After some searching, I finally located the main.cpp and the main() function.
But it doesn't allow saving over, is there anything I can do to fix this?
and no, it is NOT set to read-only
if there is no workaround, what should I do so that I can program without having to use the predefined functions? (just curious)
Which operating system? Do you have root / administrator privileges?
Certainly a case of file permissions of some sort, which depends
on the operating system and file-system involved.
Yes. Depending on what you changed you may need an empty setup() and loop(). Do you expect the program to magically transfer from the PC to the arduino?
Note: You could almost certainly have put all your code in an endless loop in setup()