You do not have to file a 1099-misc to the contractor. That requirement was rescinded a few years ago.
You cannot add the cost to your 2016 return. You have to file an amended return for 2015.
A cost of a new roof cannot usually be deducted out right, but must be depreciated over 27.5 years. However, starting in 2015, there are a couple of options that you might qualify for. See https://ttlc.intuit.com/questions/3266204-de-minimis-safe-harbor-election?jump_to=answer_5361755
