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I would recommend separating your thesis into separate files,
much like I do in my skeleton thesis
example. Try separating your chapters and appendices into
separate files and using my thesis.tex, prelude.tex, newcom.tex, and app0.tex files
(customized for your own thesis).
Or, if you already have a system for organization you prefer (perhaps your thesis is all in one file), then make sure you have these commands:
\documentclass[12pt]{report}
\usepackage{uithesis03}
at the beginning of your document (but make sure that
\usepackage{uithesis03} is AFTER any other
\usepackage statements you have). Then insert your own
customized version of prelude.tex
immediately thereafter. Regardless, make sure you issue the \appendix
command before your appendices and use the \Chapter
and \Appendix commands (rather than the built-in LaTeX
ones) for new chapters and appendices, respectively.
