Better management of file handles and pointers

[madMatchstick]

There are 6 file pointers,

FILE *control_fptr;
FILE *input_fptr;   
FILE *subcat_fptr;  
FILE *params_fptr;  
FILE *output_fptr;
FILE *out_hyd_fptr; 

input output and out_hyd are needed conditionally depending on yes_print_output and stand_alone. Yet, current code opens/sets handle (fully) regardless of these flags. This primary applies to bmi.initalize() & bmi.finalize() and eventually bmi.set_value() & bmi.get_value_ptr() as needed for serialization and other BMI enhancement tools