@rynait, since this is the easiest of the questions. Yes, you can completely rearrange the gem file to be however you want. I would like to let you know, there are over 100 gems. Enjoy.
@Mephansteras and MaximumZero, removing the stuff from the entity is a completely viable option. However... I would say to start some where small or easy. I'd go with metals first, because you already have the smelter modifiable, so it'd be as simple as adding a line or two to the existing reactions for it to start. The first question is how do you want to approach the research portion of it. One person suggested a workshop where you could dismantle minerals/gems/stones/whatever and get research points. This idea is okay, but I wouldn't want to use the research points for say actually building the items. I would prefer research points to be used up. I would suggest something along the lines of books or tomes or something. dismantle the elements, get research points, spend research points on a specific book item, book item gets used in reactions and doesn't get used up. I would basically have a couple books, one for precious metals, one for metals below iron, one for iron, one for steel, one for adamantine. At the very least IMO. You could get very specific and make one for each metal.