Index calls in libraries too

Nearly all checks are just searching for method calls and checking their inputs, which is why Brakeman indexes all the method calls into the `CallIndex`. Except it doesn't index them all, just the ones in the models, controllers, and views.

But Brakeman 3.0 will index all the calls! Well, actually it just adds the ones in "libraries".

This can be turned off with `--no-index-libs`