Cloaks have not been integrated in the polished central Mineshafter Squared system yet. Here's the temporary solution by the same developers. Upload your cape/cloak here (64 width by 32 height, or 22 by 17), and use the Universal Launcher 4.2.8+. Note: only other people using Mineshafter Squared 4.2.8+ will be able to see your capes (this is a technical limitation) - so encourage them to check this out!
Cloaks are 64 by 32 but only the first 22x17 are used. So, 22x17 cloaks are okay, but try to get 64x32 versions. Also, Spoutcraft requires 64x32 cloaks. See this Spoutcraft thread. Thanks to wiedzmin26 for helping figuring these dimensions out!
Log in to set/update your cloak. (You must have a Mineshafter Squared account. Log in with those credentials)