Updated env var names, added cache info
Updated Tested Config, Known Limitations sections
Updated PROJECT_VERSION for new alpha release
Updated PROJECT__VERSION for new dev working version
OCL compiler new flags - see notes

1. Added GMX_OCL_DUMP_INTERM_FILES - dump intermediate files for OpenCL
build:
- .IL/.ISA files for AMD
- .ptx file for NVIDIA
Ignored if caching is ON.
2. Added GMX_OCL_VERBOSE - prints extra info in build log.
Available only for NVIDIA.
Ignored if writing the log is disabled (see GMX_OCL_DUMP_LOG)
3. Renamed OCL_JIT_DUMP_FILE to GMX_OCL_DUMP_LOG - if defined, it forces
dumping OpenCL build log to file.
Flush WDDM queue if on Windows

CUDA version showed very poor performance on Windows compared to Linux.
This was due to WDDM buffering GPU jobs before actually sending them to
the GPU for execution.
This was solved by calling cudaStreamQuery, which triggers a flush for
the WDDM queue.
Fixed header comment
Merge pull request #78 from mabraham/opencl

Applied dos2unix
Merge pull request #79 from mabraham/opencl

Fix mis-use of LJ_CUTOFF_CHECK
Added sizeof_ocl_dev_info function
Added OpenCL equivalent code for existing CUDA code
Added validation for mygpu index in init_ocl_gpu
Fixed bug in calculate_lj_ewald_comb_LB_F_E
Added missing code for releasing OpenCL resources
Added OpenCL info to the log

The following details were added for now:
- if OpenCL support is enabled or disabled
- OpenCL include path
- OpenCL library path
Fixed bug in gmx_print_version_info
Updated is_gmx_supported_ocl_gpu_id

is_gmx_supported_ocl_gpu_id has been updated to reject OpenCL GPU
devices which are not supported.
Added OpenCL equivalent host code for existing CUDA code
Ran Gromacs code beautifier

If needed in future, this ran with

admin/uncrustify.sh --rev=v5.0-alpha.0 update-workdir

but (unfortunately) we need to use a custom fork of uncrustify
(details noted in that script).

Passing later Gromacs review needs this script to be happy, so
we should start now in case it makes merges easier too!