org-roam is a solution for effortless non-hierarchical note-taking with org-mode. Basically, if you already using org-mode - it's a personal wiki-like system for your files.

Org-mode supports attachments and links to external documents. So I can create a file link or use org-attach to connect a file to an entry.

Org-roam has some additional integrations like cataloging references specific URLs or bibtex references.

IIRC correctly, it's built on top of org-mode, with some tweaks toward use as a "knowledge graph"