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Hi Gioni,
Just updated to 7.0 on a couple of websites and decided to give security scanner a try. Please, have a look – https://imgur.com/a/UrESFI3
The thing goes insane and barks on nearly every file of many plugins. I gather you’re using some kind of database that contains integrity checksums of free plugins or something like that? I assume this because it looks like the scanner is going crazy only on non-free plugins (e.g. Quform, WPJM Field Editor, Yoast Premium, etc).
If that’s how it works – there’ll be tons of such false positives until you’re able to gather integrity checksums of paid plugins (which I guess is nearly impossible).