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Not currently. You could use the method mentioned in the help to exclude some projects from versioning (rename that project's AssemblyInfo file [i.e., AssemblyInfox.cs]). Then you would need to manually set the assembly version attribute for the excluded projects, which could be done via a Replace in File action. Or use a separate solution for the CF projects.
Another option is to not update/increment the File version attribute for the entire solution (and remove any existing file version attributes from existing projects), since VS.NET will set the file and/or product version values in the executable to the assembly version if they are not specified.
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