According https://wiki.liberty-eiffel.org/index.php/Eiffeltest#File_handling eiffeltest should feed any .in files to the corresponding test and testing that its output matches the .out file.
Output different from the .out file doesn't make the test fail, contents of the *.in file are not fed to the test's stdin and the program is waiting for interactive input instead.

A user has provided a minimal example of .in and .out files having no effect here https://github.com/igneus/try-eiffeltest that may be useful to add to our test suite.

This feature is actually never used in our test suite: there is just one ".in" file, namely test/lib/numeric/number/test_number07.in but its matching test ( https://git.savannah.gnu.org/cgit/liberty-eiffel.git/tree/test/lib/numeric/number/test_number07.e ), explicitly opens the input file.

As far as I can say eiffeltest does not have the actual logic implementing the handling of in and out files.