fix for Bugzilla Bug 54621

 	Incremental support ignores binary source

6 files changed, 238 insertions, 34 deletions

diff --git a/org.aspectj.ajdt.core/src/org/aspectj/ajdt/ajc/BuildArgParser.java b/org.aspectj.ajdt.core/src/org/aspectj/ajdt/ajc/BuildArgParser.java
index 6132b74d0..969d994fe 100644
--- a/org.aspectj.ajdt.core/src/org/aspectj/ajdt/ajc/BuildArgParser.java
+++ b/org.aspectj.ajdt.core/src/org/aspectj/ajdt/ajc/BuildArgParser.java
@@ -320,6 +320,7 @@ public class BuildArgParser extends Main {
             	if (args.size() > nextArgIndex) {
 					buildConfig.getAjOptions().put(AjCompilerOptions.OPTION_Inpath, CompilerOptions.PRESERVE);
 					
+					List inPath = buildConfig.getInpath();
 					StringTokenizer st = new StringTokenizer(
 						((ConfigParser.Arg)args.get(nextArgIndex)).getValue(), 
 						File.pathSeparator);
@@ -327,16 +328,16 @@ public class BuildArgParser extends Main {
 						String filename = st.nextToken();
 						File file = makeFile(filename);
 						if (file.exists() && FileUtil.hasZipSuffix(filename)) {
-							buildConfig.getInpath().add(file);    
+							inPath.add(file);    
 						} else {
 							if (file.isDirectory()) {
-								buildConfig.getInpath().add(file);
+								inPath.add(file);
 							} else 
 		            		
 							showError("bad inpath component: " + filename);  
 						}
 					}
-					
+					buildConfig.setInPath(inPath);
 					args.remove(args.get(nextArgIndex));            		
             	}
             } else if (arg.equals("-injars")) {;
diff --git a/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/compiler/AjCompilerAdapter.java b/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/compiler/AjCompilerAdapter.java
index a6eacc40a..8bb0a7c83 100644
--- a/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/compiler/AjCompilerAdapter.java
+++ b/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/compiler/AjCompilerAdapter.java
@@ -14,6 +14,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
@@ -47,8 +48,9 @@ public class AjCompilerAdapter implements ICompilerAdapter {
 	private IIntermediateResultsRequestor intermediateResultsRequestor;
 	private IProgressListener progressListener;
 	private IOutputClassFileNameProvider outputFileNameProvider;
+	private IBinarySourceProvider binarySourceProvider;
 	private WeaverMessageHandler weaverMessageHandler;
-	private List /* InterimCompilationResult */ binarySources = new ArrayList();
+	private Map /* fileName |-> List<UnwovenClassFile> */ binarySourceSetForFullWeave = new HashMap();
 	private Collection /*InterimCompilationResult*/ resultSetForFullWeave = Collections.EMPTY_LIST;
 
 	
@@ -77,7 +79,8 @@ public class AjCompilerAdapter implements ICompilerAdapter {
 							 IIntermediateResultsRequestor intRequestor,
 							 IProgressListener progressListener,
 							 IOutputClassFileNameProvider outputFileNameProvider,
-							 Map binarySourceEntries, /* fileName |-> List<UnwovenClassFile> */
+							 IBinarySourceProvider binarySourceProvider,
+							 Map fullBinarySourceEntries, /* fileName |-> List<UnwovenClassFile> */
 							 Collection /* InterimCompilationResult */ resultSetForFullWeave,
 							 boolean isXNoWeave) {
 		this.compiler = compiler;
@@ -86,15 +89,15 @@ public class AjCompilerAdapter implements ICompilerAdapter {
 		this.intermediateResultsRequestor = intRequestor;
 		this.progressListener = progressListener;
 		this.outputFileNameProvider = outputFileNameProvider;
+		this.binarySourceProvider = binarySourceProvider;
 		this.isXNoWeave = isXNoWeave;
+		this.binarySourceSetForFullWeave = fullBinarySourceEntries;
 		this.resultSetForFullWeave = resultSetForFullWeave;
 		this.eWorld = eFactory;
 		
