kvmtool: Change readdir_r to readdir

readdir_r is deprecated[1] and usage of readdir is recommended.

[1] https://sourceware.org/git/?p=glibc.git;a=commit;h=7584a3f96de88d5eefe5d6c634515278cbfbf052



Signed-off-by: Michal Rostecki <michal.rostecki@gmail.com>
Signed-off-by: Will Deacon <will.deacon@arm.com>