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Front Matter: Things about the company and about the book (numbered i,
ii, iii, etc.)
Chapter 1: Things about the program (Introduction stuff)
Chapter 2-x: How-to. Including "see Appendix A for installation/setup
Appendix A: Installation. Why? If it's a Windows application, Run
setup.exe is so well-known that most folks don't care to read about it
again. Put it at the back of the book so they don't have to look at it.
Appendix B-x: Glossary, etc. other stuff for newbies or unusual