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Should transforms apply before or after filters if an element has both?
Filters are applied to the CTM of the element. The transform changes the CTM. That doesn't (in theory) influence the filter. Practically you need to make sure that the filter is not pixelated. I don't think that this needs to be specified further . WebKit does it right already. The same for all other browsers on SVG content.
Calrify that filters are applied in the element's local coordinate system.