Criticize C argument parsing method
void parse_arguments(int count, char * arguments[]){//probably add file pointer here  to pass to load, change return type when an API is decided.
    int currentArg, paramIndex;

    for(currentArg = 1; currentArg &lt;= count; currentArg++){


Why are you counting from zero? In C arrays start from zero, but you are starting from 1. As it stands it looks like you skip the first argument and then read one past the end

        if(arguments[currentArg][0] == '-'){
            for(paramIndex = 0; paramIndex &lt; PARAMMAX; paramIndex++){
                if(strcmp(arguments[currentArg][1], arglist[paramIndex]) == 0){


Isn't arguments[currentArg][1] a char? How are you passing it to strcmp?

                    switch(paramIndex){
                        case 0:
                            //load(currentArg + 1);
                            currentArg++;


I recommend against manipulating loop counters inside your loop. It makes it harder to follow whats going on. 

                            break;
                        default:
                            break;
                    }
                    break;
                }
            }
        }
    }
}


So much indentation suggests that you should break this down into smaller functions. I'd also suggest that you store the results of the arguments into a struct. 

A general sketch of how I'd do this:

struct options
{
    char * filename;
    int numberOfRabbits;
};

struct parameter
{
    char * name; // 'x' for option '-x'
    bool requiresOption; // whether or not we should have an option
    void (*handler)(struct options * options, char * argument);
};

void parse_arguments(int count, char * arguments[], struct options * options)
{
    char * argument;
    int position = 0;
    while(position &lt; count)
    {
         struct parameter * param = determine_parameter(arguments[position++]);
         if(!parameter)
         {
              panic(); // don't know this parameter
         }
         if(param.requiresOption)
         {
               argument = arguments[position++];
         }else{
               argument = NULL;
         }
         param.handler(options, argument);
    }
}