Clean up gmx_header_config

- Remove some probably unnecessary uses for GMX_CYGWIN.
- Move GMX_CYGWIN to config.h as it is not used in installed headers
  (maybe it would be better to get rid of even the remaining uses in
  favor of some other mechanism).
- Remove gmx_header_config_gen.h and all complexity that supports it as
  there is nothing generated there any longer.
- GMX_NATIVE_WINDOWS could possibly be moved somewhere else, but
  currently it is only used in two headers, so possibly even better
  would be to just get rid of those two.

Closes #1454

Change-Id: Id27370a007eda30b7c803a3c14aa687d43555db8