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Harry caught sight of Malfoy, Crabbe, and Goyle's triumphant faces as he left, walking numbly in Professor McGonagall's wake as she strode toward the castle. He was going to be expelled, he just knew it. He wanted to say something to defend himself, but there seemed to be something wrong with his voice. Professor McGonagall was sweeping along without even looking at him; he had to jog to keep up. Now he'd done it. He hadn't even lasted two weeks. He'd be packing his bags in ten minutes. What would the Dursleys say when he turned up on the doorstep?
(Harry Potter and the Sorcerer's Stone)

Wiktionary says ‘have done’ means “to reach an end; to finish (with).” Then does ‘it’ refer to something else, for example, Harry’s Hogwart’s school life; or is the phrase ‘had done it’ used as a kind of idiom?

7

This is an instance of the idiom "Now you've done it!" The basic meaning behind it is that someone has done something bad which is the final straw/will get them in trouble for whatever reason. I don't remember exactly what happened at this point in Harry Potter, but the idea is that whatever Harry did to get McGonagall mad at him was very bad, she is extremely upset, and it's likely he's going to get expelled.

A couple other examples of this phrase's use:

John breaks a lamp.

Mary: Oh, now you've done it! You're going to be grounded for the rest of your life!

Or perhaps:

John pushes the big red button, loud sirens start going off.

Mary: Now you've done it! We're all going to die here, aren't we?

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