.getName();
+		}
+		File signatureFile = new File(filename);
+		if (deleteTempFilesOnExit)
+			signatureFile.deleteOnExit();
+		return signatureFile;
+	}
+
+	// static void verifyPackageDirExists( String packageName, String offset ) {
+	// System.err.println(">>> name: " + packageName + ", offset: " + offset);
+	// if ( packageName.indexOf( "." ) != -1 ) {
+	// File tempFile = new File("c:/aspectj-test/d1/d2/d3");
+	// tempFile.mkdirs();
+	// String currPkgDir = packageName.substring( 0, packageName.indexOf( "." ) );
+	// String remainingPkg = packageName.substring( packageName.indexOf( "." )+1 );
+	// String filePath = null;
+	// if ( offset != null ) {
+	// filePath = Config.WORKING_DIR + Config.DIR_SEP_CHAR +
+	// offset + Config.DIR_SEP_CHAR + currPkgDir ;
+	// }
+	// else {
+	// filePath = Config.WORKING_DIR + Config.DIR_SEP_CHAR + currPkgDir;
+	// }
+	// File packageDir = new File( filePath );
+	// if ( !packageDir.exists() ) {
+	// packageDir.mkdir();
+	// if (deleteTempFilesOnExit) packageDir.deleteOnExit();
+	// }
+	// if ( remainingPkg != "" ) {
+	// verifyPackageDirExists( remainingPkg, currPkgDir );
+	// }
+	// }
+	// else {
+	// String filePath = null;
+	// if ( offset != null ) {
+	// filePath = Config.WORKING_DIR + Config.DIR_SEP_CHAR + offset + Config.DIR_SEP_CHAR + packageName;
+	// }
+	// else {
+	// filePath = Config.WORKING_DIR + Config.DIR_SEP_CHAR + packageName;
+	// }
+	// File packageDir = new File( filePath );
+	// if ( !packageDir.exists() ) {
+	// packageDir.mkdir();
+	// if (deleteTempFilesOnExit) packageDir.deleteOnExit();
+	// }
+	// }
+	// }
+
+	/**
+	 * Can read Eclipse-generated single-line arg
+	 */
+	static void parseCommandLine(String[] args) {
+		if (args.length == 0) {
+			displayHelpAndExit(null);
+		} else if (args.length == 1 && args[0].startsWith("@")) {
+			String argFile = args[0].substring(1);
+			System.out.println("> Using arg file: " + argFile);
+			BufferedReader br;
 			try {
 				br = new BufferedReader(new FileReader(argFile));
 				String line = "";
-	        	line = br.readLine();
-	        	StringTokenizer st = new StringTokenizer(line, " ");
-	        	List argList = new ArrayList();
-	        	while(st.hasMoreElements()) {
-	        		argList.add(st.nextElement());
-	        	}
-	        	//System.err.println(argList);
-	        	args = new String[argList.size()];
-	        	int counter = 0;
-	        	for (Iterator it = argList.iterator(); it.hasNext(); ) {
-	        		args[counter] = (String)it.next();
-	        		counter++;
-	        	}
+				line = br.readLine();
+				StringTokenizer st = new StringTokenizer(line, " ");
+				List argList = new ArrayList();
+				while (st.hasMoreElements()) {
+					argList.add(st.nextElement());
+				}
+				// System.err.println(argList);
+				args = new String[argList.size()];
+				int counter = 0;
+				for (Iterator it = argList.iterator(); it.hasNext();) {
+					args[counter] = (String) it.next();
+					counter++;
+				}
 			} catch (FileNotFoundException e) {
 				System.err.println("> could not read arg file: " + argFile);
 				e.printStackTrace();
@@ -415,359 +420,345 @@ public class Main implements Config {
 				System.err.println("> could not read arg file: " + argFile);
 				ioe.printStackTrace();
 			}
-        }
-        List vargs = new LinkedList(Arrays.asList(args));
-
-        parseArgs(vargs, new File( "." ));  // !!!
-
-        if (filenames.size() == 0) {
-            displayHelpAndExit( "ajdoc: No packages or classes specified" );
-        }
-    }
-
-    static void setSourcepath(String arg) {
-           sourcepath.clear();
-           arg = arg + File.pathSeparator; // makes things easier for ourselves
-           StringTokenizer tokenizer = new StringTokenizer(arg, File.pathSeparator);
-           while (tokenizer.hasMoreElements()) {
-                 sourcepath.addElement(tokenizer.nextElement());
-           }
-    }
-
-    static String getSourcepathAsString() {
-       String cPath = "";
-       for (int i = 0; i < sourcepath.size(); i++) {
-           cPath += (String)sourcepath.elementAt(i) + Config.DIR_SEP_CHAR + outputWorkingDir;
-           if (i != sourcepath.size()-1) {
-              cPath += File.pathSeparator;
-           }
-       }
-       return cPath;
-    }
-
-    static void parseArgs(List vargs, File currentWorkingDir) {
-        boolean addNextAsOption     = false;
-        boolean addNextAsArgFile    = false;
-        boolean addNextToAJCOptions = false;
-        boolean addNextAsDocDir     = false;
-        boolean addNextAsClasspath  = false;
-        boolean ignoreArg           = false;  // used for discrepancy betwen class/sourcepath in ajc/javadoc
-        boolean addNextAsSourcePath = false;
-        if ( vargs.size() == 0 ) {
-            displayHelpAndExit( null );
-        }
-        for (int i = 0; i < vargs.size() ; i++) {
-            String arg = (String)vargs.get(i);  
-            ignoreArg = false;
-            if (addNextAsDocDir) {
-                docDir = arg;
-                addNextAsDocDir = false;
-            }
-            if (addNextAsClasspath) {
-                addNextAsClasspath = false;
-            }
-            if (addNextAsSourcePath) {
-                setSourcepath( arg );
-                addNextAsSourcePath = false;
-                ignoreArg = true;
-            }
-            
-            if ( arg.startsWith("@") ) {
-                expandAtSignFile(arg.substring(1), currentWorkingDir);
-            } else if ( arg.equals( "-argfile" ) ) {
-                addNextAsArgFile = true;
-            } else if ( addNextAsArgFile ) {
-                expandAtSignFile(arg, currentWorkingDir);
-                addNextAsArgFile = false;
-            } else if (arg.equals("-d") ) {
-                addNextAsOption = true;
-                options.addElement(arg);
-                addNextAsDocDir = true;
-            } else if ( arg.equals( "-bootclasspath" ) ) {
-                addNextAsOption = true;
-                addNextToAJCOptions = true;
-                options.addElement( arg );
-                ajcOptions.addElement( arg );
-            } else if ( arg.equals( "-source" ) ) {
-                addNextAsOption = true;
-                addNextToAJCOptions = true; 
-                addNextAsClasspath = true;  
-                options.addElement(arg); 
-                ajcOptions.addElement(arg);  
-            } else if ( arg.equals( "-classpath" ) ) {
-                addNextAsOption = true;
-                addNextToAJCOptions = true;
-                addNextAsClasspath = true;
-                options.addElement( arg );
-                ajcOptions.addElement( arg );
-            } else if ( arg.equals( "-encoding" ) ) {
-                addNextAsOption = true;
-                addNextToAJCOptions = false;
-                options.addElement( arg );
-            } else if ( arg.equals( "-docencoding" ) ) {
-                addNextAsOption = true;
-                addNextToAJCOptions = false;
-                options.addElement( arg );
-            } else if ( arg.equals( "-charset" ) ) {
-                addNextAsOption = true;
-                addNextToAJCOptions = false;
-                options.addElement( arg );
-            } else if ( arg.equals( "-sourcepath" ) ) {
-                addNextAsSourcePath = true;
-                //options.addElement( arg );
-                //ajcOptions.addElement( arg );
-            } else if ( arg.equals( "-link" ) ) {
-                addNextAsOption = true;
-            	options.addElement(arg);
-            } else if ( arg.equals( "-bottom" ) ) {
-                addNextAsOption = true;
-            	options.addElement(arg);
