For people whose notes number in the tens of thousands, Trilium Notes is the hierarchical note-taking application built specifically for large personal knowledge bases - actively maintained as TriliumNext. Notes arrange into arbitrarily deep trees where every note is both content and container, and cloning lets a single note live in multiple places at once - bash notes belong under both Linux and Scripting, and Trilium refuses to make you choose. A WYSIWYG editor handles rich text, tables, math, and syntax-highlighted code blocks with Markdown-style shortcuts, while dedicated note types cover Excalidraw sketches, mind maps, geo maps with GPX tracks, relation maps that visualize connections between notes, and tables with typed columns. The attribute system is the power layer: labels attach queryable metadata (#year=1999, #author), relations create named links between notes, and both inherit down the tree - feeding full-text search, saved queries, and scripting. Scripting is Trilium's deepest differentiator: JavaScript code notes run on events like note changes or hourly schedules, build custom widgets, and add server-side logic, turning the knowledge base into a programmable platform. Protected notes encrypt sensitive content, note hoisting focuses on subtrees, and the self-hosted server syncs desktop clients across devices.