Refactor for query results and failures, new protobuf protocol, fixing simulation/reachability

[seblund]

Large PR, sorry. Almost all changes depend on each other which resulted in changes all over the code base. I will do a walkthrough on request :)

Changes:

• Update protobuf to support:
  • Simulation of all system types (Quotient works now)
  • Cause of failure for all query types with as much information as possible
• Add nice result enum types for every query and cause of failure
• Introduce intermediate types between protobuf structs and TransitionSystem related structs (State, LocationTuple, Federation, etc.) with conversions between them (proto <=> intermediate <=> ts ).
• Basically rewrite simulation as the only complicated part is serialization/deserialization of states
• Change reachability to use the same Decision structs as in simulation

Most of the changes were to be able to serialize and deserialize States (Hence also LocationTuple and Federation). There are tests to ensure that the proto <=> intermediate <=> ts relation holds for thousands of different States from various systems.

[seblund]

I have resolved the conversations that I have fixed with these commits. I have also added documentation to all structs/enums/funcs in specifics.rs and query_failures.rs.

I have now added issues for documentation in general and for consistent naming of build_* methods :)