As stated in previous comments, the limitations you perceived about org-mode and org-agenda's path requirements don't actually exist. However, it's very common to have misconceptions about how org-agenda works. I had them too. I didn't really know how to approach org-agenda for a long time, so I'm going to try to distill my understanding of it at a high level to answer your broader questions.
Org Agenda Requires Design
Some assembly is required when you decide to get started with org-agenda. It's so open-ended that you have to actually DESIGN a system that will work for your needs. My favorite example, and one that I actually use every day, is Orgmode for GTD by Nicolas Petton. His org-agenda system uses 4 files:
- inbox.org - This is where he's setup org-capture to create TODO items to be refiled into the following files.
- tickler.org - This is for small tasks to be done in the near term future.
- someday.org - This is for tasks that might be nice to do in the distant future.
- gtd.org - This is for current projects.
The configuration for his system looks like this when you put it all together.
(defun c/org-agenda ()
;; GTD with org-agenda
(setq org-agenda-files '("~/Dropbox/org/inbox.org"
'("t" "Todo [inbox]" entry
(file+headline "~/Dropbox/org/inbox.org" "Tasks")
"* TODO %i%?")
'("T" "Tickler" entry
(file+headline "~/Dropbox/org/tickler.org" "Tickler")
"* %i%? \n %U")
(setq org-refile-targets '(("~/Dropbox/org/gtd.org" :maxlevel . 2)
("~/Dropbox/org/someday.org" :level . 1)
("~/Dropbox/org/tickler.org" :maxlevel . 1)))
(setq org-todo-keywords '((sequence "TODO(t)" "WAITING(w)" "|" "DONE(d)" "CANCELLED(c)")))
;; This is the only part of this setup I haven't used yet.
;; (setq org-agenda-custom-commands
;; '(("o" "At the office" tags-todo "@office"
;; ((org-agenda-overriding-header "Office")
;; (org-agenda-skip-function #'my-org-agenda-skip-all-siblings-but-first)))))
(setq org-agenda-start-with-follow-mode t))
Designing Your Own System
From the above example, I want you to pay attention to two variables:
org-refile-targets. Figuring out what should go in these variables is the heart of the design work required to use org-agenda.
Where do tasks come from?
By being in
org-agenda-files, an org document gets the ability to schedule itself in the org-agenda system. The example I gave you limits this to 3 files, but if your situation requires more, you can add them to the list. If doing that manually is too cumbersome, you may have to write a function to populate
org-agenda-files. Although my example used a flat directory structure, it's absolutely not required. They can be anywhere in the file system.
Why do you want to move items from one org file to another?
The GTD system answered this question by using refiling to express immediacy of a TODO item. Tasks start in the inbox.org and they get moved to tickler.org if they can be done soon. They move to someday.org if it doesn't have to happen right away. If the task is part of an ongoing project, they go into gtd.org. Files belonging to
org-refile-targets were given an implicit meaning.
In the example, the refile targets are all in the same directory, but they could be anywhere in the file system.
Read the documentation for these two variables, and think about how you want to use them. This will help you come up with a design that will make org-agenda work for your unique circumstance.
- C-h v org-agenda-files
- C-h v org-refile-targets
Also, I encourage you to read through the blog post I linked earlier to the GTD system. I think it's a great example of a working, cohesive system. It may not be suitable for your circumstance, but I think you can learn a lot from his example.