One great advantage of creating a single GitHub repository for Zettelkasten repos is that the search against that repo is limited to the content under that Zettelkasten, which has already been grouped in a way that makes sense to want to search independently from the other potential ZK repos. For example, say I want to search just my logs for Zettelkasten content. Here’s the same search against all my zets. I was able to copy and paste the references easily in the Markdown:
[search just my logs]: <https://github.com/rwxrob/logs/search?q=zettelkasten>
[all my zets]: <https://github.com/rwxrob/zet/search?q=zettelkasten>
If I wanted to expand to others I easily could without invoking a bunch of stuff I don’t want.
At one point I was even combining lab and codebook content in with my logs and zettel (notes) and even my schedule. That’s just stupid looking back on it now. Using this automated indexing and search capability that GitHub provides for free — without any coding on my part — is clearly the way to go — yes, even if it does create a dependency on GitHub. After all, GitHub is just too big to fail and they can never block search functionality like this to their end users (even if they do turn evil one day and charge for us to host or mirror there).