Move GPU implementation to new interface

Move GPU implementation to new interface

This prepares for OpenCL implementation by updating the existing
preprocessor-based interface for GPU functions (that has real
implementations with a GPU build and null implementations without).
Some related changes to identifier names, comments and docs.

Renamed
s/ncuda_dev/n_dev/g
s/cuda_dev/dev/g
s/nb_cuda/nb_gpu/g
s/cu_nb/nb/g
s/cu_nbv/gpu_nbv/g
s/cuda_dev_info/gmx_device_info/g
so they were more generic, for when an OpenCL implementation wants to
share the same identifiers. Related, some _gpu_ had to become
_cuda_gpu_ because it will only have a CUDA implementation, other
_cuda_gpu_ had to become just _gpu_, some _cuda_ had to become _gpu_
or _cuda_gpu_. Some CUDA became GPU.

Several CUDA header files are moved from mdlib/nbnxn_cuda to files of
more generic names in mdlib. This is not great either, but
reorganizing the whole nbnxn code into a proper module, perhaps with
submodules is not within the scope of this change.

Updated naming of some data types to be struct gmx_name_t, per
style in Redmine #1490. Used some explicit forward declarations
instead of including files to get them. Removed typedefs for
opaque pointers.

Moved gpu_timing struct from
legacyheaders/types/nbnxn_cuda_types_ext.h to timing/gpu_timing.h, and
the remaining content to mdlib/nbnxn_gpu_types.h. So we no longer
install this internal-use-only header.

The last part of init_interaction_const() in forcrec.cpp is split off,
so that the construction phase can be moved to occur before
init_nb_verlet(), so that the "constants" are known before any JIT
compilation of GPU kernels takes place. Future work will address the
question of handling JIT compilation more flexibly, or in more than
one place (e.g. when things become compile-time constants after PME
tuning).

Converted some Doxygen style to new guidelines, added basic file-level
documentation, updated include guards.

Introduced gpu_set_host_malloc_and_free so the implementation-specific
details can be handled in the implementations.

Change-Id: I888722c92daeccc7f32987d9b6cb15544351b68d