Write NetCDF files and call VULCAN robustly [DO NOT REVIEW YET]

[nichollsh]

Description

This pull request introduces a few different improvements and fixes.

Robust Atmospheric Data Handling

• Added find_latest_atmosphere_time in common.py to locate the most recent available atmosphere NetCDF snapshot, and updated run_vulcan in vulcan.py. Improving resilience to missing files.
• Refactored AGNI and JANUS climate models to use dedicated write_atmos_ncdf helper functions for writing NetCDF files
• Closes Atmosphere NetCDF files sometimes not written, and atmosphere plots sometimes not created #717

Output Writing and Configuration

• Clarified the meaning of dt_write_rel parameter in documentation and config files
• Now actsas an additional time-based write trigger combined with write_mod via logical OR, rather than logical AND.

Chemistry Model

• Adjusted VULCAN chemistry model time-stepping parameters for improved convergence and stability
• Updates atmosphere chemistry plot after running offline chemistry
• Resolves VULCAN offline chemistry crashes ('NoneType' object is not subscriptable) #773

Validation of changes

• More tests

Outline your test configuration; e.g. MacOS with Python 3.13.

Checklist

• I have followed the contributing guidelines
• My code follows the style guidelines of this project
• I have performed a self-review of my code
• My changes generate no new warnings or errors
• I have checked that the tests still pass on my computer
• I have updated the docs, as appropriate
• I have added tests for these changes, as appropriate
• I have checked that all dependencies have been updated, as required

[codecov]

Codecov Report

❌ Patch coverage is 83.33333% with 14 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.71%. Comparing base (9881061) to head (73872ac).

Files with missing lines	Patch %	Lines
src/proteus/atmos_clim/janus.py	33.33%	6 Missing ⚠️
src/proteus/proteus.py	50.00%	3 Missing ⚠️
src/proteus/utils/coupler.py	66.66%	0 Missing and 3 partials ⚠️
src/proteus/atmos_chem/vulcan.py	94.11%	0 Missing and 1 partial ⚠️
src/proteus/atmos_clim/wrapper.py	94.11%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #775      +/-   ##
==========================================
+ Coverage   92.66%   92.71%   +0.04%     
==========================================
  Files         110      110              
  Lines       15807    15867      +60     
  Branches     2846     2855       +9     
==========================================
+ Hits        14648    14711      +63     
+ Misses       1159     1148      -11     
- Partials        0        8       +8     

Flag	Coverage Δ
unit-tests	83.69% <83.33%> (+0.06%)	⬆️

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