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I finally was able to get it to work.

The first issue was caused by an outdated git plugin in Jenkins. After updating all the plugins, the job started checking out ros_buildfarm from github and used it.

The second issue seems to be that when generating the jobs with ros_buildfarm's script, the job generation configuration of ros_buildfarm_config MUST be specified as an http link.

Before I had used: --commit file:/path/to/my/local/ros_buildfarm_config/index.yaml

but it seems the provided link is saved in the jobs, which won't be able to access the file system.

So it must be: --commit http://localhost_or_wherever/ros_buildfarm_config/index.yaml