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suppose you two subprojects: core and tests. Now, in tests, there are is some test harness code that makes it easier to run your tests that others might want (in tests/src/main). Then you exercise this harness in tests/src/test. The coverage for core/src/main that you get from the tests in tests/src/tests will be excluded from the report.
The report seems to only aggregate code that is tested IN ITS OWN test directory.
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