I am not exactly sure if the model-definition plugin is at fault here or some other plugin/configuration but I discovered this after the update from 0.3 to 0.4.

My develop branch has a last build with a Jenkinsfile that worked in 0.3 but is now invalid in 0.4.
So I made a feature branch with an updated Jenkinsfile which build successfully and merged that into the develop branch which triggered an automatic develop build.

The log shows git checking out the new (merge)-commit into the WORKSPACE@scripts folder and a global library into the WORKSPACE@libs folder.
And then it starts building with the Jenkinsfile from the WORKSPACE folder which is still on the commit from the previous build with the invalid Jenkinsfile and thus the build files.