Add script fix-most-vagrant-issues

> FWIW, this cd / sync / cd can be minimized to just:
> 
> git submodule sync --recursive

Awesome! Did not know about that option.

> Also, you don't need to halt the vagrant machine beforehand

That's just there for occasional server issues I find myself and others running into. (Restarting Apache sometimes does the trick too.) Again, last resort. Doesn't actually "fix" anything.