In short: they ground them into flour which could be baked or roasted.

Longer answer: this question can't be answered historically because it predates written history. Humans have been making pottery for at least 20,000 years, so that's how long they've had pots to boil stuff in. Theoretically, you don't even need pottery. You can hollow out a stone and boil stuff in it. If your stone container is too big or unwieldy to heat directly on the campfire, you can heat the contents by dropping red hot stones from the hearth into the water to make it boil.

But we have archaeological evidence of humans eating tough plant materials like grains and beans going back much further, to at least 30,000 years or maybe 50,000 years. This comes in the form of stones used to pound the seeds into flour, and in the form of charred products showing that they were subsequently cooked.

The easiest way to cook ground beans or cereals is to add water to turn the flour into a paste and spread it on a flat stone by the campfire. This produces simple flatbreads which are a very very old invention, and still eaten in most of the world. The basic roti or chapati or tortilla is a simple flatbread. You can do the same things with beans or lentils, like a dosa made from lentil flour.