Add warning for files include by vendor path that should be from GOPATH

There are cases where the same file can be included relative to vendor or GOPATH. In GOPATH, they might look like this:

```
github.com/myproject/foo/vendor/github.com/otherproject/foo/foo.proto
```

As referenced through vendor, they would look as follows:

```
github.com/otherproject/foo/foo.proto
```

We should detect these cases and warn the user to use the shorter, vendored version.