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The rosin flux inside of the wire-type solder is amber in color compared to the clear spray flux used on the wave soldering production process. Also sometimes black oxides on the iron tip blend with the flux to make it even darker when it melts onto your work.
You could use some solvent and a toothbrush to clean off the rosin from your joints, but it really does nothing but change the way it looks, and the solvent isn't too good to breathe.
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-Clint
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