C++ version of libOpenCOR's interface: allow to create as many SED-ML documents and instances as we want for a given file

[agarny]

While working on issue #291, we modified libOpenCOR's interface so that we can create as many SED-ML documents and instances as we want for a given file. This was needed so that we can use both the standard and interactive modes independently. This all works fine using OpenCOR's Web app, but... I completely overlooked the C++ version of libOpenCOR's interface for OpenCOR itself (i.e. the desktop version). So, this needs to "fixed".