 		IMessageHandler msgHandler = world.getMessageHandler();
 		weaverMessageHandler = new WeaverMessageHandler(msgHandler, compiler);
 		world.setMessageHandler(weaverMessageHandler);
-		
-		addBinarySource(binarySourceEntries);
 	}
 	
 	public void beforeCompiling(ICompilationUnit[] sourceUnits) {
@@ -134,7 +137,6 @@ public class AjCompilerAdapter implements ICompilerAdapter {
 		} else {
 			resultsPendingWeave.add(intRes);
 		}
-		
 	}
 	
 	public void beforeResolving(CompilationUnitDeclaration unit, ICompilationUnit sourceUnit, boolean verifyMethods, boolean analyzeCode, boolean generateCode) {
@@ -178,8 +180,9 @@ public class AjCompilerAdapter implements ICompilerAdapter {
 		}
 	}
 	
-	private void addBinarySource(Map binarySourceEntries) {
+	private List getBinarySourcesFrom(Map binarySourceEntries) {
 		// Map is fileName |-> List<UnwovenClassFile>
+		List ret = new ArrayList();
 		for (Iterator binIter = binarySourceEntries.keySet().iterator(); binIter.hasNext();) {
 			String sourceFileName = (String) binIter.next();
 			List unwovenClassFiles = (List) binarySourceEntries.get(sourceFileName);
@@ -188,8 +191,9 @@ public class AjCompilerAdapter implements ICompilerAdapter {
 			result.noSourceAvailable();
 			InterimCompilationResult binarySource = 
 				new InterimCompilationResult(result,unwovenClassFiles);
-			binarySources.add(binarySource);
+			ret.add(binarySource);
 		}
+		return ret;
 	}
 	
 	private void notifyRequestor() {
@@ -209,14 +213,22 @@ public class AjCompilerAdapter implements ICompilerAdapter {
 		}
 
 		weaver.prepareForWeave();
-
-		if (isBatchCompile) {
-			resultsPendingWeave.addAll(binarySources);  
-			// passed into the compiler, the set of classes in injars and inpath...
-		} else if (weaver.needToReweaveWorld()) {
-			addAllKnownClassesToWeaveList();
+		if (weaver.needToReweaveWorld()) {
+			if (!isBatchCompile) addAllKnownClassesToWeaveList(); // if it's batch, they're already on the list...
+			resultsPendingWeave.addAll(getBinarySourcesFrom(binarySourceSetForFullWeave));
+		} else {
+			Map binarySourcesToAdd = binarySourceProvider.getBinarySourcesForThisWeave();
+			resultsPendingWeave.addAll(getBinarySourcesFrom(binarySourcesToAdd));
 		}
 
+//		if (isBatchCompile) {
+//			resultsPendingWeave.addAll(getBinarySourcesFrom(binarySourceSetForFullWeave));  
+//			// passed into the compiler, the set of classes in injars and inpath...
+//		} else if (weaver.needToReweaveWorld()) {
+//			addAllKnownClassesToWeaveList();
+//			resultsPendingWeave.addAll(getBinarySourcesFrom(binarySourceSetForFullWeave));
+//		}
+
 		weaver.weave(new WeaverAdapter(this,weaverMessageHandler,progressListener));
 	}
 	
diff --git a/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/compiler/IBinarySourceProvider.java b/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/compiler/IBinarySourceProvider.java
new file mode 100644
index 000000000..1b56159b3
--- /dev/null
+++ b/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/compiler/IBinarySourceProvider.java
@@ -0,0 +1,27 @@
+/*******************************************************************************
+ * Copyright (c) 2004 IBM Corporation and others.
+ * All rights reserved. This program and the accompanying materials 
+ * are made available under the terms of the Common Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/cpl-v10.html
+ * 
+ * Contributors:
+ *     IBM Corporation - initial API and implementation
+ *******************************************************************************/
+package org.aspectj.ajdt.internal.compiler;
+
+import java.util.Map;
+
+/**
+ * @author colyer
+ *
+ * Implementors of this interface are called by the CompilerAdapter just before
+ * it does a weave, and should return the set of binary source files (ie. those
+ * resources from injars and inpath) that are to be included in the weave. 
+ * Used to manage incremental compilation of binary sources.
+ */
+public interface IBinarySourceProvider {
+	
+	Map /* fileName |-> List<UnwovenClassFile> */ getBinarySourcesForThisWeave();
+	
+}
diff --git a/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/core/builder/AjBuildConfig.java b/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/core/builder/AjBuildConfig.java
index f9c2571db..27812ead7 100644
--- a/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/core/builder/AjBuildConfig.java
+++ b/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/core/builder/AjBuildConfig.java
@@ -17,6 +17,7 @@
 package org.aspectj.ajdt.internal.core.builder;
 
 import java.io.File;
+import java.io.FileFilter;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
@@ -24,6 +25,7 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
+import org.aspectj.util.FileUtil;
 import org.eclipse.jdt.internal.compiler.impl.CompilerOptions;
 
