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Where are the functions that handle logging the user in? Specifically, the one that checks the users plain text password at the login page against the hashed formatted one stored in the database?

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Some of the functions are in wp-includes/pluggable.php, notably wp_authenticate() though you'll notice that most of the work is done by filters hooked to authenticate. The names of those you can find in wp-includes/default-filters.php and the function definitions in wp-includes/user.php.

But be aware that functions in pluggables.php can be replaced by theme or plugin code in their entirety and functions hooked to authenticate can be removed and replaced as well as altered via the numerous hooks provided by the various functions.

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