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.
It's not always obvious the mapping between stage level and
conflict-ness. More importantly, this can lead otherwise sane
people to write constructs like `if (!git_index_entry_stage(entry))`,
which (while technically correct) is unreadable.
Provide a nice method to help avoid such messy thinking.
