There are many places throughout the codebase (mostly in the main classes) where we modify data via assignment in some object (e.g., a Suite) directly from some other class. this includes properties which are ostensibly "private" (e.g. Suite#_onlyTests).

This breaks encapsulation/information-hiding. Refactor these instances by creating methods within the classes having these properties, and call those methods from whatever code is currently doing direct assignment.

Example:

Instead, Suite could expose an instance method (e.g., appendOnlyTest) which appends the test to its _onlyTests array. The consuming code would call test.parent.appendOnlyTest(test). Going a step further, the Test class could expose an instance method (e.g. markOnly()) which would make the call.

These changes can be incremental; we don't have to do it all at once. Any new methods will need unit tests.