[Pro. PHP Dev.] Security: Includes / Classes / Configs?

Hello All,

So I have a question, which i'm sure you guys can answer.

I was taught that having your includes in /home/user/includes/ was
best practice for security reasons, however the most popular apps on
the market come with the includes folder inside the install directory
itself /home/user/public_html/includes/.

Which way is the best?

Which way is the most secure?

Which way is the most efficient?

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