tools/api: add support for 1) deprecating message types and 2) moving nested message types up

Title: add support for 1) deprecating message types and 2) moving nested message types up

Description:

• at the moment, there are already a few message types that have been deprecated, e.g.
  • bootstrap.v2.Runtime
    • tools/api already support removing it from the next API version by adding option deprecated = true;
  • trace.v3.Tracing
    • if option deprecated = true; is added, tools/api will remove the message along with its nested types, which is not desired (see next point)
• additionally, there is a case where a nested message type needs to be moved up, e.g.
  • trace.v3.Tracing.Http => trace.v4.HttpTracer
  • and, probably, even trace.v3.Tracing.Http => trace.v3.HttpTracer

Context:

• #10405