Fix for #38: use CMAKE_INSTALL_PREFIX

Except for the root CMakeLists.txt, it's a search and replace of SimTK_INSTALL_PREFIX to CMAKE_INSTALL_PREFIX. For the root CMakeLists.txt, I remove the block of code that overwrites CMAKE_INSTALL_PREFIX with the value of SimTK_INSTALL_PREFIX, and add a different block that will copy SimTK_INSTALL_PREFIX into CMAKE_INSTALL_PREFIX under certain conditions for backward compatibility.

I have tested this on OSX, but I still need to test on my Ubuntu machine. If someone can test this on Windows I would appreciate it.