The FBI is facing the entire federal government in this case. It is why we are so quiet.
The problem is with the entire government. HRC is one component of that government. A Special Access Program (SAP) is an intelligence program classified above top-secret. They are held on closed servers at secret locations. The only way to get one is if you are specifically read on to a program, have a need to know, then you must physically go to a location and pass through several layers of security to even look at the program. A good example in non-classified terms would be the locations and operations of our intelligence operatives around the globe, or our missile silo locations.