Windows Installer vs. ClickOnce Deployment
Today, one of the developers in our teams asked me does it possible to use custom actions in ClickOnce. I’ve never thought about this before and I googled a bit. I found a nice article in MSDN. It briefly describes both technologies and the beginning and you can get an overview of them. Further, it contains two really important sections "Key Differences" and "How to Choose?". These sections will answer you the question "What of the technologies to use in a specific requirements that you might have?".
Back to the question, "Does it possible to use custom actions in ClickOnce?" No, you cannot use custom actions, your package does not have file and registry access, etc. But you can do all your pre-initializations when your application will start after ClickOnce deployment. Actually, I do not like this solution very much because it will not allow to perform uninstall actions that you might need. A better solution is to try to implement a solution like those described in section "Use Both Windows Installer and ClickOnce" of the article mentioned above.
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