Lot's of code fixes from coverity and clang-tidy (#2736, #2734, #2735, #2731, #2732, #2733)

Fix the boundary condition logic at a wall for Detonation (#2722)

Reimplement the shock detection algorithm to account for sources and do a better job in multidimensions (#2711, #2710, #2709, #2704)

Start the process of moving the runtime parameters to structs (#2688)

An option for unlimited PPM reconstruction was added (#2670)

An option allowing for optional passive sources to the conserved state was added (#2678)

A script diag_parser.py was added to allow for easy parsing of the global diagnostic files output at runtime (#2666, #2667)

Problem GNUmakefiles have been standardized and now allow for the problem to be compiled elsewhere (#2640, #2641, #2642, #2643)

The true-SDC Newton solver has been made more robust and faster (#2586, #2602, #2605, #2606)

Several problems that required the initial model grid spacing to be specified in the inputs file now automatically compute it as needed, including flame_wave (#2610), convective_flame, bubble_convergence, and hse_convergence (#2624), double_bubble, gamma_law_bubble, and hse_convergence_general (#2612)

Outflow boundary conditions for the 4th order solver have been changed to no longer use the one-sided stencil (#2607)

The ca_rad_source hook in Fortran has been removed. The existing problem_rad_source() hook in C++ can be used instead. (#2626)

The compile option USE_AUX_UPDATE has been removed. If you want to manually update the auxiliary parameters, you can use an external source term or you can use the problem post-timestep hook. (#2614)

The pressure is now always included in the x-momentum flux in 1-d Cartesian, and this fixes an issue at jumps in refinement with the pressure gradient (#2468)

A bug was fixed in the 4th order diffusion operator that was introduced when it was originally converted to C++ (#2592)

The 2nd order Radau integrator had the wrong quadrature weights (#2594)

True-SDC no longer evolves density as part of the reaction system and now uses the same ODE code path as simplified-SDC. This means we don't need our own custom VODE righthand side functions (#2559, #2560, #2567, #2578, #2580, #2584)

The true SDC runtime parameter sdc_solve_for_rhoe has been removed. (#2572)

The true SDC runtime parameters sdc_solver_tol_spec, sdc_solver_tol_ener, sdc_solver_atol have been removed. Instead the Microphysics integration tolerance parameters should be used. (#2571)

The true SDC runtime parameter sdc_newton_use_analytic_jac has been removed. Instead the Microphysics integrator jacobian parameter should be used (#2573)