Annotations do not work when [linter_dir] argument is used

[markphip]

This was observed with flake8 but I assume it applies to all linters. If you restrict the linter to run in a specific directory the errors and annotations it produces do not "link" with the source code in the PR files view. I would assume that the dir could be put back on the path that is reported to make this work. In my case, I found I was OK running flake8 from my root folder so I was able to work around it but I want to try enabling mypy next and that one I need to run from a specific folder.