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This is the first PR from some refactoring I did over the break, to get rid of shared pointers for containers. It is totally appropriate that we use shared pointers for factors (although, maybe we should not!), but it never made sense (I see now) that we used shared pointers for graphs, as they are not really shuffled around like factors.
The big changes that are coming (branches have not been published yet) are mostly in linear, to get a newer and faster API for elimination -- prompted by development in hybrid branch. This PR removes shared pointers from the subgraph API, for starters.
Adding @jlblancoc as a reviewer, partly to get his opinion on above, and @ProfFan as FYI as I know he has a forked branch with lots of shared pointer changes (presumably moving to std::shared_ptr).