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Eliminate shared ptrs to Eigen matrices & vectors
Eliminate all use of shared pointers to Eigen matrices and vectors, especially as arguments and return values. The impetus was that pybind11 did not wrap the return value from the following properly (it build but could not turn the result into a Python object, and the error message made it look like the result was an Eigen::MatrixXd instead of a shared pointer to the same): ``` std::shared_ptr<Eigen::MatrixXd> makeRegularizationMatrix ```
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