Fix empty output files when no targets are found in inputs

[peterk87]

This pull request:

• Fixes #49, there's always going to be a subtyping entry for each input
• Refactors code to be more DRY, modular and, hopefully, more obvious
• Added unit tests for important utility functions

[peterk87]

Great! @gcttong If it looks good to you, then can you merge the changes? Thanks for taking a look at this PR.