I think you are working with Minecraft 1.3.1 no? If you are, there is a file contained in the zip called aux.class, which unfortunately is a reserved filename in windows. I've been trying to automate the process of modding, while manipulating the jar file myself, and have had little success. The only option I have yet to explore is find a way to extract the contents of the jar file to a temporary location, while watching for that exception. When it occurs, rename the file to a temp name, extract and move on. Then while recreating the zip file, give the file the original name in the archive. From my own experience, SharZipLib doesnt do what you need it do nicely, or at least I couldnt figure out how. I suggest using Ionic Zip (Dot Net Zip) instead, and trying the rename route on the offending files. In addition, I also posted a question about this. You can see how far I got at Extract zip entries to another Zip file
Edit - I tested out .net zip more (available from http://dotnetzip.codeplex.com/), and heres what you need. I imagine it will work with any zip file that contains reserved file names. I know its in C#, but hey cant do all the work for ya :P
public static void CopyToZip(string inArchive, string outArchive, string tempPath)
{
ZipFile inZip = null;
ZipFile outZip = null;
try
{
inZip = new ZipFile(inArchive);
outZip = new ZipFile(outArchive);
List<string> tempNames = new List<string>();
List<string> originalNames = new List<string>();
int I = 0;
foreach (ZipEntry entry in inZip)
{
if (!entry.IsDirectory)
{
string tempName = Path.Combine(tempPath, "tmp.tmp");
string oldName = entry.FileName;
byte[] buffer = new byte[4026];
Stream inStream = null;
FileStream stream = null;
try
{
inStream = entry.OpenReader();
stream = new FileStream(tempName, FileMode.Create, FileAccess.ReadWrite);
int size = 0;
while ((size = inStream.Read(buffer, 0, buffer.Length)) > 0)
{
stream.Write(buffer, 0, size);
}
inStream.Close();
stream.Flush();
stream.Close();
inStream = new FileStream(tempName, FileMode.Open, FileAccess.Read);
outZip.AddEntry(oldName, inStream);
outZip.Save();
}
catch (Exception exe)
{
throw exe;
}
finally
{
try { inStream.Close(); }
catch (Exception ignore) { }
try { stream.Close(); }
catch (Exception ignore) { }
}
}
}
}
catch (Exception e)
{
throw e;
}
}