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