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Is it possible to only run when source directive is clover:on ?

This is a bit of an odd use case, but we are trying to make changes in an adversarial environment and it would be good if we could only show coverage for marked methods.  I know there are the source directives; on, off, flush, void.  

I was wondering if there was a way to configure it to only run when clover:on is set?

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There's no such possibility, however, you can control which files should be instrumented by using include/exclude patterns, take a look at this documentation.

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