Using Org for a dissertation

[Richard Lawrence <richard.lawrence@berkeley.edu>]

Hi all,

I am a graduate student in philosophy, and I am about to begin writing
my dissertation.  I am wondering about whether I should write it in Org,
or stick to plain LaTeX.

This question has been asked before:
http://article.gmane.org/gmane.emacs.orgmode/22756

But that was two years ago; Org has changed a fair bit, and I'm
wondering if there are any updates to the advice given there.  Moreover,
I'm wondering if anyone has written a dissertation or other long
documents in Org in the meantime, and what their experiences have been.
(Henri-Paul, do you still read this list?)

I have used Org to write most of the shorter papers I have so far
written as a graduate student, and been very happy with the results.  I
prefer most of Org's editing features and conventions to bare LaTeX.  I
haven't previously had much of a need to mix TODO items and writing, but
imagine I will with a dissertation.  I *have* been relying on Org's
to-do list features for my reading: I enter new readings as TODO items
via capture, and include the bibliographic fields that make them
suitable to export via org-bibtex when it comes time to reference them.
None of the writing I've done so far has had strict formatting
requirements, however, and I have run into enough small formatting
issues in the past that I want to avoid having them grow into large
issues in the context of a dissertation.

Since I am not in the sciences, I doubt that I will have many figures or
complex tables, which I know can lead to headaches.  Here are a few of
the things I *am* worried about.  I'm sure most of them can be dealt
with; I am guessing that most of these issues reflect my ignorance or
outdated knowledge of Org features.  I'd be grateful for pointers or
workarounds for them:

1) Section labels and other in-document references.  It's nice that Org
generates these on export, but I need to be able to assign and use
labels that will not change if the document is reordered.  I know I can
simply add such labels via a \label command, but I am worried that using
them in addition to Org's autogenerated labels might cause numbering
problems in LaTeX.

2) Escaping/unrecognized commands.  I have occassionally run into
annoyances where Org escapes characters or commands that I intend to be
exported literally ("~" and "$" are perennial offenders).  Export also
tends to break when fill-paragraph breaks a LaTeX command across a line,
like:

some preceding text up to the end of the line \cite{SomeAuthorReference,
AnotherReference}.

3) Indentation around #+BEGIN_*/#+END_* environments. (I most often use
QUOTE.)  I usually have to explicitly control indentation in a way that
I wouldn't have to in LaTeX, because Org inserts blank lines around them
during export.

4) Inline footnotes.  I usually prefer to use inline footnotes, but I
think I have found in the past that Org's syntax for inline footnotes
([fn:: ...]) interacts badly with LaTeX commands, especially anything
requiring a "]" in the footnote text.

5) Bibtex and bibliographies.  I love keeping my reading list as Org
TODO entries, but would like a more automated way to export (just) the
entries I need for a particular document to a .bib file.  I would also
like to have more control over the bibliography as a section of my
document.  The \bibliography command must live under some Org heading or
other, and as far I as know it can't live under its own without
generating an extraneous heading, so I have to be careful that it ends
up at the end of the last section.

Are there other issues that people have run into when using Org to write
a longer document with strict formatting requirements?  Again, any and
all advice is greatly appreciated!

Thanks,
Richard