If you are targeting the 3.5 Framework, you do not need to sign up for ClickOnce deployments. Make sure the “Sign ClickOnce manifest” is not checked on the Icon tab of your project’s properties. This will allow you to edit the .plplication file after creating the deployment. Change the codebase attribute of the deployProvider ... tag
<deploymentProvider codebase="http://theirserver/.../Foo.application" />
This will not solve the problem of installing the application. If you are editing a file that you are deploying, the hash for the file must be regenerated.
Do you know what client setup should be? If so, maybe you can have separate configuration files for each client and do something with the pre-build event to copy the configuration files around?
Should the parameter be in the client configuration file? Could you save the settings on the server and pass it through the url parameter or get it when you call the web service after the application starts?
If these things do not work, you can provide your clients with a simple script (possibly using Mage ) so that they can regenerate and remove manifests (with their own certificate) after editing the deployment.
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