-            } else if ( arg.equals( "-windowtitle" ) ) {
-                addNextAsOption = true;
-            	options.addElement(arg);
-            } else if (arg.equals("-XajdocDebug")) {
-            	deleteTempFilesOnExit = false;
-            } else if (arg.equals("-use")) {
-            	System.out.println("> Ignoring unsupported option: -use");
-            } else if (arg.equals("-splitindex")) {
-            	// passed to javadoc
-            } else if (arg.startsWith("-") || addNextAsOption || addNextToAJCOptions) {
-                if ( arg.equals( "-private" ) ) {
-                    docModifier = "private";
-                } else if ( arg.equals( "-package" ) ) {
-                    docModifier = "package";
-                } else if ( arg.equals( "-protected" ) ) {
-                    docModifier = "protected";
-                } else if ( arg.equals( "-public" ) ) {
-                    docModifier = "public";
-                } else if ( arg.equals( "-verbose" ) ) {
-                    verboseMode = true;
-                } else if ( arg.equals( "-author" ) ) {
-                    authorStandardDocletSwitch = true;
-                } else if ( arg.equals( "-version" ) ) {
-                    versionStandardDocletSwitch = true;
-                } else if ( arg.equals( "-v" ) ) {
-                    System.out.println(getVersion());
-                    exit(0);
-                } else if ( arg.equals( "-help" ) ) {
-                    displayHelpAndExit( null );
-                } else if ( arg.equals( "-doclet" ) || arg.equals( "-docletpath" ) ) {
-                    System.out.println( "The doclet and docletpath options are not currently supported    \n" +
-                                        "since ajdoc makes assumptions about the behavior of the standard \n" +
-                                        "doclet. If you would find this option useful please email us at: \n" +
-                                        "                                                                 \n" +
-                                        "       aspectj-dev@eclipse.org                            \n" +
-                                        "                                                                 \n" );
-                    exit(0);
-                } else if (arg.equals("-nonavbar")
-                	|| arg.equals("-noindex")) {
-                	// pass through 
-                	//System.err.println("> ignoring unsupported option: " + arg);
-                } else if (addNextToAJCOptions || addNextAsOption) {
-                	// deal with these two options together even though effectively
-                	// just falling through if addNextAsOption is true. Otherwise
-                	// will have to ensure check "addNextToAJCOptions" before
-                	// "addNextAsOption" so as the options are added to the 
-                	// correct lists.
-                	if (addNextToAJCOptions) {
-                    	ajcOptions.addElement(arg);
-                    	if (!arg.startsWith("-")) {
-                    		addNextToAJCOptions = false;
-    					}
-                    	if (!addNextAsOption) {
-    						continue;
-    					}						
+		}
+		List vargs = new LinkedList(Arrays.asList(args));
+
+		parseArgs(vargs, new File(".")); // !!!
+
+		if (filenames.size() == 0) {
+			displayHelpAndExit("ajdoc: No packages or classes specified");
+		}
+	}
+
+	static void setSourcepath(String arg) {
+		sourcepath.clear();
+		arg = arg + File.pathSeparator; // makes things easier for ourselves
+		StringTokenizer tokenizer = new StringTokenizer(arg, File.pathSeparator);
+		while (tokenizer.hasMoreElements()) {
+			sourcepath.addElement(tokenizer.nextElement());
+		}
+	}
+
+	static String getSourcepathAsString() {
+		String cPath = "";
+		for (int i = 0; i < sourcepath.size(); i++) {
+			cPath += (String) sourcepath.elementAt(i) + Config.DIR_SEP_CHAR + outputWorkingDir;
+			if (i != sourcepath.size() - 1) {
+				cPath += File.pathSeparator;
+			}
+		}
+		return cPath;
+	}
+
+	static void parseArgs(List vargs, File currentWorkingDir) {
+		boolean addNextAsOption = false;
+		boolean addNextAsArgFile = false;
+		boolean addNextToAJCOptions = false;
+		boolean addNextAsDocDir = false;
+		boolean addNextAsClasspath = false;
+		boolean ignoreArg = false; // used for discrepancy betwen class/sourcepath in ajc/javadoc
+		boolean addNextAsSourcePath = false;
+		if (vargs.size() == 0) {
+			displayHelpAndExit(null);
+		}
+		for (int i = 0; i < vargs.size(); i++) {
+			String arg = (String) vargs.get(i);
+			ignoreArg = false;
+			if (addNextAsDocDir) {
+				docDir = arg;
+				addNextAsDocDir = false;
+			}
+			if (addNextAsClasspath) {
+				addNextAsClasspath = false;
+			}
+			if (addNextAsSourcePath) {
+				setSourcepath(arg);
+				addNextAsSourcePath = false;
+				ignoreArg = true;
+			}
+
+			if (arg.startsWith("@")) {
+				expandAtSignFile(arg.substring(1), currentWorkingDir);
+			} else if (arg.equals("-argfile")) {
+				addNextAsArgFile = true;
+			} else if (addNextAsArgFile) {
+				expandAtSignFile(arg, currentWorkingDir);
+				addNextAsArgFile = false;
+			} else if (arg.equals("-d")) {
+				addNextAsOption = true;
+				options.addElement(arg);
+				addNextAsDocDir = true;
+			} else if (arg.equals("-bootclasspath")) {
+				addNextAsOption = true;
+				addNextToAJCOptions = true;
+				options.addElement(arg);
+				ajcOptions.addElement(arg);
+			} else if (arg.equals("-source")) {
+				addNextAsOption = true;
+				addNextToAJCOptions = true;
+				addNextAsClasspath = true;
+				options.addElement(arg);
+				ajcOptions.addElement(arg);
+			} else if (arg.equals("-classpath")) {
+				addNextAsOption = true;
+				addNextToAJCOptions = true;
+				addNextAsClasspath = true;
+				options.addElement(arg);
+				ajcOptions.addElement(arg);
+			} else if (arg.equals("-encoding")) {
+				addNextAsOption = true;
+				addNextToAJCOptions = false;
+				options.addElement(arg);
+			} else if (arg.equals("-docencoding")) {
+				addNextAsOption = true;
+				addNextToAJCOptions = false;
+				options.addElement(arg);
+			} else if (arg.equals("-charset")) {
+				addNextAsOption = true;
+				addNextToAJCOptions = false;
+				options.addElement(arg);
+			} else if (arg.equals("-sourcepath")) {
+				addNextAsSourcePath = true;
+				// options.addElement( arg );
+				// ajcOptions.addElement( arg );
+			} else if (arg.equals("-link")) {
+				addNextAsOption = true;
+				options.addElement(arg);
+			} else if (arg.equals("-bottom")) {
+				addNextAsOption = true;
+				options.addElement(arg);
+			} else if (arg.equals("-windowtitle")) {
+				addNextAsOption = true;
+				options.addElement(arg);
+			} else if (arg.equals("-XajdocDebug")) {
+				deleteTempFilesOnExit = false;
+			} else if (arg.equals("-use")) {
+				System.out.println("> Ignoring unsupported option: -use");
+			} else if (arg.equals("-splitindex")) {
+				// passed to javadoc
+			} else if (arg.startsWith("-") || addNextAsOption || addNextToAJCOptions) {
+				if (arg.equals("-private")) {
+					docModifier = "private";
+				} else if (arg.equals("-package")) {
+					docModifier = "package";
+				} else if (arg.equals("-protected")) {
+					docModifier = "protected";
+				} else if (arg.equals("-public")) {
+					docModifier = "public";
+				} else if (arg.equals("-verbose")) {
+					verboseMode = true;
+				} else if (arg.equals("-author")) {
+					authorStandardDocletSwitch = true;
+				} else if (arg.equals("-version")) {
+					versionStandardDocletSwitch = true;
+				} else if (arg.equals("-v")) {
+					System.out.println(getVersion());
+					exit(0);
+				} else if (arg.equals("-help")) {
