Analyze Scripts not in a Gem

Currently we only analyze scripts that are part of gems. This PR adds code to the scanner that puts all loose scripts in their own source unit.
I wondered why this output was being generated, and it is indeed correct.

https://github.com/sgtest/sample_ruby_gem/blob/master/sample_ruby_gem.gemspec#L9 only lists 1 file.

To avoid confusion, I think it would be best to update sample_ruby_gem to use `s.files = ["lib/**/*.rb"]` and make a new test repo for the rubyprogram behavior.