For around 15+ years I have maintained a super-curated deep taxonomy of files and folders, symlinking stuff, and so on. I've given up around 6 years ago switching to Emacs, actually almost all my files are org-mode managed, the current approach is:

- time-based notes, like

~/org/yyyy/
notes/mm-dd.org
binders/{various,topic-based,notes}.org
work/{work,related,notes}.org

~/org/lib/{long,lasting,topic,based,notes}.org

~/data/ < org-attach tree

essentially files get attached to headings in daily notes `~/org/yyyy/notes/mm-dd.org` so they get moved to a cache-dir style tree org-attach managed under `~/data/` and I can access files easily with org-attach-reveal or linking them in the org-mode note. Things that have something in common, let's say electricity bills, have a daily note heading relevant note with linked emails (ol-notmuch), transaction (beancount), attached pdf bill etc. Since they are regular I have a binder note, so `~/org/yyyy/binders/electrictyBillNote.org` that org-transclude all relevant daily headings and since it's a topic that goes beyond the current year I also have a `~/org/lib/electrictyBillNote.org` note that transclude all the years.

At first might sound complicated but it allow both an overview of anything, just looking at years binders notes, the maximum level of details going down to daily notes, and the maximum high level zoom via `lib` notes. Essentially I have a personal history, I can slowly change my notes having only to keep stuff under `lib` consistent, and having all things relevant to a certain timeframe immediately at hands.

That's to org-roam-node-find I can directly access any attached file just hitting a key and start typing something, it's a graph not a hierarchy, but when I'm on the desired results or around something I look for I can also "explore the surroundings" thanks to the time-based structure and org-mode links, org-roam backrefs and so on.

Anything is linked or attached in notes: my mails reside also on my iron indexed via notmuch, my files org-attached, some configs are created from notes (org-babel, tangled), something is attached and linked per file, some linked to the parent dir some files reside in dired etc. Basically I have a near-semantic, full-text searchable, metadata rich, tool to manage anything.

I've tried to do more with org-ql but honestly I'm not disciplined enough, I've tried the LLM way (khoj) and find very little useful results, so far direct access using org-mode heading as titles/searchable stuff with tags and optional org-roam aliases prove to be powerful enough. Sometimes when I fails to find something this way I going the counsel-rg way (full text ripgrep) and than I add a roam_alias matching the keywords I've tried before. I've also tried briefly recoll/counsel-recoll (xapian) but I've never have to use it except for testing.

I do miss phone/sms integration but having daily notes and org-capture at hand if something relevant happen I'll note in a daily note. If it became or I know it's relevant it will also be in some year-binder, if it's useful or became useful beyond an year it goes in lib, a kind of long-term archive. That's my current best compromise between "noise" and "order". Various automation do help noting anything, org-store-link/org-insert-link do help do link an email, so org-capture initiated from a mail, similarly yasnippet and hydra do help for recurrent transactions (all babel blocks get tangled to a tree where beancount import * anything), some helpers allow to link things to open with specific apps via elisp: links and so on.

It was a journey, I've hesitated much, I still have a gazillion of things to sort and automate properly, some broken/old automation etc BUT anything works smooth enough and I never lost a single bit of information nor I've failed to find something with nearly no effort so...