+					displayHelpAndExit(null);
+				} else if (arg.equals("-doclet") || arg.equals("-docletpath")) {
+					System.out.println("The doclet and docletpath options are not currently supported    \n"
+							+ "since ajdoc makes assumptions about the behavior of the standard \n"
+							+ "doclet. If you would find this option useful please email us at: \n"
+							+ "                                                                 \n"
+							+ "       aspectj-dev@eclipse.org                            \n"
+							+ "                                                                 \n");
+					exit(0);
+				} else if (arg.equals("-nonavbar") || arg.equals("-noindex")) {
+					// pass through
+					// System.err.println("> ignoring unsupported option: " + arg);
+				} else if (addNextToAJCOptions || addNextAsOption) {
+					// deal with these two options together even though effectively
+					// just falling through if addNextAsOption is true. Otherwise
+					// will have to ensure check "addNextToAJCOptions" before
+					// "addNextAsOption" so as the options are added to the
+					// correct lists.
+					if (addNextToAJCOptions) {
+						ajcOptions.addElement(arg);
+						if (!arg.startsWith("-")) {
+							addNextToAJCOptions = false;
+						}
+						if (!addNextAsOption) {
+							continue;
+						}
 					}
-                } else if (arg.startsWith("-")) {
-                	ajcOptions.addElement(arg);
+				} else if (arg.startsWith("-")) {
+					ajcOptions.addElement(arg);
 					addNextToAJCOptions = true;
 					continue;
-                } else {
-                	System.err.println("> unrecognized argument: " + arg);
-                    displayHelpAndExit( null );
-                }  
-                options.addElement(arg);
-                addNextAsOption = false;
-            } else { 
-                // check if this is a file or a package
-//            	System.err.println(">>>>>>>> " + );
-//            	String entryName = arg.substring(arg.lastIndexOf(File.separator)+1);
-                if (FileUtil.hasSourceSuffix(arg) || arg.endsWith(".lst") && arg != null ) {
-                    File f = new File(arg);
-                    if (f.isAbsolute()) {
-                    	filenames.addElement(arg);
-                    }
-                    else {
-                        filenames.addElement( currentWorkingDir + Config.DIR_SEP_CHAR + arg );
-                    }
-                    fileList.addElement( arg );
-                }
-
-                // PACKAGE MODE STUFF
-                else if (!ignoreArg) {
-                	
-                    packageMode = true;
-                    packageList.addElement( arg );
-                    arg = arg.replace( '.', '/' );  // !!!
-
-                    // do this for every item in the classpath
-                    for ( int c = 0; c < sourcepath.size(); c++ ) {
-                      String path = (String)sourcepath.elementAt(c) + Config.DIR_SEP_CHAR + arg;
-                      File pkg = new File(path);
-                      if ( pkg.isDirectory() ) {
-                          String[] files = pkg.list( new FilenameFilter() {
-                              public boolean accept( File dir, String name )  {
-                                  int index1 = name.lastIndexOf( "." );
-                                  int index2 = name.length();
-                                  if ( (index1 >= 0 && index2 >= 0 ) &&
-                                        (name.substring(index1, index2).equals( ".java" )
-										 || name.substring(index1, index2).equals( ".aj" ))) {
-                                      return true;
-                                  }
-                                  else  {
-                                      return false;
-                                  }
-                              }
-                             } );
-                          for ( int j = 0; j < files.length; j++ ) {
-                              filenames.addElement( (String)sourcepath.elementAt(c) +
-                                                    Config.DIR_SEP_CHAR +
-                                                    arg + Config.DIR_SEP_CHAR + files[j] );
-                          }
-                      }
-                      else if (c == sourcepath.size() ) { // last element on classpath
-                          System.out.println( "ajdoc: No package, class, or source file " +
-                                              "found named " + arg + "." );
-                      }
-                      else {
-                           // didn't find it on that element of the classpath but that's ok
-                      }
-                    }  
-                }
-            }
-        }
-        // set the default visibility as an option to javadoc option
-        if ( !options.contains( "-private" ) &&
-             !options.contains( "-package" ) &&
-             !options.contains( "-protected" ) &&
-             !options.contains( "-public" ) ) {
-            options.addElement( "-package" );
-        }        
-    }
-
-    static void expandAtSignFile(String filename, File currentWorkingDir) {
-        List result = new LinkedList();
-
-        File atFile = qualifiedFile(filename, currentWorkingDir);
-        String atFileParent = atFile.getParent();
-        File myWorkingDir = null;
-        if (atFileParent != null) myWorkingDir = new File(atFileParent);
-
-        try {
-            BufferedReader stream = new BufferedReader(new FileReader(atFile));
-            String line = null;
-            while ( (line = stream.readLine()) != null) {
-                // strip out any comments of the form # to end of line
-                int commentStart = line.indexOf("//");
-                if (commentStart != -1) {
-                    line = line.substring(0, commentStart);
-                }
-
-                // remove extra whitespace that might have crept in
-                line = line.trim();
-                // ignore blank lines
-                if (line.length() == 0) continue;
-                result.add(line);
-            }
-        } catch (IOException e) {
-            System.err.println("Error while reading the @ file " + atFile.getPath() + ".\n"
-                               + e);
-            System.exit( -1 );
-        }
-
-        parseArgs(result, myWorkingDir);
-    }
-
-    static File qualifiedFile(String name, File currentWorkingDir) {
-        name = name.replace('/', File.separatorChar);
-        File file = new File(name);
-        if (!file.isAbsolute() && currentWorkingDir != null) {
-            file = new File(currentWorkingDir, name);
-        }
-        return file;
-    }
-
-
-    static void displayHelpAndExit(String message) {
-    	shownAjdocUsageMessage = true;
-        if (message != null) {
+				} else {
+					System.err.println("> unrecognized argument: " + arg);
+					displayHelpAndExit(null);
+				}
+				options.addElement(arg);
+				addNextAsOption = false;
+			} else {
+				// check if this is a file or a package
+				// System.err.println(">>>>>>>> " + );
+				// String entryName = arg.substring(arg.lastIndexOf(File.separator)+1);
+				if (FileUtil.hasSourceSuffix(arg) || arg.endsWith(".lst") && arg != null) {
+					File f = new File(arg);
+					if (f.isAbsolute()) {
+						filenames.addElement(arg);
+					} else {
+						filenames.addElement(currentWorkingDir + Config.DIR_SEP_CHAR + arg);
+					}
+					fileList.addElement(arg);
+				}
+
+				// PACKAGE MODE STUFF
+				else if (!ignoreArg) {
+
+					packageMode = true;
+					packageList.addElement(arg);
+					arg = arg.replace('.', '/'); // !!!
