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Okay, I want http://example.com/mysite, so I put a config.php with the appropriate settings in the drupal/sites/mysite folder. I made a symlink and can confirm that example.com/mysite resolves to example.com/drupal, but it still just shows my default setup.
I've made sure my permissions are correct, double-checked the config.php files and all that stuff, still no-worky. The symlink is working, but Drupal won't connect to the other DB or anything. What could I be missing?