Learn Hardcore Latin: Maneant pueri sub porticu, donec faber opus in tecto finiat. - Let the boys stay under the portico until the craftsman finishes the work on the roof.

Maneant is the present subjunctive, not the indicative. Here it is a jussive subjunctive, which Latin often uses to give a command about a third person:

manent = they remain / are remaining
maneant = let them remain

So the sentence is not simply describing what the boys do; it is telling what they are to do.

Why isn’t the command written as an imperative, like manete?

Because manete would mean stay! said directly to you all. That is a second-person plural command.

But pueri means the boys, which is third person. Latin commonly uses the jussive subjunctive for third-person commands:

manete = you all stay
maneant pueri = let the boys stay

English does something similar with let ....

What case is pueri, and how do I know?

Here pueri is nominative plural, the subject of maneant.

You can tell because:

maneant is third-person plural