With the symbolic-awareness of GTK+, vector icons are recolored (using
fg, success, warning and error colors). Unfortunately it was also
recoloring some rectangles with neither fill nor stroke, which were
using only to get appropriate icon size (these icons were therefore
displayed as just a square).

I made a quick pass in our icons to "fix" these. I expect I may have
missed some icons, or at the opposite, I may have broken other icons by
removing rectangles which should not have been removed. If you find any
such icon, please fix.
Also some icons do not look quite right just now. We will have to create
new guidelines on how to make symbolic icons and fix/redesign some, I
guess.