Logseq
A local-first knowledge base supports note-taking, PDF annotation and task management, with Markdown and Org-mode formats under AGPL-3.0.
Alternative to:

Logseq is a local-first knowledge base for people who want to organize notes and research alongside their tasks. It supports Markdown and Org-mode for working with written material.
- Notes and organization: Create and structure notes as a personal knowledge base.
- PDF annotation: Annotate PDF documents as part of your research workflow.
- Task management: Manage tasks alongside your knowledge management work.
- Extensions and themes: Adapt the workspace with community plugins and themes, or build custom extensions through the plugin API.
Logseq is open source under the AGPL-3.0 license. It has desktop, web and mobile apps, including Linux support; the mobile apps provide most desktop features.