Where I work has chosen to structure their proto definitions for company proto files under a path such as
./protos/s12/accounts/user/v1/user.proto

In this user.proto we have imports to vendored 3rd party protos that are stored in a directory prefixed with third_party.

import "google/api/annotations.proto";
import "google/api/visibility.proto";

The pb building toolchain in use is buf and that supports us having our own proto files separated out from third_party/vendored protos in the same folder structure. For example our buf.work.yaml is setup as

version: v1
directories:
  - protos
  - third_party

I am not sure if this is a widely used convention.

Currently when I try to test a simple RPC from user.proto that imports the third_party google protos the path loading stepci wants is

ENOENT: no such file or directory, open 'protos/s12/accounts/user/v1/google/api/annotations.proto'

It would be good if I could pass in some directories to the proto file section and have stepci parse all of them. Although I am not sure how feasible that is (i'm not a expert in protobuf or its usage).