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If I never associated a phone number with my account am I safe, or does it also include phone numbers from contacts lists people let Facebook copy?

Not true, you could only search for accounts using phone numbers people had entered themselves

But your phone number would still be in facebooks database...

This article is not about facebook’s database it’s about phone numbers scraped through search which ended up in a third party database

"numbers scraped" from Facebook's database. Of course this is about Facebook's database