I think I solved the problem.
I installed the github version for mac and staggered, read a lot of man pages, and finally I was able to do this :-)

What helped me was to click the β+β sign at the bottom of the screen, as shown in the screenshot. Here I could specify my repositories in a local directory.
nielsrasmus / jekyll-sites: points to the root of the jekyll assembly.
nielsrasmus / nielsrasmus.imtqy.com: points to the generated site in ~ / jekyll-sites / _site
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