It looks like the Eagle ‘45 Holes’ layer is not Chilipeppr supported yet. I have created a custom package with holes (button), as well as I have few holes on the board, but I don’t see them rendered nor present in the g-code 
did you include them in eagle cam to generate the gcode?
@sszafran if you take a look at the code for the Eagle BRD Import widget it shows what layers it uses to find SMDs, pads, vias, etc. I know it’s not looking for a layer called ‘45 Holes’. It would be cool if you were up for extending the code to allow other layers like ‘45 Holes’ to be included in the layers used.
@sszafran if you have time today, we can chat.
Technically you want layers 44-46: drills, holes, and milling if you want to be as thorough as possible. I was dealing with them yesterday trying to get a proper dxf out to render my board in CAD.
@jlauer I had a quick look at the widget code and I’ll try to get some time working on it mid-term (summer holiday?).
I am thinking also about g-code optimization, e.g. drilling order is not always the most efficient, probably depending on part definition. Autolevel probing after board drilling would be a great option, too. Just consider 2 sided board with plated through-holes, where drilling must be the first step.
@raykholo we surely will chat or talk one of the coming day.