Clean up matio.*

- Remove unnecessary includes of matio.h.
- Move t_matrix and related type definitions from types/matrix.h to
  matio.h, since this is the only header that needs them, and all users
  also need the contents of that header.
- t_rgb is an exception to the above rule.  Moved that to types/rgb.h
  for now, and adapted other users.
- Remove clear_matrix() as unused.
- Fix a file handle left open in do_dssp.
- Make several functions not declared in matio.h static in matio.cpp.
- Don't use gmx_fio_close() on a handle not opened with gmx_fio_open()
  in readcmap().
- Most of the *cmap() functions are unused (only do_dssp calls one of
  the reading functions, and no one calls the writing functions), but
  left them there for completeness.

Change-Id: Iffc9c9e6d06ce8884e1835c07e9c0f9227412725