cours/sources/clippings/github/dhanushka2001citeorder Simple command-line tool to relabel Footnotes in Markdown files in numerical order. Program and integration testing written in C. Builds for Windows, macOS, and Linux..md

---
link: "https://github.com/dhanushka2001/citeorder"
created: 2026-05-11
tags:
  - "#t/clippings/github"
---
[![Logo](https://github.com/user-attachments/assets/43f400c2-ba67-45a9-b196-53757bf9931b#gh-dark-mode-only)](https://github.com/user-attachments/assets/43f400c2-ba67-45a9-b196-53757bf9931b#gh-dark-mode-only)## citeorder

Simple command-line tool to correctly reorder Footnotes in Markdown files.

> [!tip] Tip
> For those who don't wish to use the command-line, I have made a [Chrome Extension](https://github.com/dhanushka2001/citeorder-github) which adds a toolbar inside GitHub's README.md text editor with a button to reorder footnotes.

## Motivation

Markdown processors that support footnotes (e.g. [GitHub’s Markdown engine](https://github.com/github/cmark-gfm), which implements the [GitHub Flavored Markdown](https://github.github.com/gfm) spec) automatically reorder footnotes when converting `.md` files to HTML. However, `citeorder` fixes the ordering in the `.md` file itself, making it neater and easier to manage lots of footnotes. Especially useful when needing to add new footnotes in the middle of a long `.md` file and not having to spend ages reordering every in-text and full-entry footnote manually (🥲).

In-text footnotes (`"Alice here",[^1]`) and full-entry footnotes (`[^1]: Alice`) are a many-to-one relationship. `citeorder` assumes the connections are correct, and relabels them according to the order in which the **in-text footnotes** appear.

## How to use

1. Download the precompiled executable from the latest [release](https://github.com/dhanushka2001/citeorder/releases).
	Installation via [Homebrew](https://github.com/dhanushka2001/homebrew-citeorder) (macOS/Ubuntu):
	```
	brew install dhanushka2001/citeorder/citeorder
	```
	Installation via the [AUR](https://aur.archlinux.org/packages/citeorder) (Arch):
	```
	yay -S citeorder
	```
	Or clone the repo and compile source code
	If you want to compile the source code yourself, clone the repo and compile `citeorder.c`:
	```
	git clone https://github.com/dhanushka2001/citeorder
	```
	```
	gcc -Wall -O2 citeorder.c -o citeorder
	```
2. To run, simply enter into the terminal:
	```
	citeorder input.md
	```
	where `input.md` is the Markdown file whose Footnotes you want reordered. `citeorder` will keep the original file as is and output the changes to a new file, `input-fixed.md`.
	To allow relaxed quote handling, do:
	```
	citeorder -q input.md
	```
	For more info and options, run:
	```
	citeorder -h
	```

## Example

`example.md`:

```
"Alice says hi".[^1]

[^1]: Alice

"Bob is here".[^7] "I'm Charlie",[^4] "Daniel!",[^5] here.

[^4]: Charlie
[^3]: Gary
[^5]: Daniel
[^7]: Bob

Is "Ethan"[^8] here?

[^8]: Ethan

"Bob and Charlie here again"[^7][^4]

[^6]: Fred
```

Running:

```
citeorder example.md
```

will produce `example-fixed.md`:

```
"Alice says hi".[^1]

[^1]: Alice

"Bob is here".[^2] "I'm Charlie",[^3] "Daniel!",[^4] here.

[^2]: Bob
[^3]: Charlie
[^4]: Daniel
[^6]: Gary

Is "Ethan"[^5] here?

[^5]: Ethan

"Bob and Charlie here again"[^2][^3]

[^7]: Fred
```

## Cases handled

- No changes needed.
- Stacked in-text footnotes, e.g. `"hello",[^3][^1][^5]` → `"hello",[^1][^2][^3]`.
- Single punctuation (or none) after end quote, e.g. `"A"[^3] "B",[^2] "C".[^6] "D"![^5]` → `"A"[^1] "B",[^2] "C".[^3] "D"![^4]`.
- Improper quote, e.g. `"hello[^1]`, `"hello",,[^1]`, `hello"[^1]`, `"hello" [^1]` produces an error message like: `ERROR: in-text citation [^1] not properly quoted (line 5)`. Can ignore this error with the `-q` / `--relaxed-quotes` flag.
- Full-entry footnotes with no matching in-text footnotes simply get bubbled to the end of the ordering.
- In-text footnotes with no matching full-entry footnote produce an error message like: `ERROR: in-text citation [^2] without full-entry (line 3)`.
- Duplicate full-entry footnotes, e.g.
	```
	[^4]: Alice
	[^4]: Bob
	```
	produces an error message like: `ERROR: duplicate [^4] full-entry citations (line 7 and 8)`.
- Footnotes inside inline code (`"A"[^1]`) and fenced code blocks:
	```
	"A"[^1]
	[^1]: A
	[^2]: B
	```
	are ignored.
- Footnote labels with letters/symbols are supported, and will be relabeled accordingly, e.g. `"A"[^6b]` → `"A"[^1]`.
- Spaces in the in-text or full-entry footnotes. Spaces outside the label for in-text footnotes, e.g. `"A"[^  Alice ]` are accepted by Markdown processors, and `citeorder` will convert that to `"A"[^1]`. However, for full-entry footnotes, e.g. `[^ 4b  ]: Alice`, it is not accepted, and in `citeorder` it will produce an error message like: `ERROR: [^ 4b  ] full-entry citation contains a space (line 3)`. For both in-text and full-entry footnotes, spaces **in** the label itself, e.g. `"A"[^4 b]`, `[^4 b]: Alice`, are not accepted, and in `citeorder` you will get an error message.
- In-text or full-entry footnote missing a label, e.g. `"A"[^]`, will produce an error message like: `ERROR: in-text citation [^] missing label (line 7)`.
- Multiline quote:
	```
	"T"[^4]
	"This quote takes
	up multiple lines
	but is still valid",[^3]
	"H",[^6]
	[^4]: T
	[^6]: H
	[^3]: Multiline quote
	```
	becomes:
	```
	"T"[^1]
	"This quote takes
	up multiple lines
	but is still valid",[^2]
	"H",[^3]
	[^1]: T
	[^2]: Multiline quote
	[^3]: H
	```
- Duplicate full-entry footnotes, e.g.
	```
	"A"[^dupe], "B"[^dupe]
	[^dupe]: A
	[^dupe]: B
	"C"[^dupe]
	[^dupe]: C
	"D"[^1]
	[^1]: D
	```
	can be auto-incremented using the `-d` / `--relaxed-duplicates` flag (must be only ONE duplicate footnote label, and must have an equal number of full-entry and in-text duplicates):
	```
	"A"[^1], "B"[^2]
	[^1]: A
	[^2]: B
	"C"[^3]
	[^3]: C
	"D"[^4]
	[^4]: D
	```