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Sometimes, you find a blog post that answers the exact question you wanted help with - thank you @da5nsy !
I want to try using Jekyll on my GitHub Pages site, the docs don't mention how to do that and I got worrying "not empty" conflict warnings - but this handy post walks through the steps I needed.
https://www.dannygarside.co.uk/blog/How-to-add-a-Jekyll-blog-to-an-existing-github-pages-website/
Danny Garside · How to add a Jekyll blog to an existing github pages websiteI wrote this blog at the Open Science Retreat. Thanks to the organizers for giving me the time and inspiration to finally get this done!
@neil_vass
Oh yay I'm so glad! 
Any bits which need updating?
@da5nsy
Nope, wouldn't change a thing!