Plug a memory leak caused by re-allocating a `git_index`
structure which has already been allocated by the test suite's
initializer.

Support reading and writing index v4.  Index v4 uses a very simple
compression scheme for pathnames, but is otherwise similar to index v3.

Signed-off-by: David Turner <dturner@twitter.com>

Ensure that we include conflicts when calling `git_index_read_index`,
which will remove conflicts in the index that do not exist in the new
target, and will add conflicts from the new target.

Read a tree into an index, write the index, then re-open the index and
ensure that we are treesame to the original.

Read a tree into an index using `git_index_read_index` (by reading
a tree into a new index, then reading that index into the current
index), then write the index back out, ensuring that our new index
is treesame to the tree that we read.

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.

Instead of hoping that we can get a racy entry by going real fast
and praying real hard, just create a racy entry.

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.