There is a proposed fix in git commit 8b5a2f96c956ba5b34eed47226d78fc8032de0db
What it does is that Parsers.config.parse() will now handle any permission errors softly if the file in question is a resource file (as they are most commonly with special permssions).
Error will be appended to Parsers.config.errors instead of raising an exception.
If permission denied is encountered in Model.*.get_effective_check_command there is an exception like before.
Abhinav, if you have time, please verify that the patch works as expected. In the meantime i will close the case.