web.config file transform from command line

If you add the following xml to the bottom of the .csproj file for your web application, you’ll ensure that the config transformation occurs before every build:

<Import Project="$(MSBuildExtensionsPath32)\Microsoft\VisualStudio\v10.0\WebApplications\Microsoft.WebApplication.targets" />
<Target Name="BeforeBuild">
    <TransformXml Source="Web.Base.config" Transform="Web.$(Configuration).config" Destination="Web.config" />
</Target>

Edit: In response to your comment, you should be able to use Web.config as the source parameter in the TransformXml task (see step #2). If you only want to perform the config transform in the build script, follow these instructions:

1) Import WebApplication.targets in your build script like so:

<Import Project="$(MSBuildExtensionsPath32)\Microsoft\VisualStudio\v10.0\WebApplications\Microsoft.WebApplication.targets" />

2) Execute the TransformXml build task in your build script target:

<Target Name="MyBuildScriptTarget">
    <TransformXml Source="Web.config" Transform="Web.$(Configuration).config" Destination="Web.config" />
    ...other build tasks...
</Target>