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test_sys_checkout: use actual paths in on-the-fly configs rather than…
… MANIC_TEST_BARE_REPO_ROOT env var. This will make it easier to test (in the near future) that checkout_externals actually checked out the desired repo dir. The env-var path is still tested by two tests which rely on a checked-in externals.cfg that relies on an environment variable. More clearly document that env vars are passed to checkout_externals via os.environ, and that the command line assembled in _execute_checkout_in_dir is just for manual reproducibility.
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