Update C3D-related Python, Matlab, and C++ examples

[tkuchida]

As reported on the Forum. This example in the doxygen doesn't seem to work, and the examples in the User's Guide need to be updated to reflect the recent changes to the API.

[jenhicks]

@aymanhab Is working on incorporating the examples into the build environment, so we don't need to maintain separately. When code is merged, we can update links in confluence to the correct branch/version of the code.

[jenhicks]

What if any documentation (confluence, doxygen) changes are still needed to mark this as done? @aymanhab

[aymanhab]

Confluence has some links to github code, the code changed from 4.0 to 4.1, now we include links to both by pointing to specific branches. Do we want to maintain that or stick with 4.1? if the former then we're done, if the latter, just remove the reference to 4.0 code/API

[jenhicks]

The current live confluence is for both 4.0 and 4.1. So let's leave as is and call this issue "Done".