Rafters - to peg or not to peg, that is the question

I'm building a 14'x 24' timber frame cottage, using Jack Sobon's plans for a timber frame tool shed. I can't find any reference to how the rafters (4"x6"x12', on 2' centers) are fastened to the plate (8"x8"x24'). The plans call for notching out the plate, and then fitting the rafters into the notchs. Is this sufficient, or should they be pegged in as well. If pegged, should the peg holes be draw bored like the sills and bents?

You certainly need some means to attach the rafters to the plates in order to resist wind uplift. Depending on prevailing conditions, your local building code may require a metal connector like a Simpson strap for this purpose.

Most older building constructed after the advent of machine made nails would have used them rather than pegs. Preboring of wooden peg holes is rather infeasible because of alignment tolerances. So, my suggestion would be to use large spikes --- That's what Jack does.