Move CUDA-specific files to src/gpu

[rht]

I haven't tested it since it takes some time to prepare the dependencies on my laptop running NixOS. What I have done is

1. find all filenames starting with Cuda in src/ and move them to src/gpu/
2. Find all CUDA references in the makefile and change their directory.

The objective is to group the 45 .cc files in structured clusters in folders.