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Still no solution for comments though. I guess the only solution would be to move this repository to another place that we are sure of to be crawled by Google Scholar.
There are multiple issues here for us:
More details on the problem (thanks to Elias for the pointers):
https://academia.stackexchange.com/questions/100232/google-scholar-stopped-indexing-pdfs-on-github-gitlab-pages
https://www.google.com/search?client=firefox-b-d&q=google+scholar+does+not+find+my+paper+on+github
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