For those considering a commerical solution, DEVONthink handles personal knowledge as well as PDF and other files, split into separate "databases" that can sync across local WiFi to other devices running DEVONthink.
I recently discovered it can handle Markdown files and link across entries.
Search is powerful and fast. There are very few sync issues.
Downsides: MacOS/iOS/iPadOS only, and not free or open-source (but it's a one-time purchase).
The strong point for me is that DEVONthink uses RTF (and RTFD) as the native format. RTF is, along with Markdown, a document format that I expect to be widely supported for the next 40 years, but has the advantage of being WYSIWYG and supporting more advanced formatting. RFTD supports embedded images - it is less widely supported, but there are third party editors. The "databases" are MacOS packages, and they document how to get the files out if DEVONthink becomes unavailable. Hence for me it gives a good balance of functionality and longevity.
I recently discovered it can handle Markdown files and link across entries.
Search is powerful and fast. There are very few sync issues.
Downsides: MacOS/iOS/iPadOS only, and not free or open-source (but it's a one-time purchase).
Not affiliated, just a happy user.