chore(controller): fix flake8 issues

I fixed up the coreos scheduler before adding it to the excludes, but the embedded systemd unit files is longer than our flake8 restrictions, so I decided to add it to the excludes. The API migrations are ugly as well, so I added that to it.

Other things done in this PR:

- removed duplicate `run()` function
- removed unused LOGGER_TEMPLATE and ROUTER_TEMPLATE. These templates exist at `logger/systemd/deis-logger.service` and `router/systemd/deis-router.service`.

Also, there's 2 free bugfixes for spawning applications in this PR. Bonus points for figuring out where they're hiding :)

fixes #675