Help adding new files to Jar file.

I am new to Java and am having problems haveing our Web App work after I have recreated the JAR file...this is what I did...
Changed to the following directory at a dos prompt:
D:\jdk1.3.1_01\bin
Ran the following to extract the files from the jar file.
jar xvf app2.jar
...this created 5 directories with various files.
copied new and updated graphic files to
D:\jdk1.3.1_01\bin\app2\images
Recreated the jar file using the following command (pv com javavp meta-inf borland are the 5 directories that were extracted from the original jar file above):
jar.exe cvf app2.jar pv com app2 meta-inf borland
I now have a new jar file that is a similar size, so it looks good, but when I put it in our web site, it does not recognize certain frames (that get information from the database) that it did before (the frames are blank)
Any thoughts on what I am doing wrong?
Also, are there any Windows programs that i can use to make this easier instead of using the dos commands?
Thanks...

To change the contents while inside a java program, you might be able to use Runtime.exec(String[]). Make the array with "jar.exe" as the first index, flags in the second, and remaining arguments in the remaining indecies.

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