Since nobody else seems to have mentioned it: Code Complete is probably part of the answer you’re looking for, even if it’s several years old by this point—the concepts you’re looking to learn aren’t as fleeting as the technical details that change all the time. (Although, I don’t remember if even the latest edition tackles Agile methodology, so you might need a separate resource for that if it doesn’t.)
Since nobody else seems to have mentioned it: Code Complete is probably part of the answer you’re looking for, even if it’s several years old by this point—the concepts you’re looking to learn aren’t as fleeting as the technical details that change all the time. (Although, I don’t remember if even the latest edition tackles Agile methodology, so you might need a separate resource for that if it doesn’t.)