Severing Protobuf dependency

[adamnovak]

Since libvgio defines the framing format that vg produces output in, it would be nice if it were easy to use in other projects that want to read and write vg's files (basically anything that would use libbdsg).

For that to work, it would potentially be desirable to not have to link against Protobuf to use libvgio.

This could be accomplished by moving vg's alignment format over to GAF or a binary flavor of GAF, which, together with the replacement of the vg::VG class by HashGraph/PackedGraph, would more or less remove the need for Protobuf in vg's interchange formats.

Then we could write our own varint encoder/decoder and replace/clone all the Protobuf base classes of the stream types here, and not have to use Protobuf anymore to access vg files.

On the other hand, since vg now supports system-packaged Protobuf, and since libbdsg also needs a bunch of succinct data structure libraries, it is not clear whether dropping Protobuf is really worth it, since dependencies will still exist and the marginal cost of an apt-get isn't high.