 /**
@@ -37,11 +39,12 @@ public class AjBuildConfig { // XXX needs bootclasspath?
 	public static final String AJLINT_WARN = "warn";
 	public static final String AJLINT_ERROR = "error";
 	public static final String AJLINT_DEFAULT = "default";
-
+	
 	private File outputDir;
 	private File outputJar;
 	private List/*File*/ sourceRoots = new ArrayList();
 	private List/*File*/ files = new ArrayList();
+	private List /*File*/ binaryFiles = new ArrayList();  // .class files in indirs...
 	private List/*File*/ inJars = new ArrayList();
 	private List/*File*/ inPath = new ArrayList();
 	private Map/*String->File*/ sourcePathResources = new HashMap();
@@ -68,6 +71,27 @@ public class AjBuildConfig { // XXX needs bootclasspath?
     private boolean incrementalMode;
     private File incrementalFile;
     
+	public static class BinarySourceFile {
+		public BinarySourceFile(File dir, File src) {
+			this.fromInPathDirectory = dir;
+			this.binSrc = src;
+		}
+		public File fromInPathDirectory;
+		public File binSrc;
+		
+		public boolean equals(Object obj) {
+			if ((obj instanceof BinarySourceFile) &&
+				(obj != null)) {
+				BinarySourceFile other = (BinarySourceFile)obj;
+				return(binSrc.equals(other.binSrc));
+			}
+			return false;
+		}
+		public int hashCode() {
+			return binSrc != null ? binSrc.hashCode() : 0; 
+		}
+	}
+    
 	/**
 	 * Intialises the javaOptions Map to hold the default 
 	 * JDT Compiler settings. Added by AMC 01.20.2003 in reponse
@@ -150,6 +174,15 @@ public class AjBuildConfig { // XXX needs bootclasspath?
 		return files;
 	}
 
+	/**
+	 * returned files includes all .class files found in
+	 * a directory on the inpath, but does not include
+	 * .class files contained within jars.
+	 */
+	public List/*BinarySourceFile*/ getBinaryFiles() {
+		return binaryFiles;
+	}
+	
 	public File getOutputDir() {  
 		return outputDir;
 	}
@@ -219,6 +252,22 @@ public class AjBuildConfig { // XXX needs bootclasspath?
 	
 	public void setInPath(List dirsOrJars) {
 		inPath = dirsOrJars;
+		
+		// remember all the class files in directories on the inpath
+		binaryFiles = new ArrayList();
+		FileFilter filter = new FileFilter() {
+			public boolean accept(File pathname) {
+				return pathname.getPath().endsWith(".class");
+			}};
+		for (Iterator iter = dirsOrJars.iterator(); iter.hasNext();) {
+			File inpathElement = (File) iter.next();
+			if (inpathElement.isDirectory()) {
+			    File[] files = FileUtil.listFiles(inpathElement, filter);
+				for (int i = 0; i < files.length; i++) {
+					binaryFiles.add(new BinarySourceFile(inpathElement,files[i]));
+				}
+			}			
+		}
 	}
 
 	public List getSourceRoots() {
diff --git a/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/core/builder/AjBuildManager.java b/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/core/builder/AjBuildManager.java
index dc1eef8f5..65dad3eff 100644
--- a/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/core/builder/AjBuildManager.java
+++ b/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/core/builder/AjBuildManager.java
@@ -19,6 +19,7 @@ import java.util.jar.*;
 import java.util.zip.ZipEntry;
 
 import org.aspectj.ajdt.internal.compiler.AjCompilerAdapter;
+import org.aspectj.ajdt.internal.compiler.IBinarySourceProvider;
 import org.aspectj.ajdt.internal.compiler.IIntermediateResultsRequestor;
 import org.aspectj.ajdt.internal.compiler.IOutputClassFileNameProvider;
 import org.aspectj.ajdt.internal.compiler.InterimCompilationResult;
@@ -43,11 +44,18 @@ import org.eclipse.jdt.internal.compiler.problem.AbortCompilation;
 import org.eclipse.jdt.internal.compiler.problem.DefaultProblemFactory;
 //import org.eclipse.jdt.internal.compiler.util.HashtableOfObject;
 
