Modifying the file system's implementation would be. Including a valid_testdata.txt and an invalid_testdata.txt file in your test's directory, however, is not 'modifying the file system'.

> don't want my daemons or user-facing applications to just crash, when a file is missing

If the file is important, it's the best kind of thing you can do when implementing a non-user-facing service. The last thing you want to do is to silently and incorrectly serve traffic because you are missing configuration.

You want to crash quickly and let whatever monitoring system you have in place escalate the problem in an application-agnostic manner.