Investigate running tests on installed bagel package

[alyssadai]

From what we've seen, the CLIRunner used to "call" the CLI in tests does not seem to behave exactly the same as running the installed package (e.g., in terms of the expected path structure of modules vs. non-module files - in our test environment all files in the repo are made available to the test CLI app, unlike in the actual installation).

To avoid issues like ..., we should look into whether there's a way to force the tests to run on the installed CLI (even something silly like making an actual system call with subprocess or something - but I'm sure something smarter must exist too).

Originally posted by @surchs in #379 (review)