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RE: mainfile.php
If you're paranoid about sercurity, you may want to take a look at the
Xoops Protector module. You'll need to do some mild hacking to install it, but it will protect the contents of the mainfile.php.
RE: Robots.txt
The default robots.txt file is fine the way it is for *most* installations. The only time you should ever have to chage that file is if you install piCal or if you just don't want search engines to index certain areas of your site.
The reason you want to disallow access to piCal is because the spiders will each up all your bandwidth searching through the calendars internal links month by month. To disallow piCal, just add the following to robots.txt:
Disallow: /modules/piCal/
To disallow access to any other module on your site, use the same format, just replace piCal with the module name you wish to deny access to.
ex:
Disallow: /modules/newbb/
Hope this helps.