REv3 idea: Make is_topologically_sorted the default, and eliminate tag bytes

[EdSchouten]

In #229 and #230 we added a new is_topologically_sorted flag that can be used by workers to indicate that Tree objects are topologically sorted, making it easier to process them. It also simplified the wire format of Tree objects slightly, making it easier to parse them without using a Protobuf library.

1. This proposal is to make this option the default, requiring that all workers generate such Trees.
2. It proposes that we remove the tag bytes from the records, as they no longer serve any real purpose. It is already implied that the root directory is the first to be stored.
3. As (2) causes the encoding to differ from message Tree, we should then remove this message entirely. There are no other parts of the protocol where it is used.

Note that this is just a minor cleanup. If it turns out we manage to solve issues like #170, we can close this as being irrelevant.