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 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.