Logseq

An outliner-style knowledge base where notes are built from nested blocks and linked with double brackets, so relationships between ideas are visible in the structure rather than hidden in folders. It stores graphs as plain Markdown files or in a local database, and adds daily journals, queries, tasks, flashcards, PDF annotation, and a plugin and theme ecosystem for custom workflows.

Researchers, writers, and engineers use it for linked notes, literature reviews, and planning.

Keeping it on your own machine or server keeps your thinking private and the files portable, with no account required and backups that are a folder copy.