Remove the now-unnecessary entries vector.  Add `git_array_search`
to binary search through an array to accomplish this.

Add a new build flag to disable the pool allocator

Windows defines `timeval` with `long`, which we cannot
sanely cope with.  Instead, use a custom timeval struct.

git_index_entry__init_from_stat: set nsec fields in entry stats

Improve error messages when dirs prevent ref/reflog creation