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I only remember reading the first book. It was in middle school (around 2009-2011) so I'm a little fuzzy on the details, but I know once I see or read the title I'll know it.

I remember that it followed two main characters, a girl and a boy.

The boy was high born and was from a time of magic. He was sent to wizard school in a castle where he and the other boys were taught Socrates style, having to figure out the information on their own with little teaching. They had a cafeteria area where you could eat anything you wanted as long as you could concentrate enough to conjure it from the stone, so the boy ate apples, which he remembered most of all because he fed them to his horses. Eventually, after months of the same thing, the boys began to trade food. But he decided to use the stone to conjure soap, and that's when they gave him new robes, as in him moving up in rank.

The girl was born on a farm. Her mother was sick, so she went to get a healer. They killed her mom, and stole all her valuables from the farm house. I remember more, but I think it would confuse rather than help.

Key information: I believe the stories tie into each other like one is from the past, the other the future...

The books' tone was kind of dreadful with the hope of something better, like the boy could become a great wizard and the girl could solve a problem to this magical rebellion I think or learn more magic.

This is "Skin Hunger" by Kathleen Duey.

There's a wizard school, teachers who seem clueless about how to teach magic and more apples than you can shake a stick at.

Sadima lives in a world where magic has been banned, leaving poor
villagers prey to fakes and charlatans. A "magician" stole her
family's few valuables and left Sadima's mother to die on the day
Sadima was born. But vestiges of magic are hidden in old rhymes and
hearth tales and in people like Sadima, who conceals her silent
communication with animals for fear of rejection and ridicule. When
rumors of her gift reach Somiss, a young nobleman obsessed with
restoring magic, he sends Franklin, his lifelong servant, to find her.
Sadima's joy at sharing her secret becomes love for the man she shares
it with. But Franklin's irrevocable bond to the brilliant and
dangerous Somiss traps her, too, and she faces a heartbreaking
decision.

Centuries later magic has been restored, but it is available only to
the wealthy and is strictly controlled by wizards within a sequestered
academy of magic. Hahp, the expendable second son of a rich merchant,
is forced into the academy and finds himself paired with Gerrard, a
peasant boy inexplicably admitted with nine sons of privilege and
wealth. Only one of the ten students will graduate -- and the first
academic requirement is survival.

Sadima's and Hahp's worlds are separated by generations, but their
lives are connected in surprising and powerful ways in this brilliant
first book of Kathleen Duey's dark, complex, and completely compelling
trilogy. - _{^{Amazon UK}}