\setcounter{tocdepth}{1} will put sections in your TOC. For reference,
Part = -1, Chapter = 0, section = 1, subsection = 2, subsubsection = 3
(not present in Tufte-latex), paragraph = 4, and subparagraph = 5
The mathpazo package is loaded by tufte-latex. From memory isn't there
a nofont option for tufte-latex to supress loading the "tufte" fonts?
Try loading the separate appendix pacakge. perhaps somewhere the
standard latex \appendix command was overwritten.
http://www.tex.ac.uk/cgi-bin/texfaq2html?label=appendix
Hope that helps,
Steve
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