So I rebuilt around 3 folders: Inbox, Projects, Knowledge.
Made it AI-native: - MANIFEST.md files so Claude/Copilot can index your vault - CLAUDE.md + AGENTS.md instruction files - GitHub Actions for auto-maintenance
Plain markdown, Git-tracked, works with any editor.
Blog post with the full journey: https://gokhanarkan.com/blog/over-engineered-note-taking/