Thanks.
I don’t use any plugins, or [[links]] in the body text, and exclusively use footnotes [^1]. This constraint/consistency might not be appropriate for everyone.
For the footnotes, I define 5 tag types:
-
distillation - Linking source materials to my own wording of the concept. (there may be many sources contributing to a concept). e.g. wikipedia article for cat; and the cat owner’s association of why cats are good pets.
-
formulation - Linking concepts to my own extrapolations. e.g. my claim that cats are good, and that the world would therefore be a better place if everyone had a cat.
I also permit 3 relationships between concepts (which form an ontology):
-
variation - Where similarities are defined. e.g. cats are similar to dogs; and maybe rabbits.
-
aggregation - Cat is actually “a type of” pet. Cats are also a type of big cats, like tigers and lions. (taxonomy)
-
conflict - Doesn’t really apply to concept of things; more appropriate to concepts of theory, e.g. maybe the world wouldn’t be better with more cats, as they’d somehow be a nuisance in large numbers.
Workflow is quite simple:
- Copy and past stuff into the sources folder - each page being a single article.
- Identify concepts - each page being an ideal (similar to zattlekasten).
- Link everything together
- Spot patterns and create new ideas
Here’s an example of a footnote: [^1]: #distillation [[link-to-source]] - I am using # to “tag” the footnote, hoping that in future someone will write a plugin to manage this 
The relationships I’ve defined suit my purpose well enough, however depending on your needs, you will want to think about the type of relationships you may want to capture.
My only advice is to have a “#unsure” tag. Don’t try to architect the unknown - go forth and embrace uncertainty - sometimes architecture is easier in hindsight, and consistent usage of “#unsure” means that you can easily identify the pages you need to fix. (They will show up in the “Tags Panel”).