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Is there any particular reason why index.php in most templates usually seems to go all the way from just after the start of #main to right before it's closing tag, with that closing tag contained in footer.php. In my theme it would be handy to have #main's closing tag in the index/single/page files not in footer.php ( so the split would be another couple of lines down the code from where i normally see it ).

And if there's no real difference then should i also move the header/index split up a line to get the #main div start tag into the index/single/page etc files ?

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It's a personal choice. If the containing markup is consistent across all templates it doesn't matter if they're in the template or header/footer, it's just one less bit of markup that gets repeated in every template.

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