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I wanted to know if the (auto_update_plugin) and the (auto_update_theme) filters work when put in theme's functions.php file instead of config.php file in WordPress core.

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    which config.php is this? You shouldn't be modifying WP Core
    – Tom J Nowell ♦
    Commented Jul 23, 2014 at 17:59

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The filter works when placed in active theme's functions.php file. Just tested that, and the result was positive.

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In general they should. All of config load, plugins load, and theme load happens during load process and before init hook, which is considered a point after which load is done and functionality starts.

Unless you are dealing with early load-related events, typically plugin is perfectly appropriate place.

PS not sure what you mean by config.php, hooks don't even work as early as wp-config.php yet.

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