To my mind, option 1 is preferable.
Option 2 sounds a little VC-specific and I'm not sure I'd do things that way.
The worst "smelling" option is option 3, at least the way you've presented it.
Before deciding, though, you should consider what version control system you're using. Some allow mapping of a singular file in the repository to several different places on the hard drive. We use this technique to enforce a "contract" (interface) between an Linux system and our Windows main application.
That way, all vc projects have "a copy in very project" but the source of each copy is a single file in the repository.