New plan of action:

1) Pull File Entity from Media and store in its own project page.
2) Have Embedded Media Field create a new widget for File Fields, that offers a textfield in addition to the upload button, allowing to paste URL's.
3) The update from d6 to d7 will create a new file field in place of the old, which will store the parsed URI's.

Most of this is already in place, making the process much easier than it would have been earlier.

What do you think? Is this a reasonable course of action? Am I missing something?

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