...How do other people determine that a site is actually based on Cocoon?
I don't think there's much more than what you suggest. Looking at the way the HTML is serialized can help a bit but it's really getting into forensics at this point ;-)
The configuration of a website can make it very hard to find out that it's running Cocoon, I guess we'll have to believe the people at some point, maybe after asking some details as we've done in the past.
-Bertrand
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