[brew doctor] remove check_homebrew_prefix

## Summary

This one may be a bit controversial; however, I've been running with `brew` installed to `~/.homebrew` for about 1.5 years and not only have I not had `/usr/local` related problems, but rather, I've had a reduction in issues altogether. I never have to run `brew doctor`.

## Rationale

- https://news.ycombinator.com/item?id=7750203
- https://github.com/wilmoore/homebrew-home#benefits
- https://github.com/wilmoore/homebrew-home/wiki/Rationale
- http://ascarter.net/2010/02/22/homebrew-for-os-x.html