remove density from the true SDC reaction system

[zingale]

PR summary

This makes the linear algebra basically the same as with simplified-SDC.

PR motivation

PR checklist

• test suite needs to be run on this PR
• this PR will change answers in the test suite to more than roundoff level
• all newly-added functions have docstrings as per the coding conventions
• the CHANGES file has been updated, if appropriate
• if appropriate, this change is described in the docs

[zingale]

this seems to work for the Newton solver at the moment. I still need to update the VODE solver.

[zingale]

With these changes to the Newton solver, I still get the expected convergence for the 4th order bubble_convergence test:

 $\rho$                           3.585683e+15   3.265       3.729255e+14   3.727       2.816885e+13
 $\rho u$                         1.118641e+24   3.796       8.055874e+22   3.961       5.174399e+21
 $\rho v$                         1.312304e+24   3.544       1.124944e+23   3.852       7.791824e+21
 $\rho E$                         3.690044e+32   2.949       4.780038e+31   3.669       3.757922e+30
 $\rho e$                         3.689602e+32   2.949       4.779603e+31   3.669       3.757719e+30
 $T$                              1.437942e+18   3.508       1.263904e+17   3.831       8.882729e+15
 $\rho X(\isotm{He}{4})$          3.584429e+15   3.268       3.722135e+14   3.725       2.814696e+13
 $\rho X(\isotm{C}{12})$           1.51971e+13   2.544       2.606256e+12   3.798       1.874186e+11
 $\rho X(\isotm{O}{16})$              35853340   3.265            3729538   3.727             281661
 $\rho X(\isotm{Fe}{56})$             35855820   3.265            3729107   3.727           281688.5

[zingale]

this requires: AMReX-Astro/Microphysics#1338

[zingale]

the VODE solver code path works now too.

I'll stop here in this PR. In a follow-on PR, I'll remove all the VODE stuff from Castro and instead have us directly use the Microphysics simplified-SDC update, since the mechanics are identical.

[zingale]

I think that this is ready for review. We should first merge:
AMReX-Astro/Microphysics#1338

then rerun the tests here. Note that by merging that Microphysics PR, we'll break true-SDC in the current code (but it wasn't actually correct with VODE anyway). Then this PR will fix it all up again.

[zingale]

test suite run with these changes:
http://groot.astro.sunysb.edu/Castro/test-suite/gfortran/2023-09-21-001/index.html

[zingale]

okay, I think that this is all set for review now. Microphysics has been updated and the benchmarks have been updated too. The test suite shows the expected error around tolerance.