+
+					// do this for every item in the classpath
+					for (int c = 0; c < sourcepath.size(); c++) {
+						String path = (String) sourcepath.elementAt(c) + Config.DIR_SEP_CHAR + arg;
+						File pkg = new File(path);
+						if (pkg.isDirectory()) {
+							String[] files = pkg.list(new FilenameFilter() {
+								public boolean accept(File dir, String name) {
+									int index1 = name.lastIndexOf(".");
+									int index2 = name.length();
+									if ((index1 >= 0 && index2 >= 0)
+											&& (name.substring(index1, index2).equals(".java") || name.substring(index1, index2)
+													.equals(".aj"))) {
+										return true;
+									} else {
+										return false;
+									}
+								}
+							});
+							for (int j = 0; j < files.length; j++) {
+								filenames.addElement((String) sourcepath.elementAt(c) + Config.DIR_SEP_CHAR + arg
+										+ Config.DIR_SEP_CHAR + files[j]);
+							}
+						} else if (c == sourcepath.size()) { // last element on classpath
+							System.out.println("ajdoc: No package, class, or source file " + "found named " + arg + ".");
+						} else {
+							// didn't find it on that element of the classpath but that's ok
+						}
+					}
+				}
+			}
+		}
+		// set the default visibility as an option to javadoc option
+		if (!options.contains("-private") && !options.contains("-package") && !options.contains("-protected")
+				&& !options.contains("-public")) {
+			options.addElement("-package");
+		}
+	}
+
+	static void expandAtSignFile(String filename, File currentWorkingDir) {
+		List result = new LinkedList();
+
+		File atFile = qualifiedFile(filename, currentWorkingDir);
+		String atFileParent = atFile.getParent();
+		File myWorkingDir = null;
+		if (atFileParent != null)
+			myWorkingDir = new File(atFileParent);
+
+		try {
+			BufferedReader stream = new BufferedReader(new FileReader(atFile));
+			String line = null;
+			while ((line = stream.readLine()) != null) {
+				// strip out any comments of the form # to end of line
+				int commentStart = line.indexOf("//");
+				if (commentStart != -1) {
+					line = line.substring(0, commentStart);
+				}
+
+				// remove extra whitespace that might have crept in
+				line = line.trim();
+				// ignore blank lines
+				if (line.length() == 0)
+					continue;
+				result.add(line);
+			}
+		} catch (IOException e) {
+			System.err.println("Error while reading the @ file " + atFile.getPath() + ".\n" + e);
+			System.exit(-1);
+		}
+
+		parseArgs(result, myWorkingDir);
+	}
+
+	static File qualifiedFile(String name, File currentWorkingDir) {
+		name = name.replace('/', File.separatorChar);
+		File file = new File(name);
+		if (!file.isAbsolute() && currentWorkingDir != null) {
+			file = new File(currentWorkingDir, name);
+		}
+		return file;
+	}
+
+	static void displayHelpAndExit(String message) {
+		shownAjdocUsageMessage = true;
+		if (message != null) {
 			System.err.println(message);
 			System.err.println();
-	        System.err.println(Config.USAGE);
-        } else {
+			System.err.println(Config.USAGE);
+		} else {
 			System.out.println(Config.USAGE);
 			exit(0);
-        }
-    }
-
-    static protected void exit(int value) {
-        System.out.flush();
-        System.err.flush();
-        System.exit(value);
-    }
-
-    /* This section of code handles errors that occur during compilation */
-    static final String internalErrorMessage =
-        "                                                                  \n"+
-        "If this has not already been logged as a bug raised please raise  \n"+
-        "a new AspectJ bug at https://bugs.eclipse.org/bugs including the  \n"+
-        "text below. To make the bug a priority, please also include a test\n"+
-        "program that can reproduce this problem.\n ";
-
-    static public void handleInternalError(Throwable uncaughtThrowable) {
-        System.err.println("An internal error occured in ajdoc");
-        System.err.println(internalErrorMessage);
-        System.err.println(uncaughtThrowable.toString());
-        uncaughtThrowable.printStackTrace();
-        System.err.println();
-    }
-
-    static String getVersion() {
-        return "ajdoc version " + Version.text;
-    }
-    
+		}
+	}
+
+	static protected void exit(int value) {
+		System.out.flush();
+		System.err.flush();
+		System.exit(value);
+	}
+
+	/* This section of code handles errors that occur during compilation */
+	static final String internalErrorMessage = "                                                                  \n"
+			+ "If this has not already been logged as a bug raised please raise  \n"
+			+ "a new AspectJ bug at https://bugs.eclipse.org/bugs including the  \n"
+			+ "text below. To make the bug a priority, please also include a test\n"
+			+ "program that can reproduce this problem.\n ";
+
+	static public void handleInternalError(Throwable uncaughtThrowable) {
+		System.err.println("An internal error occured in ajdoc");
+		System.err.println(internalErrorMessage);
+		System.err.println(uncaughtThrowable.toString());
+		uncaughtThrowable.printStackTrace();
+		System.err.println();
+	}
+
+	static String getVersion() {
+		return "ajdoc version " + Version.text;
+	}
+
 	public static boolean hasAborted() {
 		return aborted;
 	}
-	
+
 	public static IMessage[] getErrors() {
 		return errors;
 	}
-	
+
 	public static boolean hasShownAjdocUsageMessage() {
 		return shownAjdocUsageMessage;
 	}
-	
+
 	/**
-	 * Sets the output working dir to be <fullyQualifiedOutputDir>\ajdocworkingdir
-	 * Useful in testing to redirect the ajdocworkingdir to the sandbox
+	 * Sets the output working dir to be <fullyQualifiedOutputDir>\ajdocworkingdir Useful in testing to redirect the ajdocworkingdir
+	 * to the sandbox
 	 */
 	public static void setOutputWorkingDir(String fullyQulifiedOutputDir) {
 		if (fullyQulifiedOutputDir == null) {
 			resetOutputWorkingDir();
 		} else {
-			outputWorkingDir = fullyQulifiedOutputDir + File.separatorChar + 
-									Config.WORKING_DIR;			
+			outputWorkingDir = fullyQulifiedOutputDir + File.separatorChar + Config.WORKING_DIR;
 		}
 	}
-	
+
 	/**
-	 * Resets the output working dir to be the default which is
-	 * <the current directory>\ajdocworkingdir
