The "code audit" that you guys did to make sure nothing was backdoored was quite thorough too, considering since then remote bugs in Snort have been published. If you can't even spot the vulnerable code you introduce into your source tree by accident, how can you definitively argue that no one else snuck in subtle bugs that you also didn't catch?
I'm sure it would have been extraordinarily difficult to run 'diff' on the codebase before the intrusion and the one after, to see if any of the changes weren't accounted for.
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