Embedded tags vs. file system tags

I’m developing a collection of notes for which tagging will be essential. The basic needs are (1) be able quickly to find all documents relevant to a topic, and (2) make it possible for a document to be associated with two or more topics without duplicating the document. I’m trying to decide whether to go with file system tags or embedded tags. When I consider that most of my notes will be Markdown files, I lean toward embedded tags, because I can do complex multi-file queries with either Eagle Filer or BBEdit. (The more complex analytics possible with YAML front matter are cool, but are probably overkill for my needs.) But when I consider that perhaps as many as 25% of my documents will be image files for which it would be tedious to embed tags, I lean toward Finder tags, which can be used on any type of document, and are really easy to manage with Eagle Filer. Finder tags are not cross-platform, and I can worry about that if I think about it long enough, but I presently don’t intend for this to be anything other than a Mac-only PKM system. I’m vascillating. I don’t want to go a long way down a road only to discover that I would have been better served going a different direction. I would be interested in the opinions of people who have been there and done that.

I would generally lean towards EagleFiler/Finder tags, since those are natively supported on macOS and iOS in lots of apps. There is probably an automated way to turn those into embedded tags later if you ever need to move the files to a different system.

What sort of queries do you have in mind? BBEdit does support Finder tags in its multi-file search filters, and EagleFiler has better support for queries with non-embedded tags than embedded ones.

It’s hard to anticipate, but I could see something like: Find A or B, but only without C. On further reflection, I guess that isn’t so complex.

Well, this is embarrassing. I’ve used BBEdit for twenty years, and didn’t know I could search Finder tags. And I still can’t see where.

Perhaps not sufficient for your needs (as it doesn’t support nesting), but this is how you can do it in BBEdit:

How many times have I passed right over this without seeing it?

Thank you!