Control chemistry BoxArray - remove some avgDown

[esclapez]

When using MAGMA with relatively large mechanisms, the memory requirements prevent using grid patches bigger than 32^3. This results in a large number of boxes that deteriorates the scaling performances, especially in the linear solvers. Since PeleLMeX already utilize a specific BoxArray for the chemistry to only integrate non fine-covered boxes, this PR introduce a user-controlled parameter to specify a max grid size for this specific BA:
peleLM.max_grid_size_chem = 32
If this keyword is not provided, the usual amr.max_grid_size is used.
Additionally, this PR remove the machinery that used to handle averaging down the reaction term and advancing fine-covered region with A+D+R in place of calling the reaction integrator. This leads to small differences on I_R (<1e-12) in fine-covered regions, that can propagate to the rest of the solution when regriding (but still < 1e-12 differences on state variables). Averaging down of RhoRT and density are also removed since those call did not affect the solution.