Even though the file is empty and thus the size in the entry matches, we
should be able to detect it as a difference.

They fit there much better, even though we often check by diffing, it's
about the behaviour of the index.

This will tell us which numbers we were trying to compare, rather than
just telling us that they're different.

When confronted with a conflict in the index, `git_index_add_all`
should stage the working directory copy.  If there is no file in the
working directory, the conflict should simply be removed.

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.

When adding a conflict for some path, remove the staged entry.
Otherwise, an illegal index (with both stage 0 and high-stage
entries) would result.