Removed the optional `replace` argument, we now have 4 add methods:
`git_index_add`: add or update from path
`git_index_add2`: add or update from struct
`git_index_append`: add without replacing from path
`git_index_append2`: add without replacing from struct
Yes, this breaks the bindings.
When in the middle of a merge, the index needs to contain several files
with the same name. git_index_insert() used to prevent this by not adding a new entry if an entry with the same name already existed.
