Stop leaking details about the implementation of PDA's

This removes three functions we should probably never have created:

* `get_indices`
* `index_to_level`
* `level_to_index`

Users should not be accessing our internal representation of PDA's as part of their normal workflow. The R documentation voices it wish that users wouldn't do this, but then concedes that it happens all the time. We should not let them happen to Julia.