src/configure has modification time in the future.
The test `cd "$srcdir" && ls -1t configure configure~ | head -n 1` =
"configure" in src/configure.in seems unreliable. If the current
kernel's stat() doesn't support nanoseconds or ls doesn't compare
them, the test fails if the modification times of both files are in
the same second, which can happen if src/run_autoconfig --no-recurse
Perhaps if you use a file name that lexically precedes "configure",
such as "config-time-test", instead of "configure~".