Reorganization to separate allele/interpretation model repos has broken build

[bpow]

Commit d20a93de3c256b587e98d68649f213bbb1d11015 broke the build, since config.rb has many helpers that expected the individual models to be in subdirectories under source/ (and that commit had promoted the contents of the allele directory to be directly within source/

We will need to re-think how to make links between documentation in the two different models (or more as we add more models).

Tagging @tnavatar and @larrybabb in case they have comments.

[bpow]

I think this is now mostly fixed. If not, it should probably be an issue under the data-model-docs repo.