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I want to make some custom changes to part of the output. Will be too complicated to do it by a plugin because there are many changes and as well, I need to directly overwrite some of the functions which can't be overwrited by a plugin.

My idea is to overwrite the output by using ob_start and ob_end_flush.

I see some occurences of ob_start in 1.5.2 code as well. Should be any interference if I add my own ob_start and ob_end_flush on index.php?
Q2A version: 1.5.2

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It should be fine, since PHP allows nesting of output buffering.