Remove unused dev.testing.com.conf

Looks like this was added by me way back when during a moment when I accidently added all of my custom domains. Good time to ditch it as it helps me test this new rsync line. :)
Use rsync to copy individual site configs from nginx-config/sites
If our custom-sites directory does not yet exist, exist it.
Better grouping and documentation of config files
Copy dotfiles and bin files rather than symlinking

Another step toward a clean vagrant up without provisioning
Unlink previously symlinked files before copying

This sets things up to work on future uses of halt/up without requiring a full destroy. As long as `vagrant provision` is run, no destroy is needed.

Note that it doesn't make sense to keep this here forever. At some point we'll just have to recommend a full `vagrant destroy` to sync back up with the repo.
Formatting is great!

A nice output is nice sometimes.
Cleanup mysql configuration area to match the rest of provisioning
Update CHANGELOG to highlight big stuff from 1.0-working so far