+	 * Resets the output working dir to be the default which is <the current directory>\ajdocworkingdir
 	 */
 	public static void resetOutputWorkingDir() {
 		outputWorkingDir = Config.WORKING_DIR;
 	}
 }
-
-
diff --git a/ajdoc/src/org/aspectj/tools/ajdoc/StructureUtil.java b/ajdoc/src/org/aspectj/tools/ajdoc/StructureUtil.java
index 26ebbd260..e38538f20 100644
--- a/ajdoc/src/org/aspectj/tools/ajdoc/StructureUtil.java
+++ b/ajdoc/src/org/aspectj/tools/ajdoc/StructureUtil.java
@@ -9,7 +9,7 @@
  * Contributors: 
  *     Mik Kersten     initial implementation 
  * ******************************************************************/
- package org.aspectj.tools.ajdoc;
+package org.aspectj.tools.ajdoc;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -26,76 +26,71 @@ import org.aspectj.asm.IRelationship;
 public class StructureUtil {
 
 	/**
-	 * Calculate the targets for a given IProgramElement (and it's 
-	 * immediate children if its not a type or if the child is
-	 * CODE) and relationship kind
+	 * Calculate the targets for a given IProgramElement (and it's immediate children if its not a type or if the child is CODE) and
+	 * relationship kind
 	 * 
-	 * @return	null if a relationship of that kind is not found
+	 * @return null if a relationship of that kind is not found
 	 */
-	public static List /*String*/ getTargets(IProgramElement node, IRelationship.Kind kind) {
-		return getTargets(node,kind,null);
+	public static List /* String */getTargets(IProgramElement node, IRelationship.Kind kind) {
+		return getTargets(node, kind, null);
 	}
-	
+
 	/**
-	 * Calculate the targets for a given IProgramElement (and it's immediate
-	 * children if its not a type or if the child is CODE) and relationship 
-	 * kind with the specified relationship name.
+	 * Calculate the targets for a given IProgramElement (and it's immediate children if its not a type or if the child is CODE) and
+	 * relationship kind with the specified relationship name.
 	 * 
 	 * @return null if a relationship of that kind is not found
 	 */
-	public static List /*String*/ getTargets(IProgramElement node, IRelationship.Kind kind, String relName) {
+	public static List /* String */getTargets(IProgramElement node, IRelationship.Kind kind, String relName) {
 		List relations = new ArrayList();
-		List rels = AsmManager.getDefault().getRelationshipMap().get(node);
+		List rels = node.getModel().getRelationshipMap().get(node);
 		if (rels != null) {
 			relations.addAll(rels);
 		}
-	    for (Iterator iter = node.getChildren().iterator(); iter.hasNext();) {
+		for (Iterator iter = node.getChildren().iterator(); iter.hasNext();) {
 			IProgramElement child = (IProgramElement) iter.next();
 			// if we're not a type, or if we are and the child is code, then
 			// we want to get the relationships for this child - this means that the
 			// correct relationships appear against the type in the ajdoc
-			if (!node.getKind().isType() 
-					|| child.getKind().equals(IProgramElement.Kind.CODE) ) {
-				List childRelations = AsmManager.getDefault().getRelationshipMap().get(child);
+			if (!node.getKind().isType() || child.getKind().equals(IProgramElement.Kind.CODE)) {
+				List childRelations = node.getModel().getRelationshipMap().get(child);
 				if (childRelations != null) {
-					for (Iterator iterator = childRelations.iterator(); iterator
-							.hasNext();) {
+					for (Iterator iterator = childRelations.iterator(); iterator.hasNext();) {
 						IRelationship rel = (IRelationship) iterator.next();
 						if (!relations.contains(rel)) {
 							relations.add(rel);
 						}
 					}
-				}					
+				}
 			}
-		}			
-	    if (relations == null || relations.isEmpty()) return null;
-		List targets = new ArrayList(); 
-		for (Iterator it = relations.iterator(); it.hasNext(); ) {
-	      	IRelationship rtn = (IRelationship)it.next();
-	      	if (rtn.getKind().equals(kind)
-	      			&& ((relName != null  && relName.equals(rtn.getName()))
-	      					|| relName == null)){
-	      		List targs = rtn.getTargets();
-	      		for (Iterator iter = targs.iterator(); iter.hasNext();) {
+		}
+		if (relations == null || relations.isEmpty())
+			return null;
+		List targets = new ArrayList();
+		for (Iterator it = relations.iterator(); it.hasNext();) {
+			IRelationship rtn = (IRelationship) it.next();
+			if (rtn.getKind().equals(kind) && ((relName != null && relName.equals(rtn.getName())) || relName == null)) {
+				List targs = rtn.getTargets();
+				for (Iterator iter = targs.iterator(); iter.hasNext();) {
 					String element = (String) iter.next();
 					if (!targets.contains(element)) {
 						targets.add(element);
 					}
 				}
-	      	}
-	     }
-		return targets;		
+			}
+		}
+		return targets;
 	}
-	
-	static List /*IProgramElement */ getDeclareInterTypeTargets(IProgramElement node, IProgramElement.Kind kind) {
+
+	static List /* IProgramElement */getDeclareInterTypeTargets(IProgramElement node, IProgramElement.Kind kind) {
 		List targets = new ArrayList();
-		List stringTargets = StructureUtil.getTargets(node,IRelationship.Kind.DECLARE_INTER_TYPE);
+		List stringTargets = StructureUtil.getTargets(node, IRelationship.Kind.DECLARE_INTER_TYPE);
 		if (stringTargets == null) {
 			return null;
 		}
 		for (Iterator iter = stringTargets.iterator(); iter.hasNext();) {
 			String element = (String) iter.next();
-			IProgramElement ipe = AsmManager.getDefault().getHierarchy().findElementForHandle(element);
+			IProgramElement ipe = node.getModel().getHierarchy().findElementForHandle(element);
 			if (ipe != null && ipe.getKind().equals(kind)) {
 				targets.add(ipe);
 			}
@@ -103,41 +98,41 @@ public class StructureUtil {
 		return targets;
 	}
 
-	public static List/*String*/ getDeclareTargets(IProgramElement node) {
-	    List relations = AsmManager.getDefault().getRelationshipMap().get(node);
-		List targets = null; 
-	    if (relations == null) return null;
-		for (Iterator it = relations.iterator(); it.hasNext(); ) {
-	      	IRelationship rtn = (IRelationship)it.next();
-	      	if (rtn.getKind().isDeclareKind()) {
-	      		targets = rtn.getTargets();
-	      	}
-	     }
+	public static List/* String */getDeclareTargets(IProgramElement node) {
+		List relations = node.getModel().getRelationshipMap().get(node);
