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I write using Markdown, which can easily be converted (through John MacFarlane's excellent Pandoc) to formats such as .docx or PDF (through LaTeX). My Markdown editor of choice is Byword* (which is simple, clean and free from distractions).
If you're interested in trying this out:
(i) Download the following: Byword (if on Mac, otherwise, a different Markdown editor), a LaTeX package (e.g. TexShop/MacTex), and Pandoc (which runs from the Terminal).
(ii) Create a document in Byword and include the following metadata at the top of the document (separated by three lines on top and bottom):
title: "Your Title"
abstract: Your Abstract
author: Your Name
bibliography: [insert here the filepath to the .bib file that is your bibliography file]
fontfamily: Minion Pro
(iii) To give a citation in the Markdown document, type (for example)
where williamson2000knowledge corresponds with the citation information included in the .bib file specified in the metadata.
(iv) To use Pandoc to convert your Markdown file (which includes the metadata at the top), open the terminal and use the following
pandoc -s --latex-engine=xelatex --bibliography=yourbiblioraphy.bib -o youroutput.pdf yourinput.md
to convert the .md file to PDF through XeLaTeX, or
pandoc -s -S --reference-docx=yourdocxtemplate.docx --bibliography=yourbibilography.bib -o youroutput.docx yourinput.md
to convert the .md file to .docx.
For some reasons why writing academic papers using Markdown/Pandoc is great, see here.
*Regarding Byword: it's really probably as good as you can ask for. However, Typed is really good as well.
Addendum: before I actually even start writing, I find it's helpful to 'mindmap' the key ideas of the paper (using Mindnode). Mindnode is great because it not only makes creating a mindmap simple and intuitive, but it also conveniently exports your mindmap (at least, on the Ipad/Ipod version) as an outline in (you guessed it) Markdown. And once you've got the Markdown outline, you're ready to go (using the method described above, with pandoc, etc.)
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