Refactor vendor dir

[mara-schulke]

Changes

This pr refactors the package store from:

proto
  /vendor/
    <a>/
      Proto.toml
      vendor/<c>/..
    <b>/
      Proto.toml
      vendor/<c>/..

To

proto
  /vendor/
    <a>/
      Proto.toml
      ..
    <b>/
      Proto.toml
      ..
    <c>/
      Proto.toml
      ..

And simplifies code generation implementation.

Upsides

This drastically simplifies the package store layout, and more importantly, enables people to compile it using any protobuf code gen tool, such as protoc without any change.

Furthermore it removes the type duplication problem that occured when nesting dependencies:

Before the change, you had two version of the c library types:

mod a {
  mod c { /* ... */ }
}

mod b {
  mod c { /* ... */ }
}

Which is now resolved, since tonic generates this structure:

mod a { /* ... */ }
mod b { /* ... */ }
mod c { /* ... */ }

Downsides

This change has the implication that all dependencies may only use one single version of c which is not ideal. We can and will solve this by introducing proper version resolution mechanism soon.

[cdbrkfxrpt]

a few very minor nits aside, this lgtm