+		List targets = null;
+		if (relations == null)
+			return null;
+		for (Iterator it = relations.iterator(); it.hasNext();) {
+			IRelationship rtn = (IRelationship) it.next();
+			if (rtn.getKind().isDeclareKind()) {
+				targets = rtn.getTargets();
+			}
+		}
 		return targets;
 	}
-	
-	public static String getPackageDeclarationFromFile(File file) {
-    	IProgramElement fileNode = (IProgramElement)AsmManager.getDefault().getHierarchy().findElementForSourceFile(file.getAbsolutePath());
-    	String packageName = ((IProgramElement)fileNode.getChildren().get(0)).getPackageName();
-    	return packageName;
+
+	public static String getPackageDeclarationFromFile(AsmManager model, File file) {
+		IProgramElement fileNode = model.getHierarchy().findElementForSourceFile(file.getAbsolutePath());
+		String packageName = ((IProgramElement) fileNode.getChildren().get(0)).getPackageName();
+		return packageName;
 	}
-	
+
 	public static String genSignature(IProgramElement node) {
 		StringBuffer sb = new StringBuffer();
-		
+
 		String accessibility = node.getAccessibility().toString();
 		if (!accessibility.equals("package")) {
 			sb.append(accessibility);
 			sb.append(' ');
 		}
-		
+
 		String modifiers = "";
-		for (Iterator modIt = node.getModifiers().iterator(); modIt.hasNext(); ) {
+		for (Iterator modIt = node.getModifiers().iterator(); modIt.hasNext();) {
 			modifiers += modIt.next() + " ";
 		}
-	
-		if (node.getKind().equals(IProgramElement.Kind.METHOD) || 
-			node.getKind().equals(IProgramElement.Kind.FIELD)) {
+
+		if (node.getKind().equals(IProgramElement.Kind.METHOD) || node.getKind().equals(IProgramElement.Kind.FIELD)) {
 			sb.append(node.getCorrespondingType());
 			sb.append(' ');
 		}
@@ -146,23 +141,23 @@ public class StructureUtil {
 			sb.append("class ");
 		} else if (node.getKind().equals(IProgramElement.Kind.INTERFACE)) {
 			sb.append("interface ");
-		} 
+		}
 
 		sb.append(node.getName());
-		
-		if (node.getParameterTypes() != null ) {
-			sb.append('('); 
+
+		if (node.getParameterTypes() != null) {
+			sb.append('(');
 			for (int i = 0; i < node.getParameterTypes().size(); i++) {
-				sb.append((String)node.getParameterTypes().get(i));
+				sb.append((String) node.getParameterTypes().get(i));
 				sb.append(' ');
-				sb.append((String)node.getParameterNames().get(i));
-				if (i < node.getParameterTypes().size()-1) {
+				sb.append((String) node.getParameterNames().get(i));
+				if (i < node.getParameterTypes().size() - 1) {
 					sb.append(", ");
 				}
 			}
 			sb.append(')');
 		}
-		
+
 		return sb.toString();
 	}
 
@@ -174,24 +169,24 @@ public class StructureUtil {
 			// !!! using exceptions for logic, fix
 			isIntName = false;
 		}
-//		System.err.println(">>>>>>>> " + node.getName());
+		// System.err.println(">>>>>>>> " + node.getName());
 		return isIntName || node.getName().startsWith("new ");
-//		return isIntName;
-//		if (!isIntName) {
-//			 
-//			return node.getName().startsWith("new ");
-//		} else {
-//			return false; 
-//		}
+		// return isIntName;
+		// if (!isIntName) {
+		//			 
+		// return node.getName().startsWith("new ");
+		// } else {
+		// return false;
+		// }
 	}
 
 	/**
-	 * @return	same path, but ending in ".java" instead of ".aj"
+	 * @return same path, but ending in ".java" instead of ".aj"
 	 */
 	public static String translateAjPathName(String path) {
-    	if (path.endsWith(".aj")) {
-    		path = path.substring(0, path.lastIndexOf(".aj")) + ".java";
-    	} 
-    	return path;
+		if (path.endsWith(".aj")) {
+			path = path.substring(0, path.lastIndexOf(".aj")) + ".java";
+		}
+		return path;
 	}
 }
diff --git a/ajdoc/src/org/aspectj/tools/ajdoc/StubFileGenerator.java b/ajdoc/src/org/aspectj/tools/ajdoc/StubFileGenerator.java
index c0f154f1b..e07a294bb 100644
--- a/ajdoc/src/org/aspectj/tools/ajdoc/StubFileGenerator.java
+++ b/ajdoc/src/org/aspectj/tools/ajdoc/StubFileGenerator.java
@@ -14,7 +14,11 @@
 
 package org.aspectj.tools.ajdoc;
 
-import java.io.*;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
@@ -25,208 +29,193 @@ import org.aspectj.asm.IProgramElement;
 /**
  * @author Mik Kersten
  */
-class StubFileGenerator{
-
-    static Hashtable declIDTable = null;
-
-    static void doFiles (Hashtable table,
-                        File[] inputFiles,
-                        File[] signatureFiles) throws DocException {
-        declIDTable = table;
-        for (int i = 0; i < inputFiles.length; i++) {
-            processFile(inputFiles[i], signatureFiles[i]);
-        }
-    }
-    
-
-    static void processFile(File inputFile, File signatureFile) throws DocException {
-        try {
-        	String path = StructureUtil.translateAjPathName(signatureFile.getCanonicalPath());
-            PrintWriter writer = new PrintWriter(new BufferedWriter(new FileWriter(path)));
-             
-            String packageName = StructureUtil.getPackageDeclarationFromFile(inputFile);
-            
-            if (packageName != null && packageName != "") {
-                writer.println( "package " + packageName + ";" );
-            }
-
-           	IProgramElement fileNode = (IProgramElement)AsmManager.getDefault().getHierarchy().findElementForSourceFile(inputFile.getAbsolutePath());
-        	for (Iterator it = fileNode.getChildren().iterator(); it.hasNext(); ) {
-        		IProgramElement node = (IProgramElement)it.next();
-        		if (node.getKind().equals(IProgramElement.Kind.IMPORT_REFERENCE)) {
-        			processImportDeclaration(node, writer);
-        		} else {
+class StubFileGenerator {
+
+	static Hashtable declIDTable = null;
+
+	static void doFiles(AsmManager model, Hashtable table, File[] inputFiles, File[] signatureFiles) throws DocException {
+		declIDTable = table;
+		for (int i = 0; i < inputFiles.length; i++) {
+			processFile(model, inputFiles[i], signatureFiles[i]);
+		}
+	}
+
+	static void processFile(AsmManager model, File inputFile, File signatureFile) throws DocException {
+		try {
+			String path = StructureUtil.translateAjPathName(signatureFile.getCanonicalPath());
+			PrintWriter writer = new PrintWriter(new BufferedWriter(new FileWriter(path)));
+
+			String packageName = StructureUtil.getPackageDeclarationFromFile(model, inputFile);
