Updated .gitignore
Updated Monarch to current master
Updated Monarch and updated CMakeLists.txt to use PROJECT_SOURCE_DIR instead of CMAKE_SOURCE_DIR
Updated Monarch to the current, libthorax-dependent version.
Updated KTTSGenerator to use libthorax's time utilities.
Updated PackageBuilder.cmake to include submodule updates.
Merge branch 'refs/heads/Submodules' into develop