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Basically SWFUpload offers up no user interface of it's own but instead works as a stub that brings up the standard OS Open File dialog. Then once the user has selected their files, they Flash component returns the list of file to the page and all the user interaction is handled through via markup and javascript via a sophisticated Javascript API.
This approach mitigates any accessibility issues with Flash since the UI will be primarily HTML, assuming that the OS handles the accessibility of the File Open dialog. We will still have our hands-full with making the markup accessible but at least it's a problem that we understand.
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Background for this decision:
The file and folder upload options are:
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