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bkuhn
Order matters in \usepackage{hyperref}.

The problem exhibited only in PDF files, wherein \ref{} links to
appendix chapters referred instead to regular chapters.

http://tex.stackexchange.com/questions/77886/fncychap-and-hyperref-messes-up-page-references
suggest that loading hyperref second fixes the problem. This indeed
worked.
# Standard LaTeX ancillary output files
*.aux
*.dvi
*.toc
# Log files by name, since .log may be of interest in some other context.
comprehensive-gpl-guide.log
# bkuhn often makes an x.ps file in intermediate testing.
x.ps
# Emacs temporary files
*~
\#*\#
.\#*
auto-save-list
public_html
*.idv
*.lg
*.tmp
*.xref
*.log