The shell is where you put all your side effects. Things like user input or writing to files.
That way you can use pure functions on the inside. Pure functions don't allow for side effects.
That way you can use pure functions on the inside. Pure functions don't allow for side effects.
For a functional shell, your program's entry point would be composed of pure functions describing effectful actions to take. The necessary computations get bubbled up to the entry point during evaluation, at which point the runtime / compiled program executes them.
(At least, this is the abstracted perspective you should view the purely functional source code from. The final program itself in practice is, of course, effectful throughout).
This is why there's now more focus on algebraic effects as an alternative for keeping a functional core, imperative shell. Monads/transformers are just an ugly solution that even hardcore functional programmers don't want to use.