Added --only-files option to specify specific paths to scan

I think the option is pretty self-explanatory, you give it a list of paths and it will only scan those. It differs slightly from the `--skip-files` option in that it allows paths as well as single files.

I also did a bit of refactoring so it works with `--skip-files` as well like so:
```
brakeman --only-files app/controllers/ --skip-files app/controllers/foo_controller.rb
```

I wasn't sure where to add tests for this, except maybe in a separate file under `test/tests`, if you have any suggestions on that let me know.