-public class AjBuildManager implements IOutputClassFileNameProvider,ICompilerAdapterFactory {
+public class AjBuildManager implements IOutputClassFileNameProvider,IBinarySourceProvider,ICompilerAdapterFactory {
 	private static final String CANT_WRITE_RESULT = "unable to write compilation result";
 	private static final String MANIFEST_NAME = "META-INF/MANIFEST.MF";
 	static final boolean COPY_INPATH_DIR_RESOURCES = false;
     static final boolean FAIL_IF_RUNTIME_NOT_FOUND = false;
+    
+    private static final FileFilter binarySourceFilter = 
+		new FileFilter() {
+			public boolean accept(File f) {
+				return f.getName().endsWith(".class");
+			}};
+			
 	private IProgressListener progressListener = null;
 	
 	private int compiledCount;
@@ -57,6 +65,8 @@ public class AjBuildManager implements IOutputClassFileNameProvider,ICompilerAda
 	private boolean batchCompile = true;
 	private INameEnvironment environment;
 	
+	private Map /* String -> List<UCF>*/ binarySourcesForTheNextCompile = new HashMap();
+	
 	private IHierarchy structureModel;
 	public AjBuildConfig buildConfig;
 	
@@ -146,6 +156,7 @@ public class AjBuildManager implements IOutputClassFileNameProvider,ICompilerAda
                     bcelWorld.setModel(AsmManager.getDefault().getHierarchy());
                     // in incremental build, only get updated model?
                 }
+                binarySourcesForTheNextCompile = state.getBinaryFilesToCompile();
                 performCompilation(buildConfig.getFiles());
                 if (handler.hasErrors()) {
                     return false;
@@ -157,13 +168,17 @@ public class AjBuildManager implements IOutputClassFileNameProvider,ICompilerAda
 //                }
                 // System.err.println("XXXX start inc ");
                 List files = state.getFilesToCompile(true);
-                for (int i = 0; (i < 5) && !files.isEmpty(); i++) {
+                binarySourcesForTheNextCompile = state.getBinaryFilesToCompile();
+                boolean hereWeGoAgain = !(files.isEmpty() && binarySourcesForTheNextCompile.isEmpty());
+                for (int i = 0; (i < 5) && hereWeGoAgain; i++) {
                     // System.err.println("XXXX inc: " + files);
                     performCompilation(files);
                     if (handler.hasErrors() || (progressListener!=null && progressListener.isCancelledRequested())) {
                         return false;
                     } 
                     files = state.getFilesToCompile(false);
+                    binarySourcesForTheNextCompile = state.getBinaryFilesToCompile();
+                    hereWeGoAgain = !(files.isEmpty() && binarySourcesForTheNextCompile.isEmpty());
                 }
                 if (!files.isEmpty()) {
                     return batchBuild(buildConfig, baseHandler);
@@ -425,19 +440,26 @@ public class AjBuildManager implements IOutputClassFileNameProvider,ICompilerAda
 		
 		for (Iterator i = buildConfig.getInpath().iterator(); i.hasNext(); ) {
 			File inPathElement = (File)i.next();
-			List unwovenClasses = bcelWeaver.addJarFile(inPathElement,buildConfig.getOutputDir(),true);
-			state.binarySourceFiles.put(inPathElement.getPath(),unwovenClasses); // good enough for ajc to lump these together
+			if (!inPathElement.isDirectory()) {
+				// its a jar file on the inpath
+				// the weaver method can actually handle dirs, but we don't call it, see next block
+				List unwovenClasses = bcelWeaver.addJarFile(inPathElement,buildConfig.getOutputDir(),true);
+				state.binarySourceFiles.put(inPathElement.getPath(),unwovenClasses);
+			} else {
+				// add each class file in an in-dir individually, this gives us the best error reporting
+				// (they are like 'source' files then), and enables a cleaner incremental treatment of
+				// class file changes in indirs.
+				File[] binSrcs = FileUtil.listFiles(inPathElement, binarySourceFilter);
+				for (int j = 0; j < binSrcs.length; j++) {
+					UnwovenClassFile ucf = 
+						bcelWeaver.addClassFile(binSrcs[j], inPathElement, buildConfig.getOutputDir());
+					List ucfl = new ArrayList();
+					ucfl.add(ucf);
+					state.binarySourceFiles.put(binSrcs[j].getPath(),ucfl);
+				}
+			}
 		}
 		
