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The first thing you need to do is run the included configure script to define some initial configuration, just type
./configure --with-mysql=<your MySQL root> --with-webdir=<your web directory> --with-cgidir=<your cgi directory>
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--with-mysql=<your MySQL root>
Why does it even matter? I can use MySQL without knowing this. Why does ZoneMinder need to know this anyway? With MySQL running as a Service, why can't it produce querries like anything else?