Small updates for 6.0

[mxgrey]

There were a few TODO tags related to version 6.0. This takes care of two of them:

1. Now, when we clone a Skeleton, the full State of the original Skeleton gets copied into the new Skeleton. (Before now, only Properties were getting copied)
2. Initial positions and initial velocities are now included in the constructors of SingleDofJoint and MultiDofJoint.

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This change is

[jslee02]

Reviewed 7 of 31 files at r1.
Review status: all files reviewed at latest revision, all discussions resolved.

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[jslee02]

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Review status: all files reviewed at latest revision, all discussions resolved, some commit checks pending.

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