This fixes git_index_add and git_index_append to behave more like
core git, preserving old filemode data in the index when adding
and/or appending with core.filemode = false.

This also has placeholder support for core.symlinks and
core.ignorecase, but those flags are not implemented (well,
symlinks has partial support for preserving mode information in
the same way that git does, but it isn't tested).