An application might want to use C11 features. The user would assume
that setting `CFLAGS=-std=gnu11` in the Makefile would work. It does not
since the board's Makefile.include shadows the `-std` flag.

This patch removes the `-std=gnu99` from the various Makefile.includes,
and sets the flag in the common Makefile.include of RIOT instead.
If an `-std` flag was provided by an earlier Makefile (the application,
the board, or the CPU [whilst only the former one should]), then no
additional flag is set. It is first tested if the supplied compiler
understands `-std=gnu99`, then `-std=c99`.