First steps might be to look for
and replace them by simple \internal tags -- except for cases where the code is too complicated for Doxygen.
Also, some deprecated (unused) code samples can be dropped.
You can configure Eigen with -DEIGEN_TEST_BUILD_DOCUMENTATION=ON to have the documentation built when building the test-suite, and you can activate EIGEN_INTERNAL_DOCUMENTATION if you want the \internal documentation to be built.
Bug 728 and Bug 833 should probably be solved along with this.
Overall, this is not super-important but should be done eventually.
I started fixing some warnings (only on devel branch so far):
A major issue at the moment is that doxygen does not like template specializations, most importantly that makes documenting TriangularView difficult, because doxygen does not know if it should inherit from TriangularViewImpl<...,Dense> or TriangularViewImpl<...,Sparse>.
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