This has probably been answered before, but I couldn't find it searching on the forum (or Google). I created my own custom theme (copied the default one) and started modifying it. I needed to make some CSS changes, but couldn't work out why they were not being applied. Then I looked in the header.tpl file and noticed this:
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<link href="catalog/view/theme/default/stylesheet/stylesheet.css" rel="stylesheet">
Cheers,
Allen