-//		if (buildConfig.getSourcePathResources() != null) {
-//			// XXX buildConfig.getSourcePathResources always returns null (CompileCommand.java)
-//			for (Iterator i = buildConfig.getSourcePathResources().keySet().iterator(); i.hasNext(); ) {
-//	//			File resource = (File)i.next();
-//				String resource = (String)i.next();
-//				bcelWeaver.addResource(resource, (File)buildConfig.getSourcePathResources().get(resource), buildConfig.getOutputDir());
-//	//			bcelWeaver.addResource(resource, buildConfig.getOutputDir());
-//			}
-//		}
 		
 		bcelWeaver.setReweavableMode(buildConfig.isXreweavable(),buildConfig.getXreweavableCompressClasses());
 
@@ -575,7 +597,7 @@ public class AjBuildManager implements IOutputClassFileNameProvider,ICompilerAda
 		options.produceReferenceInfo(true); //TODO turn off when not needed
 		
 		try {
-			compiler.compile(getCompilationUnits(filenames, encodings));
+		 	compiler.compile(getCompilationUnits(filenames, encodings));
 		} catch (OperationCanceledException oce) {
 			handler.handleMessage(new Message("build cancelled:"+oce.getMessage(),IMessage.WARNING,null,null));
 		}
@@ -865,11 +887,19 @@ public class AjBuildManager implements IOutputClassFileNameProvider,ICompilerAda
 						factory,
 						getInterimResultRequestor(),
 						progressListener,
-						this,
+						this,  // IOutputFilenameProvider
+						this,  // IBinarySourceProvider
 						state.binarySourceFiles,
 						state.resultsFromFile.values(),
 						buildConfig.isNoWeave());
 	}
+
+	/* (non-Javadoc)
+	 * @see org.aspectj.ajdt.internal.compiler.IBinarySourceProvider#getBinarySourcesForThisWeave()
+	 */
+	public Map getBinarySourcesForThisWeave() {
+		return binarySourcesForTheNextCompile;
+	}
 	
 }   // class AjBuildManager
 
diff --git a/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/core/builder/AjState.java b/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/core/builder/AjState.java
index 232f93126..82dfe6263 100644
--- a/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/core/builder/AjState.java
+++ b/org.aspectj.ajdt.core/src/org/aspectj/ajdt/internal/core/builder/AjState.java
@@ -26,6 +26,9 @@ import java.util.Map;
 import java.util.Set;
 
 import org.aspectj.ajdt.internal.compiler.InterimCompilationResult;
+import org.aspectj.bridge.IMessage;
+import org.aspectj.bridge.Message;
+import org.aspectj.bridge.SourceLocation;
 import org.aspectj.util.FileUtil;
 import org.aspectj.weaver.bcel.UnwovenClassFile;
 import org.eclipse.jdt.internal.compiler.CompilationResult;
@@ -59,6 +62,8 @@ public class AjState {
 	
 	Set addedFiles;
 	Set deletedFiles;
+	Set /*BinarySourceFile*/addedBinaryFiles;
+	Set /*BinarySourceFile*/deletedBinaryFiles;
 	
 	List addedClassFiles;
 	
@@ -101,6 +106,14 @@ public class AjState {
 		deletedFiles = new HashSet(oldFiles);
 		deletedFiles.removeAll(newFiles);
 		
+		Set oldBinaryFiles = new HashSet(buildConfig.getBinaryFiles());
+		Set newBinaryFiles = new HashSet(newBuildConfig.getBinaryFiles());
+		
+		addedBinaryFiles = new HashSet(newBinaryFiles);
+		addedBinaryFiles.removeAll(oldBinaryFiles);
+		deletedBinaryFiles = new HashSet(oldBinaryFiles);
+		deletedBinaryFiles.removeAll(newBinaryFiles);
+		
 		this.newBuildConfig = newBuildConfig;
 		
