Thanks everyone for taking time to provide such excellent advice. I’ve moved everything under topics rather than by application. I have cleanup to do but I’ve made a good start.
Thanks again!
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One thing that I try to teach people using computers is to create file names/folder names and subject headings that are clear and memorable.
Name the thing so that a glance will tell you what it is about. This is also true for email Subject fields. Be specific. Unless it’s a long-standing, familiar, or standard acronym, one that you will not have to fumble to remember, do not use it for a folder/directory name, and maybe, not for a file name…
In my case, that means that I would use UCLA on a folder name, but not ITPB (IT Planning Board) because I might not remember the expansion.
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I keep all files in a folder listed by topic, because I normally have multiple files of the different types for a given topic. For example, recently I collected data in a spreadsheet on the specific project assessment, than I cut and pasted the relevant parts into a document where I wrote up the context and the summary, and later I took the information and put it in a slide deck. All of those would go in the same folder.
The only time where I don’t do that is for images, because it is not uncommon for me to use images in multiple contexts, Especially when I’m making a slide deck or a video and I w already know I am likely to reuse photos of a classroom or a park or It’s too car collision, etc. All of those photos go in the images folder, but with descriptive names so they’re easy to locate for future use.
I try to file by topic without using tags at all. Everything directly stored on iCloud Drive so it can be accessed easily via Finder, Files, EagleFiler or Notebooks, which I recently purchased and find very convenient.
Now, the question is: where do I store a user manual for a synthesizer? Does it go under “Music”, along with the sheet music and MIDI files or under “Manuals”, with the fridge and microwave oven manuals? I used Johnny Decimal to establish a taxonomy but my main rule of thumb when storing the file is: When will I look for it when the time comes? Usually the gut feeling is right, but always make sure there are good searching capabilities 
I only have one exception to the rule. My health issues log --slowly increasing year by year, alas-- is in a Numbers document, in fact it’s the only Numbers document I have so I just have to open Numbers. Convenience won here.
Great topic. There are probably as many filing schemes as there are computer users! In the end it is quite individual depending on the person and their thought process.
I can certainly understand the motivation for storing files based on the app that creates/edits them, since when I want the spreadsheet for “xyz” I can be pretty sure that Numbers is the way I will want to edit it. However, I find that in general I prefer to create folders for specific projects and put all of the files for that project into one folder. The reason for this is that, practically, if I need to find all of the files for a specific project or task, that is much easier to do when they are all in one folder than when they are dispersed into different locations based on the app that created the each one.
For example, if I remembered that I had a Numbers spreadsheet for something, obviously I could find that in the Numbers folder (eg in iCloud), but would I necessarily remember that I also had a Page document, several images, etc and go looking for them in the various folders for each of those apps? If I created an image in Affinity Photo and another in Photoshop, how would I know where to search for the images?
On the other hand, if I know that I created a spreadsheet in Numbers but cannot remember the project folder name or location, I can always do a Spotlight search for Numbers documents and find it, so there is useful metadata based on the app, but not on the project.
There are, of course, many ways to get around this. For example, you could use an app like Hook to “hook” together all of the files associated with a given project regardless of location in the file system. You could create a tag for every project and hopefully be rigorous enough to assign that tag to every file you create in the project, and then pull together the files via Spotlight search or a Finder smart folder. You could embed the project name into every file you create for that project and again use Smart Folders or Spotlight. Since you do get the metadata of the creating application “for free” I find that easier than these approaches, and it avoids having hundreds or thousands of Finder tags.
I keep my finder tags set relatively small as a result. One thing I do is use tag whatever I am currently working on with “active” and I have a smart folder to easily see everything with this tag. I even have buttons on my StreamDeck to add and remove this tag. This is helpful to make it easy to quickly get to the things I am currently working on.
One interesting idea is to tag the project folders with a small number of tags, say major work and personal areas, and you can then in Finder chose to group by tags, which will break up your Finder listing by these different areas, which I have just begun to experiment with.
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I really don’t use Hook to its full potential, mostly just generating links to files and documents.
I use Ulysses and I prefer to use its own file system for the additional features. I’m going to try to use Hook to link together my writing with external files and resources.