Support for multi-version, make clean check smoke

 - add chisel-dependent.sbt to sub-projects (remove
   libraryDependencies from build.sbt)
 - add target and subdirectory Make fragment generators to Makefile
 - add FameTransform and SimpleALU executables to examples/Makefile
 - add support for SBT_FLAGS to counter/Makefile
 - add CHISEL_*_VERSION definitions and use them in target-specific
   variables - overrideable with "chiselVersion=..." on the command
   line.