Heat the olive oil in a large skillet over medium heat. Add the onions and 1/4 teaspoon salt and cook, stirring occasionally, until soft and translucent, about 25 minutes. Increase the heat to medium high and cook, stirring often, until golden brown, 5 to 10 minutes more.
While the onions cook, add the farro to the boiling water along with 1 teaspoon salt. Boil until tender but still very toothsome, about 20 minutes. Add the asparagus and cook until crisp-tender, about 2 minutes; drain well.
Add the farro and asparagus to the caramelized onions along with the parsley, vinegar and red pepper flakes. Season with salt and pepper. Transfer to a bowl and serve.