Replace most strdup with gmx_strdup

Replace most strdup with gmx_strdup

gmx_strdup existed but code was using a mixture of it and strdup.
Advantages of using gmx_strudup everywhere:
- consistency
- error handling for out of memory
- strdup might not be available (e.g. Cygwin)

Left strdup in testutils which had already error handling. And fatalerror.cpp
which cannot use gmx_strdup because it could lead to an infinite loop.

If all strdup are removed gnu++0x in gmxTestCXX11.cmake is not required
anymore.

Change-Id: I6ed3e17e34b833b01222d4b45c680db7aadada34