 		return true;
@@ -126,6 +139,27 @@ public class AjState {
 		return ret;
 	}
 
+	private Collection getModifiedBinaryFiles() {		
+		return getModifiedBinaryFiles(lastSuccessfulBuildTime);
+	}
+
+	Collection getModifiedBinaryFiles(long lastBuildTime) {
+		List ret = new ArrayList();
+		//not our job to account for new and deleted files
+		for (Iterator i = buildConfig.getBinaryFiles().iterator(); i.hasNext(); ) {
+			AjBuildConfig.BinarySourceFile bsfile = (AjBuildConfig.BinarySourceFile)i.next();
+			File file = bsfile.binSrc;
+			if (!file.exists()) continue;
+			
+			long modTime = file.lastModified();
+			//System.out.println("check: " + file + " mod " + modTime + " build " + lastBuildTime);			
+			if (modTime >= lastBuildTime) {
+				ret.add(bsfile);
+			} 
+		}
+		return ret;
+	}
+	
 	private boolean pathChange(AjBuildConfig oldConfig, AjBuildConfig newConfig) {
 		boolean changed = false;
 		List oldClasspath = oldConfig.getClasspath();
@@ -153,7 +187,13 @@ public class AjState {
 			if (!oldPath.get(i).equals(newPath.get(i))) {
 				return true;
 			}
-			File f = new File((String)oldPath.get(i));
+			Object o = oldPath.get(i);  // String on classpath, File on other paths
+			File f = null;
+			if (o instanceof String) {
+				f = new File((String)o);
+			} else {
+				f = (File) o;
+			}
 			if (f.exists() && !f.isDirectory() && (f.lastModified() >= lastSuccessfulBuildTime)) {
 				return true;
 			}
@@ -188,6 +228,28 @@ public class AjState {
 		return thisTime;
 	}
 
+	public Map /* String -> List<ucf> */ getBinaryFilesToCompile() {
+		if (lastSuccessfulBuildTime == -1 || buildConfig == null) {
+			return binarySourceFiles;
+		}
+		// else incremental...
+		Map toWeave = new HashMap();
+		List addedOrModified = new ArrayList();
+		addedOrModified.addAll(addedBinaryFiles);
+		addedOrModified.addAll(getModifiedBinaryFiles());
+		for (Iterator iter = addedOrModified.iterator(); iter.hasNext();) {
+			AjBuildConfig.BinarySourceFile bsf = (AjBuildConfig.BinarySourceFile) iter.next();
+			UnwovenClassFile ucf = createUnwovenClassFile(bsf);
+			if (ucf == null) continue;
+			List ucfs = new ArrayList();
+			ucfs.add(ucf);
+			binarySourceFiles.put(bsf.binSrc.getPath(),ucfs);
+			toWeave.put(bsf.binSrc.getPath(),ucfs);
+		}
+		deleteBinaryClassFiles();
+		return toWeave;
+	}
+	
 	private void deleteClassFiles() {
 		for (Iterator i = deletedFiles.iterator(); i.hasNext(); ) {
 			File deletedFile = (File)i.next();
@@ -203,6 +265,16 @@ public class AjState {
 		}
 	}
 	
+	private void deleteBinaryClassFiles() {
+		// range of bsf is ucfs, domain is files (.class and jars) in inpath/jars
+		for (Iterator iter = deletedBinaryFiles.iterator(); iter.hasNext();) {
+			AjBuildConfig.BinarySourceFile deletedFile = (AjBuildConfig.BinarySourceFile) iter.next();
+			List ucfs = (List) binarySourceFiles.get(deletedFile.binSrc.getPath());
+			binarySourceFiles.remove(deletedFile.binSrc.getPath());
+			deleteClassFile((UnwovenClassFile)ucfs.get(0));
+		}
+	}
+	
 	private void deleteResources() {
 		List oldResources = new ArrayList();
 		oldResources.addAll(resources);
@@ -263,7 +335,8 @@ public class AjState {
 		}				
 	}
 
-	private void deleteClassFile(UnwovenClassFile classFile) {
+	
+	private void deleteClassFile(UnwovenClassFile classFile) {		
 		classesFromName.remove(classFile.getClassName());
 		
 		buildManager.bcelWeaver.deleteClassFile(classFile.getClassName());
@@ -274,6 +347,18 @@ public class AjState {
 		}
 	}
 	
+	private UnwovenClassFile createUnwovenClassFile(AjBuildConfig.BinarySourceFile bsf) {
+		UnwovenClassFile ucf = null;
+		try {
+			ucf = buildManager.bcelWeaver.addClassFile(bsf.binSrc, bsf.fromInPathDirectory, buildConfig.getOutputDir());
+		} catch(IOException ex) {
+			IMessage msg = new Message("can't read class file " + bsf.binSrc.getPath(),
+									   new SourceLocation(bsf.binSrc,0),false);
+			buildManager.handler.handleMessage(msg);
+		}
+		return ucf;
+	}
+	
 	public void noteResult(InterimCompilationResult result) {
 		File sourceFile = new File(result.fileName());
 		CompilationResult cr = result.result();