I assume that you'd like to run your tests again, because you have changed something in your application, isn't it? If yes, then it means that application must be rebuilt it and new clover.db has to be copied to the application server. And because of fact that application is re-deployed it means that Clover's coverage recorders will be restarted as well.
Marek, does your answer mean that there is no ability to have clover generate historical coverage reports when the code being tested is being changed constantly? After all, whenever we rebuild our code, we generate a new set of clover.db files. Your answer indicates to me that Clover's only historical ability is when you have new/changed tests, not new/changed product code being tested. If that is true, then the historical abilities are completely useless for us (we have at least a dozen change sets going into our build every day).
@jimbabka: I think you've misunderstood my answer.
I wrote that it is not possible to nullify hit counters at runtime (i.e. when an application is running) programatically (like the inline "///CLOVER:FLUSH" directive which allows to flush data to disk).
It is of course possible to restart the application (or server) and start recording again.
Clover historical report is a different feature. It requires history snapshot file, which contains zipped XML coverage report. Historical report compares these XML files (and not clover.db files). So it is of course possible to compare builds between each other - and there's no difference whether application classes or test classes were modified.
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