transaction: Add back support for file: uris in RuntimeRepo keys

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This used to work, and the gnome-software test suite relies on it,
so add it back. I believe it regressed in
 https://github.com/flatpak/flatpak/pull/2740

This fixes https://github.com/flatpak/flatpak/issues/2955

Closes: #2956
Approved by: alexlarsson

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