I took a look in my framework folder and it looks like the 4.0 framework has a different _CopyFilesMarkedCopyLocal. Try this modified version and let me know if it works for you (diff from orig highlighted):

<Target
    Name="_CopyFilesMarkedCopyLocal"
    Condition="'@(ReferenceCopyLocalPaths)' != ''"
    >

    <PropertyGroup>
        <!-- By default we're not using Hard Links to copy to the output directory, and never when building in VS -->
        <CreateHardLinksForCopyLocalIfPossible Condition="'$(BuildingInsideVisualStudio)' == 'true' or '$(CreateHardLinksForCopyLocalIfPossible)' == ''">false</CreateHardLinksForCopyLocalIfPossible>
    </PropertyGroup>

    <Copy
        SourceFiles="@(ReferenceCopyLocalPaths)"
        DestinationFiles="@(ReferenceCopyLocalPaths->'$(OutDir)%(DestinationSubDirectory)%(Filename)%(Extension)')"
        SkipUnchangedFiles="$(SkipCopyUnchangedFiles)"
        OverwriteReadOnlyFiles="$(OverwriteReadOnlyFiles)"
        Retries="$(CopyRetryCount)"
        RetryDelayMilliseconds="$(CopyRetryDelayMilliseconds)"
        UseHardlinksIfPossible="$(CreateHardLinksForCopyLocalIfPossible)"
        Condition="'$(UseCommonOutputDirectory)' != 'true' And ('$(Obfuscate)'!='true' Or '$(ShouldMergeAssemblies)'!='true')"
        >

        <Output TaskParameter="DestinationFiles" ItemName="FileWritesShareable"/>

    </Copy>

     <!-- Since this target is already overriden, let's use this to copy the mapping file. -->
    <Copy SourceFiles="@(ObfuscationMapFiles)" DestinationFiles="@(ObfuscationMapFiles->'$(OutDir)%(DestinationSubDirectory)%(Filename)%(Extension)')" SkipUnchangedFiles="true" Condition="'$(Obfuscate)'=='true'">
      <Output TaskParameter="DestinationFiles" ItemName="FileWrites" />
    </Copy>

</Target>

I was able to run my project but cookcomputing namespace not working,
GetPages GetPageList = (GetPages)CookComputing.XmlRpc.XmlRpcProxyGen.Create(typeof(GetPages));

Create method not invoking the page, what should i do, anything i missed?

Third paragraph should read:
Line 2580 in Microsoft.Common.targets is inside the “GenerateApplicationManifest” target.

This seems like a great solution but I can’t seem to get it working, not sure if I’m doing something wrong.

I get the following error message when builing my project:
C:\Windows\Microsoft.NET\Framework\v4.0.30319\Microsoft.Common.targets(2580,9): error MSB3171: Problem generating manifest. Could not load file or assembly ‘C:\ProjectName\obj\Release\AppName.exe’ or one of its dependencies. An attempt was made to load a program with an incorrect format.

Line 2580 in Microsoft.Common.targets is inside the section.

I’ve noticed that when I remove the following from your .targets file, the project compiles but it is then obviously working with the original exe and not the obfuscated version:

I’m also not quite sure what you mean with the following related to the _CopyFilesMarkedCopyLocal, GenerateManifests and DoubleCheckDependencies targets
“Borrowed from target in ‘Microsoft.Common.targets’ included with MSBuild 2.0. You may need to make sure it matches the targets file included with your version of MSBuild.”

Does this mean that I have to overwrite the target in your .targets file with what’s found in the Microsoft.Common.targets file (located in C:\Windows\Microsoft.NET\Framework\v4.0.30319)?

These are probably obvious questions but I’m not at all familiar with the way .target files work.

Thanks in advance
Stefan

You see, when the compiler is invoked in a configuration called Release either by a build or a publish, it compiles and assembles all the necessary files in the “obj\Release” folder. This is called the “intermediate output path” which you’ll see used in the Obfuscation.targets file.

If you’re performing a publish, once the build is complete vs will build the publish using these intermediate files and generate and sign the publish manifest. We do the obfuscation in the intermediate folder because after the publish manifest is generated, the published files may not change.

Only after everything is completely built are things copied to the “bin\Release” folder or the publish destination.

By the way, are you using the community edition of Dotfuscator? Keep in mind that its obfuscations are extremely weak and probably won’t do much to protect your program. Download .NET Reflector to see just how much of your program is still susceptible to disassembly.