Replace std::exception with std::runtime_error

std::exception would compile on windows (VS10), but not on linux)
Refactoring to make it possible toshare code between VSD and Console version.

The arguments and error handling for the Virtual Skeleton Database needs to be
different from the console version. Thus we introduced to main methods,
and refactored the code such that the common functionality of both version
is in common src/header files.