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This seems very familiar to a bash application I created that follows the zettelkasten note taking method. The source can be found here https://github.com/AndrewCopeland/zettelkasten
Each note is saved as a markdown file in GitHub and can be searched and linked easily from the zk cli.
Try https://gitjournal.io/ . It's open source and works very well for me. Don't forget to donate if you like it, the dev is super nice!
Seems like a simpler version of TiddlyWiki¹, which is free.
It might worth a try for those who prefer less features
Related software and previously discussed on HN - ZimWiki
It lets you run a Wiki out of a vault in your drive, which can be moved to a new machine or exported as PDF/HTML
Author here.
It currently supports Markdown, Txt Files, and OrgMode. The OrgMode is thanks to an app called Orgzly [0] whose Widgets are being used within GitJournal. Also, I'm additionally working on letting you open any text file [1], but I won't make a release of this until early next week.
I'm literally working on removing more of the code which assumed all notes would be in Markdown format, and make GitJournal open to supporting any.
If you try it out, please let me know how it did for your use case. I'm just getting started with OrgMode, and would love to improve GitJournal.