Is there a way to automatically register widgets when a new site is registered with a multi site setup? E.g. inside wpmu_new_blog?
In your themes
This option that signals that an install is immanent can be used in a hook of the
Keep in mind that switching themes kills the widgets configuration. So this is for first-time use only.
A full working example on how to register widgets on theme activation can be found in the Semiologic Reloaded Theme. It's available for download, feel free to suit yourself.
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Much easier. There's the_widget(); function already present. Just consult the codex.