Fix naming workarounds

1. Agree on an approach for colliding names and what slots should be called.

'Ref' is added to colliding slot names. Some variables are called things like '--RefRef' if they are a reference to a class that is itself a reference.

The most robust approach would have ODM adopt case-insensitive unique names between classes, types, enums and references, while subscribing to the lowercase first naming of as forced by the current LinkML generators e.g. GraphQL

Slots could then be renamed to this new schema via creation of a lookup/mapping file

2. Figure out why LinkML fails when ODM class is not renamed (see `ODMLinkMLTransformer.hardcoded_modifications()`)

Start by reading ODMLinkMLTransformer.hardcoded_modifications() and reproduce the LinkML failure when an ODM class is not renamed. The work is done when the naming approach for colliding names and slots is agreed, the required lookup or mapping file is defined, and the reported failure is resolved.

Written by the indexing model from the issue text.