Your best bet is to first create a standardized directory structure (e.g. c: \ www \ example.com). Then in each directory of the site there is a directory for your root and for conf files. You will then use this in your main nginx.conf http {} section.
include c:/www/*/conf/nginx.conf;
Then, each nginx.conf site will be loaded when starting or releasing a reboot for nginx. So, if you have these two paths for the site, you are set up.
c:\www\example.com\conf\ c:\www\example.com\htdocs\
Web files are in htdocs, and nginx.conf is in conf. Just like that.
I have never used nginx for Windows, so I assume that its "conf" uses slashes like * nix.
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