All of these links work fine in the documentation website (https://docs.cbioportal.org) since the domain name is the root. For example, following the above path, you would end up at the correct page:
Changing all these links to relative should fix it so it works in both the github repo and the documentation website. E.g. since the Architecture Overview is in the root:
[OncoKB Data Access](integration-with-other-webservices/OncoKB-Data-Access.md)
REPRO
EXPECTED
NOTE
All of these links work fine in the documentation website (https://docs.cbioportal.org) since the domain name is the root. For example, following the above path, you would end up at the correct page:
PROPOSED SOLUTION
Changing all these links to relative should fix it so it works in both the github repo and the documentation website. E.g. since the Architecture Overview is in the root: