Refactor hierarchy

[kejacobson]

Refactor to use MphysGroup, library of scenarios/coupling groups, promote by tags, and MultipointParallel.
Reduce Builder to only necessary methods, change elements to subsystems.

Converted solvers:

• TACS
• VLM
• MELD
• FUN3D

Example directories with converted scripts:

• aero_only
• struct_only
• aerostructural

[anilyil]

@kejacobson I pushed a fix for the adflow functionals with the current shape_by_conn behavior. I merged that change here as well. I also created a new tagged version 0.2 to act as a checkpoint before we merge in your refactor stuff.

I think this PR is good to go. I would rather not delay this any further. I will work on the mach refactor on the side and merge that as a separate PR.

[anilyil]

I have been working to refactor all of the mach stuff and I think I am done with my first iteration. You can check out the branch here: https://github.com/anilyil/mphys/tree/refactor_mach That branch is branched from this PR's branch, so we can either merge here or back to mphys/master after merging the PR. I have updated all of the example runscripts that has adflow in it. I have also updated the tests. Currently, I have these two tests failing locally:

The following tests failed:
test_meld_derivs.py:TestXferClasses.test_derivatives
test_tacs_derivs.py:TestTACs.test_derivatives


Passed:  59
Failed:  2
Skipped: 0

I remember someone mentioning that I need complex builds of tacs/meld for these, so I am not sure. I didnt try to understand why these tests were failing; let me know the build steps I need to run these and I can try to run them as well. The remaining tests pass.

@joanibal I left some TODOs for you in mphys adflow regarding thermal hooks. I also left general TODOs in our codes for possible issues and possible optimizations we can look at. I think we can make that of secondary importance since all examples run now. It is probably a better idea to work on merging these refactor PRs, make a release, then make incremental updates to the mach wrappers.

Let me know when this PR is ready to merge @kejacobson. Then we can figure out the work on my branch as well.