Update BOUT++

[dschwoerer]

Purpose

Update BOUT++ to the latest next branch. Additionally PR boutproject/BOUT-dev#3463 is included to simplify normalisation.

Change Summary

boutproject/BOUT-dev#3463 -> Add API for normalisation of metrics (NOT yet merged)
boutproject/BOUT-dev#3457 -> Fix properly selection of bout::ConductionMethod
boutproject/BOUT-dev#3452 -> Only the first commit is currently included in hermes-3, not the cleanup
boutproject/BOUT-dev#3453 -> Only the first commit is currently included in hermes-3, not the
boutproject/BOUT-dev#3425 -> This is a major change. All coordinates access needs to be done with functions, no public members. This allows to ensure internally cached variables are always up to date, and can also be computed only when they are needed.

Validation

Only CI

AI Assistance

None

Documentation

None

Review Notes

A lot of churn, but most changes are just renaming e.g. coords->dx to coords->dx(). This has been done mostly with bout-upgrader v6 v6_upgrader <files>...

[codecov]

Codecov Report

❌ Patch coverage is 48.57143% with 108 lines in your changes missing coverage. Please review.
✅ Project coverage is 57.65%. Comparing base (dba2bb1) to head (e0e62a0).
⚠️ Report is 7 commits behind head on master.

Files with missing lines	Patch %	Lines
src/div_ops.cxx	62.50%	24 Missing ⚠️
src/neutral_boundary.cxx	0.00%	22 Missing ⚠️
src/recalculate_metric.cxx	0.00%	22 Missing ⚠️
src/sheath_boundary_insulating.cxx	0.00%	12 Missing ⚠️
src/recycling.cxx	33.33%	10 Missing ⚠️
src/vorticity.cxx	55.55%	4 Missing ⚠️
src/neutral_full_velocity.cxx	40.00%	3 Missing ⚠️
src/relax_potential.cxx	40.00%	3 Missing ⚠️
src/evolve_density.cxx	0.00%	2 Missing ⚠️
src/sound_speed.cxx	50.00%	2 Missing ⚠️
... and 4 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #639      +/-   ##
==========================================
- Coverage   57.73%   57.65%   -0.08%     
==========================================
  Files          97       97              
  Lines       10013    10021       +8     
  Branches     1442     1443       +1     
==========================================
- Hits         5781     5778       -3     
- Misses       3652     3663      +11     
  Partials      580      580              

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