cmc_v2.c
-All changes only regard the integration of the new external reaction routines.
- It seems like Darryl made some changes to these files, as they now use "apply_ext_forces" instead of "apply_ground_reactions" and"setExpGRF" instead of "get_ground_reactions"

ext_react.c
-This file is new and contains all functions necessary to handle external reaction forces and torques

main_cmc.c
-A huge variety of changes. Some due to the new definition of the external forces, some minor changes at the screen output.
-This version does not use a generic muscle file.
-It places and SIMM-Event in the output motion file, to mark the transition between initialization phase and actual algorithm output.
-The data is written to the output file while the algorithm is still in the initialization phase.

main_forsim.c
-minor changes in order to use the new definitions of external forces. Not completed yet.

nrutil.h
-The macros SQR and SIGN are already defined in "macros.h", they might are unnecessary here.

scale_v2.c
-Some useful additions for the screen output, which will now also include the
names of the segments.

sdufuncs.c
-The functions here have been primarily changed, so the work with the new functions for handling the external reactions. Previously, these functions were part of this file. They have been removed, and their call in "sduforce" and "clac_derivatives" was adapted. 

user_functions.h
-Changed the function headers for the handling of external reactions
-Included a CMC-Struct in the call for setExpStates
The prototypes for the output functions only show up in the version on
UWGait, probably they have been added later.

user_output.c
-Added some code to write the limits off the muscle forces
(includes changing the header of "create_output_motion_dt" and "store_motion_frame_dt" to allow passing of the CMC-Struct.)
-Changed the code to output the external reaction forces. These routines have been chaged so they work with the new routines provided by "ext_react.c". This includes the simplification of the function headers, as it is now unnecessary to pass the force and torque vector structs to the output function.
-Fixed the code for transforming forces from the reference frame to the output frame
-Changed the column names from "..._joint_force_..." to "..._force_..." for joint reaction forces, so they actually show up in SIMM

user_routines.c:
Changed void setExpState(...)
-Added code to deal with fixed genCoords (they are set to zero)
-Added calls to "sdassamble" and "sdinitvel". As these functions need information about which coords are tracked, a CMC-struct is now passed to the function. If the pointer to this struct is NULL, the calls are disabled
-Some code to print out the state vector.
	
user_structs.h
	Added "muscleForceLimits" to the dtOutputOptions