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Keep user's settings after altering assembly/file version

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Background
I have a simple WinForms application written in C#. I debated deployment solutions for a while but ultimately decided to abandon ClickOnce as a few of the constraints were crucially restrictive.

Instead, I've adapted a simple solution of versioning the application via the assembly/file versions (I keep them in sync) in the application's properties. I'm deploying via a Setup Project (*.msi). I store the latest assembly version number in an XML file online, as well as the latest installer file. At run-time, I simply check the Application.ProductVersion against the latest version online and open an update dialog if an update is available.

Problem
This has worked pretty well thus far, but I've recently noticed a major problem with this approach. When the assembly version of the application is updated, a new version of the user's settings file (user.config) is created in AppData/Company/Product/Version/blahblahblah. This obviously forces the user to reset everything in the new version.

Suggested Solutions
I'm not sure how to proceed. The application only has 1 release thus far and the current user base is basically whoever I can beg to test it, so switching up strategies is no big deal. I've considered:

1.) Write my own settings system and thus have complete control over where/how the settings file is stored and used.
2.) Re-think my versioning/update strategy so that the update is not based on the assembly version. I'm not sure how I would do this, but my testing seemed to reveal that even building and installing a new version with the same assembly version would still break user.config.

I guess what I'm truly asking if there is any way to preserve the default settings system since it's so easy to use while also adapting it to my deployment strategy.


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