Should I use the ISP mode or create custom configuration files and report directories for each client?
You can either (a) use ISP mode as intended and give people their ISP mode account login information so that they can go to our web interface and see their reports that way, and not worry about putting them in your regular web server space at all, or (b) totally ignore ISP mode and start creating your own custom configuration files and report directories for each client, anywhere you want to put them. Advanced mode is a good place to start on that, and you can then use command line stuff like “wusage -c /path/to/conf/file” to update any given configuration. To summarize, you can create the accounts through the ISP mode administrative interface. Or you can ignore ISP mode and go for advanced mode, which allows you to put report directories and configuration files anywhere you want them and update them from your own scripts.
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