Speed up the full build.

Now, by default, instead of fully building everything,
we skip dexing the modules that aren't going to be included
in the current build.

This will slow down some of the incremental builds (like tests),
but it improves the regular eng build from 27.5 minutes on my
Mac Pro to 25 minutes.  That's not as much of an improvement
as I had hoped for, but it's still better.

There is also a change in here that puts the java-source-list
file which is used to get around limited command line lengths
in the proper directory.  Before this change, it was an
accident that the directory for that file existed!