On new homes we install the felt, the shingles, the flashings, etc. The labor cost is $40 per sq. to install the felt, shingles, and supply the nails on most homes. Flashing is extra. Materials can be provided at whatever the current pricing may be.
On new homes I generally come out as soon as the decking is installed to temporally dry the house in with felt. The felt generally keeps the inside dry while the cornice is being installed & painted and the mechanical pipes are being ran through the roof. Then I return and install the shingles and ridge cap with the exception of any brick areas above the roof line to dry the house in even more, after the brick work has been completed I return to finalize the roof with flashing and whatever else needs to be done.