In our code writing index entries, we carry around a `disk_size`
representing how much memory we have in total and pass this value to
`git_encode_varint` to do bounds checks. This does not make much sense,
as at the time when passing on this variable it is already out of date.
Fix this by subtracting used memory from `disk_size` as we go along.
Furthermore, assert we've actually got enough space left to do the final
path memcpy.