Learn Farsi: شش پوشه‌ی جدید روی میز است.

This is exactly how numbers work in Farsi! Whenever you use a number like شش (six), the noun that follows it must stay singular. You never make the noun plural after a specific number, so the sentence literally says six new folder.

What is the extra letter ی doing at the end of پوشه‌ی?

That is the ezafe connector, which links the noun پوشه (folder) to its adjective جدید (new). Because the word پوشه ends in a silent letter that makes an eh sound, we must add the letter ی (which makes a ye sound) to smoothly connect the two words.

Why does the sentence end with است (is) instead of a plural verb for are?

In Farsi, non-human objects usually take a singular verb, even when there are multiple of them. Combined with the rule that numbers require a singular noun, using the singular verb است at the very end of the sentence is the most grammatically correct and natural way to say this.

I see روی for on and میز for desk. Where is the word for the?

Farsi does not have a direct equivalent for the English word the. The word میز can mean desk or the desk depending on the context. Here, we know it translates to the desk because it refers to a specific place where the folders are sitting.