Fix broken interaction of JarJar and Emma.

Fix broken interaction of JarJar and Emma.

JarJar, like DX, can't handle the local var corruption that Emma
performs.  To fix this, I'm moving the JarJar step before the Emma
step.

Couple other minor changes:
* Improved the comment about emma hardcoding its output filename,
  since this took me about an hour to track down.
* Changed one line from "Copying $<" to "Copying $@".  It seems to be
  the convention that such lines print the destination, not the
  source, so I made it consistent.

Change-Id: I9f5c36b4f5af15daf15025b89860e942f15bb668