[BUG] JMP Bugs involving <anatomical_markers>, <marker_names>, and JMPBody scaling

[bfregly]

Describe the bug
Run JMP using settings file JMPScaleModelMoveMarkersAll.xml, which

1. Scales femur, tibia, humerus, ulna, and radius on both sides and
2. Moves pelvis markers in Y direction.
3. Uses a list of markers to track via <marker_names>
4. Takes in a .osim file with additional markers in it that are not included in the list of <marker_names>.

Three possible bugs are evident for this JMP run:

1. JMP still tracks markers in the .osim model file not in the <marker_names> list, as shown by the HUGE cost function values. Re-run JMP using settings file JMPScaleModelMoveMarkersRemoved.xml, wich uses a .osim file where the unwanted markers have been manually removed. The cost function values are now MUCH smaller and more reasonable, but they should be the same if <marker_names> was working properly.
2. The medial and lateral knee markers do not remain over their respective anatomical locations on the femurs when the femurs were scaled, indicating that <anatomical_markers> did not work.
3. The radius in each arm (which has the Elbow and Wrist markers attached to it) was supposed to be scaled but was not scaled at all, while the hand in each arm was not supposed to be scaled but was scaled (see the output .osim model file).

To Reproduce
Steps to reproduce the behavior:
See above.

Expected behavior
Extra markers in a .osim model file should not influence JMP solution when omitted from the <marker_names> list.
<anatomical_markers> set to true should cause marker locations in both segments to scale with the body segments.
JMPBodies with <scale_body> set to true should be scaled, and bodies not included in the list of JMPBodies should not be scaled.

Screenshots
See below.

Desktop (please complete the following information):

• OS: Windows
• OpenSim Version: 4.5
• MATLAB Version: 2023a
• NMSM Pipeline Version: v1.1

Additional context
Add any other context about the problem here.
Bug2.zip

[cvhammond]

<anatomical_markers> is an experimental tag for research related to understanding the feasibility of using JMP for scaling beyond small adjustments after the OpenSim GUI Scale Tool. It has not been tested thoroughly and is beyond the scope of the expected use of JMP.

With that being said, it doesn't make sense to move markers and have anatomical markers set to true, but because this is an experimental tag, no safe-guards have been set up to stop this.