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My coworkers and I face similar problems currently. However, there are certain methods that have been written by people like Clement de Chaisemartin and Xavier d'Haultfoeuille which attempt to mitigate this issue. You'll be interested in the commands did_multiplegt, flexpaneldid. There are more DD commands written almost by the day, so it wouldn't surprise me if someones got another solution I'm unaware of.
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