Organize repo structure into Tool and Example

[ramou]

The Tool directory should include the script at the top level and the models used in the same models directory underneath. This is what gets "installed" and/or cloned by somebody who wants to use the tool.

The Example directory would include the other elements, the example inputs/outputs and resulting files so folks can test if they're getting the same results. This will be even more relevant once we do CI, but currently, there's some issue where we're not getting the expected results ourselves and Munira hasn't been able to shed any light.