Fix Eigen::Ref<MatrixXd> Jacobian output args in MATLAB wrapper

[thatdudegrantt]

Fixes borglab/gtsam#2492

Problem

When calling methods like Pose3.transformFrom with Jacobian output
arguments from MATLAB, every overload using Eigen::Ref<Eigen::MatrixXd>
was permanently unreachable, producing:

Error using gtsam.Pose3/transformFrom
Arguments do not match any overload of function gtsam.Pose3.transformFrom

Root cause: Eigen::Ref<Eigen::MatrixXd> is parsed as a TemplatedType
with typename.name == 'Ref', not a plain Type with is_ref set. The
wrapper codegen had no special handling for this pattern and emitted:

isa(varargin{2}, 'Eigen.RefMatrixXd')

Eigen.RefMatrixXd is not a MATLAB class, so this check always returns
false. On the C++ MEX side, the wrapper also incorrectly tried to
unwrap_shared_ptr<MatrixXd> from in[], which would segfault even
if dispatch somehow succeeded.

Fix

gtwrap/matlab_wrapper/mixins.py

• Add eigen_ref_types tuple ('MatrixXd')
• Add is_eigen_ref() to detect Ref<MatrixXd> TemplatedType args

gtwrap/matlab_wrapper/wrapper.py

• _wrap_method_check_statement: exclude Ref args from length(varargin)
  count and isa() checks; add nargout == N gate instead
• _unwrap_argument: allocate Eigen::MatrixXd locals for Ref args
  instead of reading from in[]
• _wrapper_unwrap_arguments: don't advance arg_id for Ref args
  (they don't consume an in[] slot); capture eigen_ref_args before
  method can be reassigned to a string for templated methods
• wrap_collector_function_return: write Jacobian locals to out[1],
  out[2], ... after the primary return value
• generate_collector_function: exclude Ref args from checkArguments
  nargin count

Generated output (before/after)

Before (broken so Eigen.RefMatrixXd never matches):

if length(varargin) == 3 && isa(varargin{1},'double') && ... && isa(varargin{2},'Eigen.RefMatrixXd')

After (correct, now dispatches on real inputs + nargout):

if length(varargin) == 1 && isa(varargin{1},'double') && size(varargin{1},1)==3 && size(varargin{1},2)==1 && nargout == 3

C++ MEX after:

Eigen::MatrixXd Hself = Eigen::MatrixXd();
Eigen::MatrixXd Hpoint = Eigen::MatrixXd();
out[0] = wrap< Point3 >(obj->transformFrom(point, Hself, Hpoint));
out[1] = wrap< Eigen::MatrixXd >(Hself);
out[2] = wrap< Eigen::MatrixXd >(Hpoint);

Testing

Added test_eigen_ref_jacobians to tests/test_matlab_wrapper.py with
fixture tests/fixtures/eigen_ref.i covering four cases:

• Instance method with primitive input + 2 Ref args (transformFrom)
• Instance method with zero real inputs + 1 Ref arg (inverse)
• Instance method with class-type input + 2 Ref args (between)
• Static method with 1 Ref arg (Expmap)

All 11 tests pass.

Environment

• OS: Windows 11 x64
• Python: 3.14.5
• wrap commit: (your current branch tip)

[dellaert]

Awesome, @thatdudegrantt !!!