Using Continuous Integration, you want to run FxCop against the build. Using Visual Studio's new "Website" project (Rick Strahl has some commentary about it), the aspnet_compiler creates DLLs with random names embedded. This is good, because it's unlikely that that DLL is cached anywhere. But it's bad, because FxCop wants to know what the DLL names are.
There's probably a better way to handle it, but we simply run aspnet_compiler twice: the first time with the -fixednames parameter, running FxCop against that build, then the second time without the -fixednames parameter generating uncached DLLs.
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