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.