I am using the command

./node_modules/documentation/bin/documentation.js build src_gen/libs_frontend/*.js src_gen/libs_backend/*.js --github -f html -o docs

Using the default theme. With version 4.0.0-beta.18 and previous versions (tested with every version from 4.0.0-beta.14 to 4.0.0-beta.18) the github links correctly appear. However, with 4.0.0-beta.19 the github links are no longer shown (even though I'm still using the same command). This happens with every repository I have tested with, but if you need a sample example see https://github.com/habitlab/habitlab