git_buf_clear does not free allocated memory associated with a
git_buf. Use `git_buf_free` instead to correctly free its memory
and plug the memory leak.

If the underlying filesystem doesn't support better than one
second resolution, then don't expect that turning on `GIT_USE_NSEC`
does anything magical to change that.

The index::nsec::staging_maintains_other_nanos test was created to
ensure that when we stage an entry when GIT_USE_NSECS is *unset* that
we truncate the index entry and do not persist the (old, invalid)
nanosec values.  Ensure that when GIT_USE_NSECS is *set* that we do
not do that, and actually write the correct nanosecond values.

Test that nanoseconds are round-tripped correctly when we read
an index file that contains them.  We should, however, ignore them
because we don't understand them, and any new entries in the index
should contain a `0` nsecs field, while existing preserving entries.