-I ../../.. is meant to navigate from `GOPATH/src/github.com/hashicorp/nomad` to `GOPATH/src`

This is fine but it assumes a few things about how the dev has setup nomad, which is also fine if that is the expected dev environment, however the `../../..` is not as explicit as "GOPATH/src" and it would also enable a few more scenarios so it seems strictly better to me.

Random example: nomad is a subrepo of ours, but with this change we can symlink from GOPATH/src/github.com/hashicorp/nomad and `make proto` will work.