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LaTeX has limitations?

You misunderstood file structure as document structure I meant it as in logical organization on a drive.

To split a document up into multiple files. But the disadvantage is that Latex only has single includes - so you can not split a document up that much.

(This is also a problem if you use images with equations such as those created by xfig (i.e. pure latex or PSTex PicTex). Usually most people would like to include an image as a separate file.

org-mode in Emacs is nice for outline-oriented note-taking, and it can export to LaTeX.

Gah that thing almost drove me over to Emacs. By almost I mean, I couldn't get full vim functionality in Viper and gave up, some commands just can't be replicated. But org-mode is a very very nice tool. The current vim alternatives like viki and vim-outline do not compare.