Generating protobuf Go files with `go generate` and a vendored protobuf package (specifically, vendored with godep).

doc.go

//go:generate protoc --go_out=import_prefix=github.com/your_github_acct/your_repo/Godeps/_workspace/src/:. your_proto_file.proto

package yourprotopkg

how it looks in shell

$ pwd
/home/your_acct/src/github.com/your_github_acct/your_repo/
$ ls
Godeps doc.go your_proto_file.proto 
$ go generate . # or `go generate github.com/your_github_acct/your_repo/`
$ ls
Godeps doc.go your_proto_file.pb.go your_proto_file.proto
$ grep "import proto" ./your_proto_file.pb.go
import proto "github.com/your_github_acct/your_repo/Godeps/_workspace/src/github.com/golang/protobuf/proto"

With this, no more futzing with godep save -r every time you regenerate your protobufs.