@TruthWK - amen to "
Limited and inconsistent hierarchy. In OneNote, Evernote and other apps I've tried, you always have Notebooks, Stacks, Lists, Projects, Sections, Links, etc."
This is one of my biggest complaints about such apps. Ironically, at least one of OneNote's predecessors just had folders that could be nested arbitrarily deep, that IIRC mapped 1:1 to filesystem folders/directories. But I was told that naive users found that confusing, so OneNote and EverNote evolved to a metaphor of notebooks, which can be stacked, have sections, etc. But physical notebooks can't have pages aded or moved around = so perhaps their actual metaphor are three ring binders?
Related: OneNote only allows you to have pages (content, text) in sections. You can't have a "README" page at the top level of a notebook to say what the notebook is about. Section groups cannot have pages, only sections. I have therefore started crteated sections called "README-xxx", which typically only hold one or a few pages of content, the actual README text.
Damn, I wish that they had stayed with the "folders" metaphor. Physical manila folders can be nested (to a limited extent). You can put explanatory notes on the folder cover, or as a few loose pages in a folder holding other folders. Etc. Even back when I was using paper, I evolved to using manila folders in a filing cabinet, as opposed to notebooks or binders. You can put notebooks or binders in folders, but vice versa not so much.
Additional wish: I wish that I could set any level of the hierarchy to be peesented vertical or horizontal. E.g. possibly all levels vertically presented. Currently OneNote only presents page names vertically, but insists that sections and section groups be presented horizontally. This may be one reason why they limit the hierarchy.
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As mentioned above, I am currently using OneNote as my "digital filing system".
I have tried using the filesystem folder / directory structure, as several people on this topic seem to be doing. I don't do that so much now because much of my work involves clippings of arbitrary content, like screen shots of diagrams, clippings of web pages, etc. Just saving a copy of a web page in a filesystem folder is a pain, unless you have the "save as single page" feature in your browser - which for years was available only in Internet Explorer, not Chrome or FireFox.
More important, when you save an item in the filesystem you have to give it a filename, and it can be a pan to create unique filenames. Dumping clippings on OneNote content pages doesn't require so many names. Similarly, you don't have to unique names for emails in your mailreader's Inbox and archived folders.
BTW, I also tried using the bookmarks section of my web browser as my GTD filing system.
So, right now I mostly use OneNote, and probably my saved stuff is 40% text, 40% images, 20% other file types. OneNote can OCR saved screen clippings, allowing searching.
I use email, and filesystem folders/directories, for additional information. Project support stuff, I believe, is the GTD term.
I may link from OneNote to a file:// URL, and/or to files in Google Drive. But the problem with such links is that, if the location is changed, the link is usually not updated. (Permalinks?) So I often link to the file, but put a page snipping in OnweNote. Ditto email.