I know that having the wires run the length of the bike is a hassle, but it's so much more practical to have the battery with me at all times since the rear pannier pocket holds the battery and it's charger quite snugly, also leaving enough room for the Blackburn flea 2.0 and it's usb charging base.

When I reach my work, I unclip the pannier, the battery connector for the MS clone, and I have everything with me. Also true when I'm running errands, with the exception of the light itself which is securely bolted to the bike instead of that !#!$!@@ rubber band that came with it.