What is the best way to flex and bison to stop processing when an error is encountered. If I call yyerror, it does not stop scanning and parsing my file. While the input is syntactically correct, there is an user error, such as they tried to load the same file twice. Once I am out of flex/bison, then my program will return an error to the user and the program should keep running. I assume that throwing a C++ exception would probably break something?
YYABORT is the standard way of getting out; it causes yyparse to return immediately with a failure (1). You can then throw an exception or do whatever you want. You'll need to reset flex's input if you want to parse something else, but if you do, you can just call yyparse again and parsing will start over from the beginning.