Q: Clean transfer between old and new MacBook Pro????

I have a 2009 MacBook Pro, planning to buy a 2016 MacBook Pro.  I also use an Apple Airport Extreme Time Capsule to do my backups. I assume the data will simply transfer between my Airport Time Capsule and the new Pro.   Before I buy new, I want to make sure I understand how to move my content and leave behind junk programs and all the loose ends that must accumulate over the years in the old computer.  Or is cleaning things up part of the file transfer protocol.