Consider making client config backwards and forwards compatible automatically through usage of protobuf

At the moment, the bootstrap client is configured through raw CLI flags / raw JSON config file. This isn't necessarily forwards or backwards compatible.

In the case where the caller specifies a new CLI flag on an older version of the client, the client invocation would break - instead the client should simply ignore the new config flag that it doesn't recognize.

One solution to this would be to use a versioned protobuf schema and contract instead of raw CLI flags / JSON config file

Start by reading the client implementation and the proto definitions described in the repository, then trace how raw CLI flags and JSON configuration are parsed. Define the versioned configuration contract and verify that newer options are ignored by older clients while older configuration remains accepted. Done means the compatibility behavior is specified and covered by appropriate tests.

Written by the indexing model from the issue text.