+
+			if (packageName != null && packageName != "") {
+				writer.println("package " + packageName + ";");
+			}
+
+			IProgramElement fileNode = model.getHierarchy().findElementForSourceFile(inputFile.getAbsolutePath());
+			for (Iterator it = fileNode.getChildren().iterator(); it.hasNext();) {
+				IProgramElement node = (IProgramElement) it.next();
+				if (node.getKind().equals(IProgramElement.Kind.IMPORT_REFERENCE)) {
+					processImportDeclaration(node, writer);
+				} else {
 					try {
-        			  processTypeDeclaration(node, writer);
-					} catch (DocException d){
+						processTypeDeclaration(node, writer);
+					} catch (DocException d) {
 						throw new DocException("File name invalid: " + inputFile.toString());
 					}
-        		}
-        	}
-           	
-            // if we got an error we don't want the contents of the file
-            writer.close(); 
-        } catch (IOException e) {
-            System.err.println(e.getMessage());
-            e.printStackTrace();
-        } 
-    }
-
-    private static void processImportDeclaration(IProgramElement node, PrintWriter writer) throws IOException {
-    	List imports = node.getChildren();
-    	for (Iterator i = imports.iterator(); i.hasNext();) {
+				}
+			}
+
+			// if we got an error we don't want the contents of the file
+			writer.close();
+		} catch (IOException e) {
+			System.err.println(e.getMessage());
+			e.printStackTrace();
+		}
+	}
+
+	private static void processImportDeclaration(IProgramElement node, PrintWriter writer) throws IOException {
+		List imports = node.getChildren();
+		for (Iterator i = imports.iterator(); i.hasNext();) {
 			IProgramElement importNode = (IProgramElement) i.next();
 			writer.println(importNode.getSourceSignature());
-		}  	 
-    }
-    
-    private static void processTypeDeclaration(IProgramElement classNode, PrintWriter writer) throws DocException {
-    	
-    	String formalComment = addDeclID(classNode, classNode.getFormalComment());
-    	writer.println(formalComment);
-    	
-    	String signature = genSourceSignature(classNode);// StructureUtil.genSignature(classNode);
-		if (signature == null){
+		}
+	}
+
+	private static void processTypeDeclaration(IProgramElement classNode, PrintWriter writer) throws DocException {
+
+		String formalComment = addDeclID(classNode, classNode.getFormalComment());
+		writer.println(formalComment);
+
+		String signature = genSourceSignature(classNode);// StructureUtil.genSignature(classNode);
+		if (signature == null) {
 			throw new DocException("The java file is invalid");
 		}
-    	
-//    	System.err.println("######" + signature + ", " + classNode.getName());
-    	if (!StructureUtil.isAnonymous(classNode) && !classNode.getName().equals("<undefined>")) {
-	    	writer.println(signature + " { " );
-	    	processMembers(classNode.getChildren(), writer, classNode.getKind().equals(IProgramElement.Kind.INTERFACE));
-	    	writer.println();
+
+		// System.err.println("######" + signature + ", " + classNode.getName());
+		if (!StructureUtil.isAnonymous(classNode) && !classNode.getName().equals("<undefined>")) {
+			writer.println(signature + " { ");
+			processMembers(classNode.getChildren(), writer, classNode.getKind().equals(IProgramElement.Kind.INTERFACE));
+			writer.println();
 			writer.println("}");
-    	}
-    }
+		}
+	}
 
-	private static void processMembers(List/*IProgramElement*/ members, PrintWriter writer, boolean declaringTypeIsInterface) throws DocException {
-    	for (Iterator it = members.iterator(); it.hasNext();) {
+	private static void processMembers(List/* IProgramElement */members, PrintWriter writer, boolean declaringTypeIsInterface)
+			throws DocException {
+		for (Iterator it = members.iterator(); it.hasNext();) {
 			IProgramElement member = (IProgramElement) it.next();
-		
-	    	if (member.getKind().isType()) { 
-	    		if (!member.getParent().getKind().equals(IProgramElement.Kind.METHOD)
-	    			 && !StructureUtil.isAnonymous(member)) {// don't print anonymous types
-//	    			System.err.println(">>>>>>>>>>>>>" + member.getName() + "<<<<" + member.getParent());
-	    			processTypeDeclaration(member, writer);
-	    		}
+
+			if (member.getKind().isType()) {
+				if (!member.getParent().getKind().equals(IProgramElement.Kind.METHOD) && !StructureUtil.isAnonymous(member)) {// don't
+					// print
+					// anonymous
+					// types
+					// System.err.println(">>>>>>>>>>>>>" + member.getName() + "<<<<" + member.getParent());
+					processTypeDeclaration(member, writer);
+				}
 			} else {
-		    	String formalComment = addDeclID(member, member.getFormalComment());;
-		    	writer.println(formalComment);
-		    	
-		    	String signature = ""; 
-		    	if (!member.getKind().equals(IProgramElement.Kind.POINTCUT)
-		    	    && !member.getKind().equals(IProgramElement.Kind.ADVICE)) {
-					signature = member.getSourceSignature();//StructureUtil.genSignature(member);
-					if (member.getKind().equals(IProgramElement.Kind.ENUM_VALUE)){
+				String formalComment = addDeclID(member, member.getFormalComment());
+				;
+				writer.println(formalComment);
+
+				String signature = "";
+				if (!member.getKind().equals(IProgramElement.Kind.POINTCUT)
+						&& !member.getKind().equals(IProgramElement.Kind.ADVICE)) {
+					signature = member.getSourceSignature();// StructureUtil.genSignature(member);
+					if (member.getKind().equals(IProgramElement.Kind.ENUM_VALUE)) {
 						int index = members.indexOf(member);
-						if ((index + 1 < members.size()) &&
-								((IProgramElement)members.get(index+1)).getKind().equals(IProgramElement.Kind.ENUM_VALUE)){
+						if ((index + 1 < members.size())
+								&& ((IProgramElement) members.get(index + 1)).getKind().equals(IProgramElement.Kind.ENUM_VALUE)) {
 							// if the next member is also an ENUM_VALUE:
 							signature = signature + ",";
 						} else {
 							signature = signature + ";";
 						}
 					}
-                } 
-		    	
-		    	if (member.getKind().isDeclare()) {
-//		    		System.err.println("> Skipping declare (ajdoc limitation): " + member.toLabelString());
-		    	} else if (signature != null &&
-		    		signature != "" && 
-		    		!member.getKind().isInterTypeMember() &&
