I've just released FxCop Integrator 1.1.1, it contians a code analysis bug fix related "Web Site" project. In this version, you can analyze a solution contains "Web Site" project.
FxCop Integrator 1.1.1 is available here.
And, I plan to release v1.2.0 in Jan 16 2011. This version will support Ruleset and changing some FxCop options. So you will be able to customize code analysis behavior.
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