Fixed some minor README formatting issues.

The README was not updated to reflect the new directory hierarchy.
Added and documented two new features:

 - The `usm copy-script` feature makes migration easier since it is not
   necessary to copy the script from bin/usm into ~/.usm-env
 - The `usm ls` command now takes an optional software argument which will
   list the versions of one particular software.
Merge remote-tracking branch 'origin-write/master'