"Ephesians 6:5; the book of Phileomon (Paul sends Onasis back to his master); Numbers 31:8; Matthew 18:25; Colossians 4:1 actually gives instructions to owners of slaves and how they should treat them ...".
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When these words were written, slavery was a part of many cultures back then....it was an issue that many lived with. How is that saying its "hunky dory", using your words? And, BTW, how does it say to treat slaves? Fairly. Same can apply to an employer/employee relationship!
I'm not willing to go that far. What we have taxonomically classified as "bird" or "fowl" is a sematic construct. There is plenty wrong with "the Bible being the word of God" without picking at sematics, imo. Things like slavery, genocide, mysogeny, choosing one "race" to favor above all others, etc.
We covered slavery (somewhat). As far as the others....read Acts of the Apostles 10:34-35.
Regarding God's ancient people the Israelites, too bad many of those other nations had to attack the Israelites! (They should have meditated on the outcome of the Egyptians, in defying Jehovah and His people. Even many Egyptians left with the Israelites.) If only these other nations had acted like the Gibeonites, they would have experienced Jehovah's mercy and survived, as Acts says!