Hacking Linux Exposed
has a (now) 3-part series on "Stealthily Managing IPTables Remotely
". Part 1
explains how to get Net::Pcap to sniff certain types of packets. Part 2
explains how to run programs based on those sniffed packets. Part 3
describes how to send commands to the above.
Although it's not "port knocking", it's close and gives a good idea of possible capabilities for both methods. In either case, it can be used for good or evil.
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