So, I'm using the CodeIgniter framework for OAv2. Best practice states you should move any sensitive files (think config.php) out of your web directories. So, a few hours and a few periods of WTF, and I have the application separated into two main sections.
Inside /var/www is index.php along with the JavaScript, css and images files. In another directory (outside the web) is the rest of the framework and application. It's working well. I think the directory structure I'll use will be along the lines of:
/var/www
/usr/bin/OAv2/codeigniter
/usr/bin/OAv2/scripts
Oh - as for Windows installs.... well, they're secondary. I plan to be able to run everything from a Debian/Ubuntu install. There should be no need for a Windows machine. This includes auditing a Windows Domain. Having said that, I'll probably expend a limited amount of effort to get it working under Windows....
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