Changes to the API

Direct storage of TimeControl affects functions in pargs.h and trxio.h

During command line argument parsing, time control flags (-b, -e and -dt) are set to an input gmx::TimeControl struct (in gromacs/fileio/timecontrol.h) instead of to global variables. The following functions are affected:

parse_common_args takes an extra gmx::TimeControl* input, which can be nullptr. If time control is desired a non-nullptr object must be passed.

read_first_frame and read_first_x both take an extra gmx::TimeControl* input, which can be nullptr if time control is not desired.

check_times takes an extra gmx::TimeControl& input containing the time control parameters to check against.