Logseq

Logseq is an outliner for notes and knowledge, where every page is a tree of bullets and each bullet is a block addressable on its own. Files are kept as plain Markdown or Org-mode in a local folder, so the graph is a directory you can read, edit elsewhere and put under version control.

The daily journal is the usual entry point: you write into today's page and link out to topics with double brackets as you go. Those links are bidirectional, so each page shows the blocks that referenced it, and a page accumulates content without you creating it deliberately. Blocks can be embedded or referenced from other pages instead of copied, and queries collect blocks matching tags, page references or properties into a live list.

Also included are PDF annotation with highlights linked back into notes, a whiteboard canvas, and a plugin and theme system. There are desktop and mobile clients; keeping them in step relies on a file syncing service of your own or on Logseq's own sync.