indentation of class hierarchy not working in generated index.md

[cmungall]

E.g https://cmungall.github.io/chem-schema/

the md says

 * [ChemicalEntity](ChemicalEntity.md) - An entity that can be described using using chemical properties.
    * [Atom](Atom.md) - A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it.
       * [AtomIonicForm](AtomIonicForm.md) - an atom type in which charge state is specified. Also known as (atom) ionic species
          * [MonoatomicIon](MonoatomicIon.md) - An atom that has a charge
             * [AtomAnion](AtomAnion.md) - A monoatomic ion that is negative
             * [AtomCation](AtomCation.md) - A monoatomic ion that is positive
          * [UnchargedAtom](UnchargedAtom.md) - An atom that has no charge
       * [ChemicalElement](ChemicalElement.md) - generic form of an atom, with unspecified neutron or charge
       * [FullySpecifiedAtom](FullySpecifiedAtom.md) - An atom (class) that has subatomic particle counts specified
       * [Isotope](Isotope.md) - A specific subtype of an atom with a specified neutron number
       * [Nuclide](Nuclide.md) - an atomic species characterized by the specific constitution of its nucleus
          * [Radionuclide](Radionuclide.md) - an atom that has excess nuclear energy, making it unstable

but this is flattened. I don't know if this is an issue with how we are making the markdown or in mkdocs...

[cmungall]

hmm, this may be an issue with mkdocs, it renders fine with github rendering:

https://github.com/cmungall/chem-schema/blob/master/scratch/test.md

[cmungall]

ah, this clarifies

Python-Markdown/markdown#3

action: use 4 spaces, not 3