The second half of this page will give you a general outline as to how to
secure you server - fixing stupid default PHP settings, getting rid of unused scripts,
turning off suexec for sure, etc.:
https://bettercgi.com/strongbox/pass...adyhacked.html
Of course there have been 1,200 page books written on the topic, so that one page
isn't comprehensive. You may need to talk to someone who has read the 1200 page books.
If they can;t get it, talk to someone who has WRITTEN one of the 1200 page books.
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Strongbox - The next generation in site security
Throttlebox - The next generation in bandwidth control
Clonebox - Backup and disaster recovery on steroids