OK, I've written the missing spec for the A-T custom config (it's in the at the end of Apache::TestRun pod), please check that it's sane and that I haven't missed some possible cases. This is a top level spec with many details explained in the code.
Next I did another iteration on the code, changing a lot of logic, since there were several problems. And also making code more robust were needed.
I think that this time there should be little or no problems at all. I've looked at the problems you have reported before and I think they are all covered now. Please correct me if I'm wrong.
Also I tested many different cases (but not all), so here is what I've done. I'm not sure whether it's a good idea to save this test somewhere.:
[...]
if you work though this test and care to expand it, please add env vars tests which I've forgotten about (a way too many possible inputs). I've just noticed a bug and fixed it (APACHE env var was ignored).
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