I've been writing a long document in org-mode recently. I decided to use org-mode for two reasons: firstly, I wrote the outline plan in org anyway and switching tools was irritating; second, I want both PDF and HTML output. My tool of choice would have been latex and auctex where it not for the HTML requirement.
Setting it up was a little difficult, but in general it's going okay now. However, I am really missing the notion of "master" documents from auctex. I have a "main" file which just includes other files each of which contain a specific section. Now, the export functionality works, but many org commands appear not to work propertly. So, for example, footnotes adds new footnotes starting from 1 in each file, but in the HTML export the earlier footnotes get overwritten. Likewise, there is no good tool for putting in crosslinks, compared to reftex in latex. Am I missing things here? Or would it make more sense to move to latex, with all the hacking that this entails for the HTML output. Phil
