I have all the source code for a completed Arduino project but I actually want to compile it into a stand alone app or program for use on Pc or OsX if possible, and I do not know where to start.
As a java programmer, I'd address this by writing a java front-end and somehow using Java Native Interface to talk to the compiled C. You'd have to simulate all the hardware in the target environment - you'd write some Java that would pretend to be an EEPROM, which would pesist the data to local disk storage.
For OSX, you are probably looking at "Swift".
Alternatively, you might be able to write some sort of X front-end in C, and simply (ha!) link in the object files.
Ultimately, you have to write a simulation layer for the hardware.
I actually want to compile it into a stand alone app or program for use on Pc or OsX if possible, and I do not know where to start.
That's easy. Start over. Compiling code for a microcontroller that can turn pins on an off, read pin states, etc. makes little sense for a PC that can't.