native: Stop using readdir()

This function is not threadsafe, and is deprecated in favor of the threadsafe
readdir_r variant.

Closes #12692
native: Move from usleep() to nanosleep()

Using nanosleep() allows us to gracefully recover from EINTR because on error it
fills in the second parameter with the remaining time to sleep.

Closes #12689
native: Fix usage of a deallocated mutex

When the timer_helper thread exited, it would attempt to re-acquire the global
task count mutex, but the mutex had previously been deallocated, leading to
undefined behavior of the mutex, and in some cases deadlock.

Another mutex is used to coordinate shutting down the timer helper thread.

Closes #12699