I just did a search for a domain, and it did indeed return results
from shortened URLs, so it seems to still work (or they fixed the
problem).

The only reasonable way I have found to consume the feed of a specific
domain is to use the search API. You'll need to periodically perform a
search, and keep track of the most recent ID that you found in the
previous search so you'll know when to stop. You may also need to
adjust the time between searches based on how many results you get.

You could probably also use the streaming API with a filter for the
domain, though I am not sure if that will work with the shortened
URLs, and it would of course require keeping a connection open.

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