Toss diced eggplant with 1 teaspoon of salt and place in a colander over a bowl for 30 minutes.
Cook eggplant in 2 T. of extra virgin olive oil over medium-high heat until golden, about 8 minutes. Remove from pan into a bowl and set aside.
Cook squash in 2 T. of extra virgin olive oil until lightly golden, about 4 minutes. Remove from pan and place into bowl with eggplant.
In a small bowl crush, by hand, the 1 pint of grape tomatoes; season with ½ t. of Kosher salt.
Tie rosemary and thyme sprigs together into an herb bundle.
Cut onions pole-to-pole and through the equator. Lie half of the onion flat on a cutting board and slice to reveal julienned-sized onions.
In the same pan, pour the remaining ½ cup of olive oil. On medium-low heat, saute the julienned onions with the rosemary and thyme herb bundle until onions are translucent and slightly golden, about 8 minutes.
Add to the onions, the coarsely chopped bell peppers. Continue to cook on medium-low heat for about 12 minutes.
Sprinkle crushed red pepper flakes and sliced garlic over this mixture; stir to combine for about 2 minutes.
Reduce heat to low and add crushed tomatoes. Cook while stirring occasionally until tomatoes are softened, about 8 minutes.
Add eggplant, squash and remaining tomatoes; stir slightly to evenly distribute with the other vegetables.
Adjust seasoning to your preference. (I added about 2 teaspoons of Kosher salt.) Simmer, covered, for about 12 minutes.
Remove from heat. adjust seasonings and remove remnants of herb bundle.
Top with basil chiffonade, parsley and capers, if desired.
Serve in a bowl.
Recipe by My Dragonfly Cafe at https://mydragonflycafe.com/rustic-ratatouille/