-					!member.getKind().equals(IProgramElement.Kind.INITIALIZER) &&
-					!StructureUtil.isAnonymous(member)) {   
-		    		writer.print(signature);
-		    	} else {
-//		    		System.err.println(">> skipping: " + member.getKind());
-		    	}  
-		      
-		    	if (member.getKind().equals(IProgramElement.Kind.METHOD) ||
-		    		member.getKind().equals(IProgramElement.Kind.CONSTRUCTOR)) {
-		    		if (member.getParent().getKind().equals(IProgramElement.Kind.INTERFACE) ||
-		    			signature.indexOf("abstract ") != -1) {
-		    			writer.println(";");
-		    		} else {
-		    			writer.println(" { }");
-		    		}
-		    		
-		    	} else if (member.getKind().equals(IProgramElement.Kind.FIELD)) {
-//		    		writer.println(";");
-		    	}
+				}
+
+				if (member.getKind().isDeclare()) {
+					// System.err.println("> Skipping declare (ajdoc limitation): " + member.toLabelString());
+				} else if (signature != null && signature != "" && !member.getKind().isInterTypeMember()
+						&& !member.getKind().equals(IProgramElement.Kind.INITIALIZER) && !StructureUtil.isAnonymous(member)) {
+					writer.print(signature);
+				} else {
+					// System.err.println(">> skipping: " + member.getKind());
+				}
+
+				if (member.getKind().equals(IProgramElement.Kind.METHOD)
+						|| member.getKind().equals(IProgramElement.Kind.CONSTRUCTOR)) {
+					if (member.getParent().getKind().equals(IProgramElement.Kind.INTERFACE) || signature.indexOf("abstract ") != -1) {
+						writer.println(";");
+					} else {
+						writer.println(" { }");
+					}
+
+				} else if (member.getKind().equals(IProgramElement.Kind.FIELD)) {
+					// writer.println(";");
+				}
 			}
 		}
-    }
-
-    /**
-     * Translates "aspect" to "class", as long as its not ".aspect"
-     */
-    private static String genSourceSignature(IProgramElement classNode) {
-    	String signature = classNode.getSourceSignature();
-		if (signature != null){
+	}
+
+	/**
+	 * Translates "aspect" to "class", as long as its not ".aspect"
+	 */
+	private static String genSourceSignature(IProgramElement classNode) {
+		String signature = classNode.getSourceSignature();
+		if (signature != null) {
 			int index = signature.indexOf("aspect");
-			if (index == 0 || (index != -1 && signature.charAt(index-1) != '.') ) {
-				signature = signature.substring(0, index) +
-				"class " +
-				signature.substring(index + 6, signature.length());
+			if (index == 0 || (index != -1 && signature.charAt(index - 1) != '.')) {
+				signature = signature.substring(0, index) + "class " + signature.substring(index + 6, signature.length());
 			}
 		}
-    	return signature;
+		return signature;
+	}
+
+	static int nextDeclID = 0;
+
+	static String addDeclID(IProgramElement decl, String formalComment) {
+		String declID = "" + ++nextDeclID;
+		declIDTable.put(declID, decl);
+		return addToFormal(formalComment, Config.DECL_ID_STRING + declID + Config.DECL_ID_TERMINATOR);
+	}
+
+	/**
+	 * We want to go: just before the first period just before the first @ just before the end of the comment
+	 * 
+	 * Adds a place holder for the period ('#') if one will need to be replaced.
+	 */
+	static String addToFormal(String formalComment, String string) {
+		if (string == null || string.equals("")) {
+			return formalComment;
+		}
+		// boolean appendPeriod = true;
+		if ((formalComment == null) || formalComment.equals("")) {
+			// formalComment = "/**\n * . \n */\n";
+			formalComment = "/**\n * \n */\n";
+			// appendPeriod = false;
+		}
+		formalComment = formalComment.trim();
+
+		int atsignPos = formalComment.indexOf('@');
+		int endPos = formalComment.indexOf("*/");
+		int periodPos = formalComment.indexOf("/**");
+		int position = 0;
+		String periodPlaceHolder = "";
+		if (periodPos != -1) {
+			position = periodPos + 3;// length of "/**"
+		} else if (atsignPos != -1) {
+			string = string + "\n * ";
+			position = atsignPos;
+		} else if (endPos != -1) {
+			string = "* " + string + "\n";
+			position = endPos;
+		} else {
+			// !!! perhaps this error should not be silent
+			throw new Error("Failed to append to formal comment for comment: " + formalComment);
+		}
+
+		return formalComment.substring(0, position) + periodPlaceHolder + string + formalComment.substring(position);
 	}
-	
-    static int nextDeclID = 0;
-    static String addDeclID(IProgramElement decl, String formalComment) {
-        String declID = "" + ++nextDeclID;
-        declIDTable.put(declID, decl);
-        return addToFormal(formalComment, Config.DECL_ID_STRING + declID + Config.DECL_ID_TERMINATOR);
-    }
-
-    /**
-     * We want to go:
-     *   just before the first period
-     *   just before the first @
-     *   just before the end of the comment
-     *
-     * Adds a place holder for the period ('#') if one will need to be
-     * replaced.
-     */
-    static String addToFormal(String formalComment, String string) {
-       if(string == null || string.equals("")) {
-          return formalComment;
-       }
-        //boolean appendPeriod = true;
-        if ( (formalComment == null) || formalComment.equals("")) {
-            //formalComment = "/**\n * . \n */\n";
-            formalComment = "/**\n * \n */\n";
-            //appendPeriod = false;
-        }
-        formalComment = formalComment.trim();
-
-        int atsignPos = formalComment.indexOf('@');
-        int    endPos = formalComment.indexOf("*/");
-        int periodPos = formalComment.indexOf("/**");
-        int position  = 0;
-        String periodPlaceHolder = "";
-        if ( periodPos != -1 ) {
-            position = periodPos + 3;// length of "/**"
-        }
-        else if ( atsignPos != -1 ) {
-            string = string + "\n * ";
-            position = atsignPos;
-        }
-        else if ( endPos != -1 ) {
-            string = "* " + string + "\n";
-            position = endPos;
-        }
-        else {
-            // !!! perhaps this error should not be silent
-            throw new Error("Failed to append to formal comment for comment: " +
-                formalComment );
-        }
-
-        return
-            formalComment.substring(0, position) + periodPlaceHolder +
-            string +
-            formalComment.substring(position);
-    }
 
 }