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ATG patch is usually supplied as a JAR file. Open the JAR file using jar/winzip or some similar application. Patch will have a ReadMe file which will tell you details about the installation and un-installation of the patches. Typically the steps you should be performing are:
1. Shutdown ATG along with any HTTP servers that you may be running.
2. Copy ATG patch JAR file to the "patch" directory which is already present within ATG root directory.
3. From the command prompt, extract the patch archive using "jar xvf patch.jar“ which would create a patch specific directory under "patch" directory in ATG root.
4. Change to the newly created directory and run the patch install script from bin directory.
5. The patch install script will install and update various files in your ATG installation.
6. In case you assembled and deployed your application using runAssembler tool then you may need to redeploy as various ATG classes and configuration files get updated by the patch.