I tried to use the wizard action Create Lookup Field including entity. After that I tried to delete the artifacts it created and got into troubles. Sure, that is a thin ice.
I thought the solution would be load a previous stable version in Git but that did not help. After I start the Architect again I get this warning:
git checkout does not delete the files added, it just gets back all the old files. You have to delete all the new files or use additional statements. So this is not an ORIGAM issue but a GIT usage issue.