Hahaha. I understand why one would be confused if they hadn't played in a while. I would be too. You need an upgrade from Xur or you need to obtain the weapon again. Also, exotic shards are needed for the last upgrade in exotic weapons an armor.
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So for example I got my shadow price at 300 attack. Is there something I can buy from Xur to make it 331?
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Sadly it's only exotics. All the vendor gear is different now. For example, The Devil You Know was replaced by a new hand cannon called The Devil You Don't. So there are two new auto rifles available from the Vanguard. You will also need something called a Vanguard Commendation to purchase any weapons and some armor from the Vanguard. The way you acquire these is simply by leveling up the Vanguard. Each new level achieved grants you one commendation. Hope all this helped. If you have any further questions I'd be happy to help.
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You can only upgrade exotic. You also have to wait for Xur to have the upgrade in stock.