Adding checks for things that commonly go wrong during template conversion.
Adding checks for things that commonly go wrong during template conversion.

1. Checking that `index.md` has `root` set to '.'
2. Checking that `_config.yml` has `root` set to '..'

butterflyology/rr-intro,dleehr/organization-RR-Jupyter,butterflyology/rr-intro,dleehr/organization-RR-Jupyter,Reproducible-Science-Curriculum/rr-automation,Reproducible-Science-Curriculum/rr-automation,butterflyology/rr-intro,Reproducible-Science-Curriculum/rr-literate-programming,dleehr/organization-RR-Jupyter,dleehr/organization-RR-Jupyter,dleehr/organization-RR-Jupyter,Reproducible-Science-Curriculum/rr-literate-programming,butterflyology/rr-intro,butterflyology/rr-intro,dleehr/organization-RR-Jupyter,butterflyology/rr-intro