First, let me say that I tried to search around for an answer to this (and I will clarify where those failed).

So my problem is that when I enter the daily for for agenda, M-x Org-Agenda a, I see duplicated tasks for what I believe is anything with a deadline or scheduled timestamp.

All tasks shown in view have a timestamp

I have tested this, and it seems normal TODOs get neglected where as anything with a timestamp, with a TODO or without, get presented twice in my daily agenda.

Removed deadline from study guide, no longer shown as result

I have tried using M-x customize variable org-agenda-todo-ignore-timestamp, which successfully eliminates duplicates at the cost of not showing any items with a scheduled/deadline time stamp, which I would still like to see in my agenda view. Though it doesn't apply here, I also checked to see if M-x customize variable org-agenda-todo-list-sublevels was responsible.

Any ideas? I'm fairly new to org-mode and its various related functions/minor modes, so I very well could just be misusing the agenda function. I am currently using emacs24.5 but experienced it also while using emacs24.3. I'm also attaching the only code in my init.el file that involves org-mode directly besides some capture templates and use-package declarations.

I really appreciate the help!

init.el code:

;---------key bindings---------------------------

(define-key global-map "\C-cc" 'org-capture)

;--------------org mode----------------------------
(desktop-save-mode 1)
(setq org-agenda-files '(""))
(setq org-agenda-files
  (mapcar 'abbreviate-file-name
      (split-string
    (shell-command-to-string "find ~/Tresors/Personal/org-mode -name \"*.org\"") "\n")))
(setq line-spacing '0.25)
(setq org-log-done 'time)
(setq org-default-notes-file (concat "~/Tresors/Personal/org-mode/notes.org"))
(setq org-journal-dir "~/Tresors/Personal/journal/"); note, org mode takes CcCj, CcCf,CcCb (i think as mode specific only, but fyi incase universal)
(setq org-startup-indented t)
(setq org-hide-leading-stars t)

solved my problem myself.

First, I had duplicate setq org-agenda-files, which obviously isn't good to start with. That wasn't the core of the problem, however.

By default, org-agenda doesn't search all sub-directories for .org files, so I tried that function as a work around. For further clarification, the documentation on orgmode.org states specifically

The information to be shown is normally collected from all agenda files, the files listed in the variable org-agenda-files. If a directory is part of this list, all files with the extension .org in this directory will be part of the list.

The immediate cause of my problem was using a recursive function to search for .org files. This just caused weirdness to happen.

Solution: You can set multiple directories for the org-agenda-files variable one after the other in quotes separated only with a space, which I implemented as such:

(setq org-agenda-files '("~/Parent/Parent/org-mode/notes" "~/Parent/Parent/org-mode/to-dos" "~/Parent/Parent/org-mode/references"))

All directories are now accounted for and are showing their relevant tasks on my agenda without duplicates! Hope this helps anyone else who bumps into the same silly mistake.

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