While there is an easy fix for unit tests, the one for I/O tests is cumbersome. My guess is that it the removal of something called prybar is the reason for I/O test problems.
If you could try and see if I/O tests work using the prybar template, that would be great.
The current solution for fixing I/O tests is just to replace the contents for both the .replit and replit.nix files (provided in the post below):
Note that this might break code intelligence, and using an older template is obviously not the best.