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    <p>Beware MSBuild and VSBuild DO differ. <a href="https://stackoverflow.com/a/1830650/57883">Afterpublish is VERY limited</a></p> <p><a href="https://stackoverflow.com/questions/8404114/how-make-msbuild-build-custom-target-specified-in-csproj-building-sln">Try having msbuild save the emitted sln</a> Also <a href="https://stackoverflow.com/questions/5556168/msbuild-script-utilizing-solution-information">here</a>.</p> <p>Have you verified the file is getting transformed at the expected time? Add in a <code>&lt;message importance="high" text="Doing Custom Transform" /&gt;</code> before your transformxml call, then another message with different text <code>Finished Custom Transform</code> after this call. <a href="https://stackoverflow.com/a/9059685/57883">This post</a> speaks directly to your desire to do things involving the specialized publishing targets.</p> <p>General msbuild debugging information:</p> <p>Hopefully this behavior IS msbuild dependant instead of VSBuild, since the two build processes differ. If you are in luck and this is following the same behavior as MSBuild would follow the msbuild debugging process:</p> <p>As with any magical behavior in msbuild, in your <code>CSProj</code> file look for any <code>import target=</code> code and go find those files. Following these through will lead you to the part that is making the decision about any of this.</p> <p>Also you can attach VS's debugger to your build process - <a href="http://blogs.msdn.com/b/visualstudio/archive/2010/07/06/debugging-msbuild-script-with-visual-studio.aspx" rel="nofollow noreferrer">http://blogs.msdn.com/b/visualstudio/archive/2010/07/06/debugging-msbuild-script-with-visual-studio.aspx</a> + <a href="http://blogs.msdn.com/b/visualstudio/archive/2010/07/09/debugging-msbuild-script-with-visual-studio-2.aspx" rel="nofollow noreferrer">http://blogs.msdn.com/b/visualstudio/archive/2010/07/09/debugging-msbuild-script-with-visual-studio-2.aspx</a></p> <p><a href="http://msdn.microsoft.com/en-us/library/ee216359.aspx" rel="nofollow noreferrer">Determining build order</a> </p> <p>Also in crank up the build verbosity temporarily <a href="http://blogs.msdn.com/b/msbuild/archive/2005/09/29/475157.aspx" rel="nofollow noreferrer">http://blogs.msdn.com/b/msbuild/archive/2005/09/29/475157.aspx</a></p>
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