Merge release-5-0 into master

Conflicts:
	cmake/gmxCFlags.cmake (adjacent changes)

Change-Id: I45088d7b5256613971b9926fc5fa50511a2ed743

diff --cc CMakeLists.txt
Simple merge

diff --cc cmake/gmxCFlags.cmake
index d779a2cb583d1ffe60b3399b5f468b1c054b0881,64f10ced525823ccce41a625191a700d9a02b037..4521a8aa0281f0908d27833d2b02d5e920a31baa
--- 1/cmake/gmxCFlags.cmake
--- 2/cmake/gmxCFlags.cmake
+++ b/cmake/gmxCFlags.cmake
@@@ -110,9 -110,14 +110,12 @@@ MACRO(gmx_c_flags
          # Since 4.8 on by default. For previous version disabling is a no-op. Only disabling for Release because with assert
          # the warnings are OK.
          GMX_TEST_CFLAG(CFLAGS_WARN_REL "-Wno-array-bounds" GMXC_CFLAGS_RELEASE_ONLY)
 -        # Since gcc 4.8 strict - false postives with old gmx_fatal. TODO: Remove in master
 -        GMX_TEST_CFLAG(CFLAGS_WARN_UNINIT "-Wno-maybe-uninitialized" GMXC_CFLAGS)
+         if(CYGWIN)
+             GMX_TEST_CFLAG(CFLAGS_WARN_SUBSCRIPT "-Wno-char-subscripts" GMXC_CFLAGS)
+         endif()
          # new in gcc 4.5
          GMX_TEST_CFLAG(CFLAGS_EXCESS_PREC "-fexcess-precision=fast" GMXC_CFLAGS_RELEASE)
 -        GMX_TEST_CFLAG(CFLAGS_COPT "-fomit-frame-pointer -funroll-all-loops"
 +        GMX_TEST_CFLAG(CFLAGS_COPT "-funroll-all-loops"
                         GMXC_CFLAGS_RELEASE)
          GMX_TEST_CFLAG(CFLAGS_NOINLINE "-fno-inline" GMXC_CFLAGS_DEBUG)
      endif()

diff --cc src/gromacs/math/utilities.c
Simple merge

diff --cc src/gromacs/selection/scanner.cpp
Simple merge

diff --cc src/gromacs/selection/scanner.l
Simple merge

diff --cc src/gromacs/selection/tests/selectioncollection.cpp
Simple merge

diff --cc src/gromacs/utility/cstringutil.h
Simple merge