Only use in-line footnotes unless your document is very very small

Footnotes in org-mode are really, really great. Before you really get into using them, take a bit of time to think about how you want to use them.
If you have 5 footnotes or less, then don’t think anymore about it. If more then read on.
This topic is not unique to org first of all, it just isn’t something that you consider much until it is too late. Once you get into the org lifecycle, you start tossing and slinging document and code fragments with ease, especially while refactoring. This is all find and well, until you realize that your footnotes will be left sad and alone, abandoned for some cruel fate. In particular, it will break your document.
The better way is to define them all in-line; that will allow simple and easy refactoring in a quite pleasant manner.
Forgot a key point, as I only revisited this today: also generate random IDs. The kind folks in the org community on-list explained this to me. That prevents name collisions. Here is what you need:

(setq org-footnote-define-inline +1)
(setq org-footnote-auto-label 'random)
(setq org-footnote-auto-adjust nil)

ADDENDUM: 2014-06-22T09:07:09-0500
As FUCO1 pointed out, there was something wrong with my approach as I was still using randomly generated IDs. That was my intent. What I wanted was in-line and still reference-able footnote definitions, but without adding them to the Footnote section/heading. After reading the code, I see now the right setting; it was the above plus no auto-adjusting the footnotes. I just updated the code to correct that.

Emacs Lisp programmers must know about pcase

Pattern matching is available in a bunch of programming languages. For some reason, I never thought to look for a library in Emacs Lisp for it, and it is here in pcase.
There is this weird thing that happens when you start using Emacs Lisp. Unlike other languages where you start learning it for “its great features”, most of us only learned it to configure Emacs. Because of this, our brains kind of turn off when it comes to using the language. Or perhaps instead, our expectations change. They are just, lower, and it makes our minds slower. That is why you see so many posts like “if you are programming Emacs Lisp then you must…”.

The story

The creativity that you apply and capture to assemble your system… this is where
all of the fun stuff is. Let me elaborate, everything in your artifacts are
valuable because they tell the story. Actually, they tell the story about a
story, a story that has yet to occur and also a story that has previously
occurred. It is here, where the actions lives, that all of those things are
learned, practiced, suffered accordingly from, and reveled in! In other words,
it is yet another story, a fun one.

If you haven’t noticed by now, either by hearing rumors, reading accounts, or
learning of it yourself: human beings are story-oriented. Your ability to
successfully function in and contribute to society will be directly proportional
to your ability to listen to stories, tell others’ stories, live your life such
that you have new stories to tell, and capture them in some form of persistent
storage. Stories grant us the power to learn from others wisdom that was
painfully acquired thousands of years ago, and it gives you a chance to
contribute the results of your hard work, for the future of humanity, too. A
belief system about the value of story-telling is essential, critical, and
mandatory to successfully achieve your goals with literate programming.

As I change, the story will change, and the action will change. The cycle will
never end.

Nevertheless, I will attempt to do my best here with the good part of me being
a flawless, rational, and logical human being to:

  • Deliver a supportable system
  • Deliver an adaptable system
  • Deliver an expandable system

A tiny org-mode literate programming Makefile

Basic build for a document:

INIT=.emacs.el
$(INIT): TC3F.org
	caffeinate -s time emacs --batch --no-init-file --load .org-mode.emacs.el --find-file TC3F.org --funcall org-babel-tangle --kill
TC3F.txt: $(INIT)
	caffeinate -s time emacs --batch --no-init-file --load .org-mode.emacs.el --find-file TC3F.org --funcall org-ascii-export-to-ascii --kill
TC3F.html: $(INIT)
	caffeinate -s time emacs --batch --no-init-file --load .org-mode.emacs.el --find-file TC3F.org --funcall org-html-export-to-html --kill
TC3F.pdf: $(INIT)
	caffeinate -s time emacs --batch --no-init-file --load .org-mode.emacs.el --find-file TC3F.org --funcall org-latex-export-to-pdf --kill
all: TC3F.txt TC3F.html TC3F.pdf
clean:
	rm $(INIT)
	rm TC3F.txt
	rm TC3F.html
	rm TC3F.pdf

Addendum: 14-06-13
Added caffeinate command.