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Application settings cannot be upgraded

My C# application uses the default C# settings mechanism. The problem here is, that everytime I change my application's version number, all settings are gone and reset to their defaults.
Thus I implemented the upgrade mechanism described here.
Problem 1:
The weird thing is, that this seems to have no effect. After the upgrade code is executed, all settings still have their default values and none of the old values have been loaded.
Does the upgrade mechanism not work?
Problem 2:
Also after saving the settings, a new settings folder is created in AppData/Local (the name differs in the URI part). So after a couple of versions there are dozens of these folders lurking around, which does not feel right.
Is it normal behavior that an application creates new settings folders for each version?

Where to store user preferences for a C# Windows app

Can anyone provide a best-practices example for where to store user preferences for a C# Windows app?
So far I've heard a number of options:
Some people are saying to store it in
SQLite. Is SQLite bundled with .NET
2.0 and immediately available for use to me?
Others have said to use the built-in
Application Settings... but I've
heard that the per-user settings here
disappear if you upgrade the app (an
obvious problem).
I've also considered just storing it
in a .xml file somewhere on disk...
but where it the "correct" place to
store that .xml file for the user?

SQLite is not included with .NET2, but you could ship it with your application
The built-in settings system works fine for simple apps - you do need to add a couple of lines of boilerplate to deal with version changes but it's not complicated.
You could put your xml file here:
Environment.GetFolderPath(
Environment.SpecialFolder.LocalApplicationData)
There is a lot of 'it depends' about your question, as you don't say how much of what types of data you need to store, nor if you have any other reasons to care where it goes.

The per-user settings "disappearing" can be solved thus: .NET ApplicationSettingsBase Should I call Upgrade() every time I load?

Storing user application settings in isolated storage seems to be a best practice.
http://msdn.microsoft.com/en-us/library/system.io.isolatedstorage(v=vs.80).aspx
Storing settings as an xml file is perfectly fine.

How to keep user settings on uninstall

I'm using .NET user settings feature and I'm facing a problem.
When the application is uninstalled, then installed back, the user settings are lost.
I understand it's by design, and I want to be able to give the choice to the user in the installer.
Could you please give me some pointers to articles or documentation that will helps me?
Thanks a lot

.NET User Settings are not removed on uninstall. In fact the settings of all previous versions of the software are preserved in Local Settings directory.
When the new version is installed, a new version of the settings is created and default settings are used.
To ensure your application will merge new settings with previous configuration, you have to call Settings.Default.Upgrade() method.
So the solution is to manually remove settings on uninstall if we don't want to preserve them. Since what I needed was preserving previous settings, all I do now is creating a new setting called UpgradeRequired with true has the default value, then add this code at application startup:
if (Properties.Settings.Default.UpdateRequired)
{
Properties.Settings.Default.Upgrade();
Properties.Settings.Default.UpdateRequired = false;
}

You could possibly write the settings you wish to save out to the registry or write them as an XML file to a location that won't be impacted by the uninstall.

If you want to keep using User Settings i would suggest writing a custom installer class, and implement the onUninstalling method, to go find the file and copy it to another location known to the onInstall method of your custom installer. So that the next time the installer runs it could find the file.

I don't think you want to actually persist data on the users machine after an uninstall. Leaving files around is an evil practice, a big no-no. You should expose a feature in the application itself to either export those settings to a location of their choice and to then import it again after re-installing the app or to synchronize those settings onto a server so they're automatically available upon re-install, etc. On an uninstall you should leave no trace behind.

single exe with changeable settings

I am trying to make a simple application which will be used to point a web browser control to some of our web applications at my work. I would like to have only one exe file but also have an admin window to change some of the settings and have them persist when the application is closed. Is that possible? I have looked at the application settings resources part but as I understand that makes a file that loads the settings.
I don't want to have to parse a file or have anything but ONE file so please don't suggest doing that if it is possible.

Just use application settings - that will create a single file, you won't have to do any parsing, it'll all be fine.
It'll be separate to the exe file, but unless you meant that "ONE file" to include the executable and rewrite that on the fly, it should fit your description easily.
For example, let's build a console app that just remembers how many times it's been launched:
Create a new console application project
Go to the properties page, and click into the Settings tab.
Click on the link to create a settings file
Type in the table to create a setting called "LaunchCount" of type int. Make it either user scope or application scope, depending on whether you want it to be persisted per user or system-wide.
Hit Ctrl-S to save.
In the Main method in Program.cs, write this code:
Settings settings = Settings.Default;
settings.LaunchCount++;
Console.WriteLine("Launch count: {0}", settings.LaunchCount);
settings.Save();
Add the appropriate using directive for Settings (put the cursor in Settings and hit Ctrl-.)
Run the app several times, and observe the number increasing.

You can't have persisted settings without having a separate file...safely. You must either have a separate file, which is the standard and suggested approach approach, like the one created with Application settings, or you must use something like the registry to save settings.
Keep in mind, though, that using the registry is highly discouraged due to security reasons. Plus most companies don't allow access to registries anyway which means that anyone without this access could not use the settings feature.

There are several ways to do this. You can use a command-line argument to do that. Launch the app from the shell and put in your command line argument and change how it launches.
A UNIX-y approach is to look at the name of the exe and change behavior based on that. If I recall correctly, rsh and rlogin are the same executable - they just look at argv[0] to decide how to run. In windows, this is straight forward - look at System.Environment.GetCommandLineArgs - if there is a non-empty string in the 0th element of that, it will be your executable name.
For persisting settings, see Jon Skeet's answer.

I have to say that this is generally a bad idea, but I've done this before a long time ago in VB6. I created a Resource within the exe and then (somehow) directly manipulated it.
The problem is, is that this is usually not possible within the .NET framework due to it being memory resident. These guys tryed it out in .net and they ended up creating an program in IL to do the heavy lifting... Modify Emdeded String in C# compiled exe
Go with a settings file as Jon suggested!

C# .NET Application Settings and Upgrading

I use Settings.Default.MySettingName & Settings.Default.Save to save and load settings. When I change my version number how am I able to get the settings from the old version and apply to them my new version? I just can't quite figure it out.

Settings.Upgrade() looks like it has some promise - check out this post - and note that this method should be called once-and-only-once by your application.