How to modify .NET config files during installation?

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We use WIX to change the application’s configuration file. It works really well, you’ll need to add wixUtilExtension.dll in the reference.

WIX sample:

<Component Id="ChangeConfig" Guid="[YOUR_GUID_HERE]">
   <File Id="App.config" Name="MyApplication.exe.config" Vital="yes" KeyPath="yes" Source="[Path to project dir]\app.config" />
   <util:XmlFile Id="AppConfigSetConnStr" Action="setValue" Permanent="yes" File="[#App.config]"            
        ElementPath="/configuration/connectionStrings/add[\[]@name="MyDatabaseName"[\]]" Name="connectionString" 
        Value="Your Connection string values here" />

</Component>

It actually depends on what you are using to create the installer, What are you using ?
Have alook at the WIX Tutorial.

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