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Welcome to Geeklog Sunday, May 19 2013 @ 06:47 PM EDT
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It works just like the theme-specific functions for the site header and footer, i.e. in your theme's functions.php, implement functions Foo_startBlock and/or Foo_endBlock (assuming your theme's name is "Foo"). Those functions will have to do all the work, so you have to effectively re-implement COM_startBlock and COM_endBlock.