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Assuming you have followed MSI patching <a href="http://msdn.microsoft.com/en-us/library/windows/desktop/aa370579(v=vs.85).aspx" rel="nofollow noreferrer">guidelines</a> when creating the initial web setup project and the one you want to derive a patch from... Basic guidelines (plenty of others to follow if you search): <ul> <li>Make sure your web project has a valid version number (1.2.3.4)</li> <li>Build installer for your initial release</li> <li>Time passes....</li> <li>Make changes as required for c)</li> <li>Update web project version - DLL(s) need to have version incremented</li> <li>Update web setup project properties - version needs to increase. Probably minor (XXX.YYY.ZZZ) <- increment Y. (by default this is 1.0.0)</li> <li>Update package code in setup project properties</li> <li>Build installer with changes</li> <li>Make administrative installs of each setup (msiexec /a websetup.msi)</li> <li>Use patch creation utility to create patch comparing the "old" to the "new" administrative installs you just created. (this step depends on the tool you want to use. I've used Installshield in the past, as well as straight msimsp.exe - old guide <a href="http://www.codeguru.com/csharp/.net/net_general/tipstricks/article.php/c9663/Creating-Installer-Patches-with-MSI-30.htm" rel="nofollow noreferrer">here</a>)</li> </ul> You can limit the files impacted by the patch (assuming they didn't change) by removing them from both the previous and the latest admin installs. Really, patching your website shouldn't be any different than any other set of files installed by MSI. Note that microsoft seems to be moving towards website deployment via msdeploy instead of building installers for them. For internal deployment, it works much easier.
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1. POHow to create a Patch file for a web application using asp.net
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