Replace use of deprecated readdir_r
clang 3.8+ warn about the deprecation of readdir_r. The main issue
here is support for concurrent access to the same directory stream,
which is never something GROMACS is likely to do. Currently the only
use is implementing enumerateFilesWithExtension which is used
single-threaded by pdb2gmx for discovering force fields in the
database. So we can replace the use of readdir_r with readdir, which
is simpler, and offers other advantages listed in man readdir_r.
Documented the new restriction on the interface of
DirectoryEnumerator. There are no current uses of nextFile that
would be affected by the change.
Change-Id: I0b80554493ff80e8857f0431192e22cfe7db5b22