Apache plugin problem/BUG?
I don't know if this should work like this but I've observed an issue in apache2_plugin.inc.php:
When the user has more files than the standard index in /usr/local/ispconfig/server/conf-custom/index/ folder, the rest of the files (favicon.ico, .htaccess, robots.txt) are NOT copied in the web folder of the new site.
The problem seems to be when ispconfig is about to copy the standard index page.
Adding the 423,424,425 lines (the ones with "if(is_file" ) below the 416 line fixed this possible problem.
I'm not sure if this is a BUG or not, but it seems like a bug to me...
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