Program: 100546
Project: 100546
Buggy source:
/** 
 * Call this to copy any unmodified classes to the output. This is called automatically by close(); you should only call this if you want to write an entry to the JAR file *after* the unmodified classes. This will only ever be called once per output JAR.
 */
final public void writeUnmodifiedClasses() throws IOException {
  passUnmodifiedClasses=false;
  makeOutputJar();
  for (int i=0; i < inputs.size(); i++) {
    Input in=inputs.get(i);
    if (!in.isClass()) {
      if (in instanceof JarInput) {
        JarInput jin=(JarInput)in;
        ZipEntry entry=jin.getEntry();
        InputStream s=jin.open();
        try {
          ZipEntry newEntry=new ZipEntry(entry.getName());
          newEntry.setComment(entry.getComment());
          newEntry.setExtra(entry.getExtra());
          newEntry.setTime(entry.getTime());
          putNextEntry(newEntry);
          copyStream(s,outputJar);
          outputJar.closeEntry();
        }
  finally {
          s.close();
        }
      }
 else {
        throw new Error("String_Node_Str" + in);
      }
    }
 else {
      String name=in.getClassName();
      if (name == null) {
        BufferedInputStream s=new BufferedInputStream(in.open(),65536);
        try {
          Object cl=makeClassFromStream(s);
          String entryName=toEntryName(getClassName(cl));
          if (!entryNames.contains(entryName)) {
            putNextEntry(new ZipEntry(entryName));
            BufferedOutputStream clOut=new BufferedOutputStream(outputJar);
            writeClassTo(cl,null,clOut);
            clOut.flush();
            outputJar.closeEntry();
          }
        }
  finally {
          s.close();
        }
      }
 else {
        String entryName=toEntryName(name);
        if (!entryNames.contains(entryName)) {
          BufferedInputStream s=new BufferedInputStream(in.open());
          try {
            putNextEntry(new ZipEntry(entryName));
            BufferedOutputStream clOut=new BufferedOutputStream(outputJar);
            copyStream(s,clOut);
            clOut.flush();
            outputJar.closeEntry();
          }
  finally {
            s.close();
          }
        }
      }
    }
  }
}

Fixed version (ground truth):
/** 
 * Call this to copy any unmodified classes to the output. This is called automatically by close(); you should only call this if you want to write an entry to the JAR file *after* the unmodified classes. This will only ever be called once per output JAR.
 */
final public void writeUnmodifiedClasses() throws IOException, IllegalStateException {
  passUnmodifiedClasses=false;
  makeOutputJar();
  for (int i=0; i < inputs.size(); i++) {
    Input in=inputs.get(i);
    if (!in.isClass()) {
      if (in instanceof JarInput) {
        JarInput jin=(JarInput)in;
        ZipEntry entry=jin.getEntry();
        InputStream s=jin.open();
        try {
          ZipEntry newEntry=new ZipEntry(entry.getName());
          newEntry.setComment(entry.getComment());
          newEntry.setExtra(entry.getExtra());
          newEntry.setTime(entry.getTime());
          putNextEntry(newEntry);
          copyStream(s,outputJar);
          outputJar.closeEntry();
        }
  finally {
          s.close();
        }
      }
 else {
        throw new Error("String_Node_Str" + in);
      }
    }
 else {
      String name=in.getClassName();
      if (name == null) {
        BufferedInputStream s=new BufferedInputStream(in.open(),65536);
        try {
          Object cl=makeClassFromStream(s);
          String entryName=toEntryName(getClassName(cl));
          if (!entryNames.contains(entryName)) {
            putNextEntry(new ZipEntry(entryName));
            BufferedOutputStream clOut=new BufferedOutputStream(outputJar);
            writeClassTo(cl,null,clOut);
            clOut.flush();
            outputJar.closeEntry();
          }
        }
  finally {
          s.close();
        }
      }
 else {
        String entryName=toEntryName(name);
        if (!entryNames.contains(entryName)) {
          BufferedInputStream s=new BufferedInputStream(in.open());
          try {
            putNextEntry(new ZipEntry(entryName));
            BufferedOutputStream clOut=new BufferedOutputStream(outputJar);
            copyStream(s,clOut);
            clOut.flush();
            outputJar.closeEntry();
          }
  finally {
            s.close();
          }
        }
      }
    }
  }
}