Have you considered looking into Trilium[1]? I'm not sure if it meets all your criteria, especially as the meaning of certain features from program to program

Have you considered looking into Trilium[1]? I'm not sure if it meets all your criteria, especially as the meaning of certain features from program to program can vastly differ. However, if I've correctly understood what you're looking for, it matches at least some of them. Natural hierarchy: notes can be organized into any tree that you like because notes can be cloned (not just copied) into any location. Very easy to create references with automatic back-references: bi-directional linking is built in and is as simple as typing @notename or Ctrl+L. It also includes automatically generated link-maps and self created reference-maps to see all the links between each document. Embedded documents: You can embed any document into any other document and have it referenced live and thus updated anywhere it's embedded. Self-hosting: You can either run it on a local machine or host your own sync server (which also allows you to access it from a browser), super simple to setup. Large file support: I haven't run into any issues with this, seems reasonably limitless. Full point-in-time history: From the official wiki: "supports seamless versioning of notes by storing snapshots ("revisions") of notes at regular intervals.". You get to choose this interval. Programmatic access: Full built-in scripting support. Every link/bookmark I add could download the webpage and cache it: You can definitely script this yourself but the web-clipper extension for Trilium allows you to save directly from the browser into a new note (text, screenshot, or local copy of site). Not exactly what you're looking for but a derivative that could be modified to suit your needs. There are so many other features that make it the best note-taking application for me (saved search queries represented & updated as notes in the note tree, full theming support, encrypted notes with timeout function, customizable keyboard shortcuts, active developer that you can speak to, etc). My multi-year search for an advanced customizable note taking application has finally come to an end. Frankly, I like the application so much that I created an HN account just so I could pass the link on to you. The best way to understand the benefits of Trilium is to give yourself 10 minutes to read the documentation[2] and take it for a test run. [1]https://github.com/zadam/trilium/ https://github.com/zadam/trilium/ [2]https://github.com/zadam/trilium/wiki https://github.com/zadam/trilium/wiki