How can I create an instrumented build that can be deployed and gather code coverage data?

I've got code coverage for my .net msbuild builds working using dotCover.  That works great for running unit tests, however I have a need to create instrumented dll's, deploy them, run additional tests and collect code coverage data for them.  Is this possible?  Are there steps documented anywhere?  I haven't found anything in my searching online and the artifacts produced from a build with code coverage enabled still appear to be the non instrumented versions.  Even if the results were not visible within TC, if I could get the data using the dotCover client that would be fine.

I will also have the same need for Java code coverage, but I'm starting with our .net stuff first.  Thanks.

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