Why has this conditional section really not focused on conditionals and instead been a computers section?
I don't remember having seen the suffix -us yet.
Does "dosierujon" mean Directory, in the way Unix uses the term?
In other sentences, dosierujo could be translated with directory instead of folder. I would ask you to allow this here as well, because, well, you cannot say dosierujo without DOS.
Why does "dosierujon" take the accusative ending after "en?"
I believe it is the directional accusitive
Yes, this changes the preposition from "in" to "into", yet we still don't have to say "into" in English, as it is unlikely that you are in the folder and putting that somewhere.
It is very common to say "tion" (rather than "ĝin") in Esperanto in cases where in English we would say "it" (rather than "that"). I think DuoLingo should really not reject translations that use "it" for "tion" or vice versa.
Why is it meti instead of metu?
The second, third ... verb in the sentence takes infinitive form. You can't say 'Bonvolu metu' that's not how Esperanto works. Instead, it's 'Bonvolu meti".