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.

This was not converted when we converted the rest, so do it now.