Refactor repository structure to match fz-Model template and integrate reference CATHARE script

[Copilot]

Aligns fz-cathare with the standard fz-Model plugin template structure for consistency across the Funz plugin ecosystem. Integrates the reference CATHARE calculator script from the original plugin-Cathare project and adds complete CNV22 test case example.

Structural Changes

• examples/: Created examples/input.txt with parametric variable examples (flattened structure)
• examples/CNV22/: Added complete CATHARE test case with input files (CNV22, CNV22g) and output files (FORT07, listing, etc.)
• calculators/: Added Cathare.sh executable script based on reference implementation; renamed Localhost_Cathare.json → localhost_Cathare.json
• tests/: Added test_plugin.py for structure validation
• docs/: Created example_usage.ipynb Jupyter notebook with interactive examples
• ci/: Added .github/workflows/ci.yml with test, lint, and docs jobs

Removed

• CHANGELOG.md and PORTING_SUMMARY.md - removed to match template (only README.md remains)
• examples/Cathare/ subdirectory - flattened to examples/ directory
• Mock references - removed from Cathare.sh; now uses production workflow

Updated Components

• example scripts: Removed sys.path workarounds, updated paths to reference examples/CNV22/output
• .gitignore: Added results/, *.out, *.msg, PID, .fz/tmp/
• README: Directory structure diagram, CNV22 example documentation, expanded testing documentation, updated calculator references
• Cathare.sh: Based on reference script from plugin-Cathare supporting full workflow (reader → cathar → postpro) with error checking and CATHARE_HOME environment variable support

CATHARE Calculator Script

The Cathare.sh script is based on the original plugin-Cathare implementation and includes:

• Full CATHARE workflow: version check, reader (with mask support), permanent initial calculations, main calculation, post-processing
• Environment variable support: CATHARE_HOME (defaults to /opt/CATHARE2_V25_3_MOD931)
• Error checking at each step (reader, calculation, post-processing)
• Automatic cleanup of temporary files
• Portable exit codes

CNV22 Example

Complete CATHARE test case in examples/CNV22/:

• input/: CNV22 main input file and CNV22g graphical specification
• output/: Reference output files including FORT07 with EVOLUTION data, listing files, restart files
• Demonstrates output parsing with real CATHARE results
• FORT07 contains multiple EVOLUTION sections (ML, MV, P0, P8, QL, QV) correctly parsed by plugin

Template Alignment

Component	Status
Only README.md (no extra .md files)	✓
CI workflow	✓
examples/ directory (flat structure)	✓
Calculator shell script	✓
Lowercase calculator config	✓
test_plugin.py	✓
example_usage.ipynb	✓
Reference CATHARE script	✓
CNV22 complete example	✓

All existing test data in tests/CNV22/ and FORT07 parsing functionality preserved unchanged.

Original prompt

refactor repository to match template fz-Model

---

💬 We'd love your input! Share your thoughts on Copilot coding agent in our 2 minute survey.

[yannrichet-asnr]

@copilot go closer to template fz-Model: most .md files are not needed, CI missing, notebook missing, subdir examples/cathare not needed. Do not include mock anywhre, just assume Cathare code is available.

[Copilot]

@copilot go closer to template fz-Model: most .md files are not needed, CI missing, notebook missing, subdir examples/cathare not needed. Do not include mock anywhre, just assume Cathare code is avail...

Done in commit b7cef3f:

✓ Removed CHANGELOG.md and PORTING_SUMMARY.md (only README.md remains)
✓ Added .github/workflows/ci.yml with test, lint, and docs jobs
✓ Notebook example_usage.ipynb already exists
✓ Flattened examples structure: examples/input.txt (removed Cathare subdirectory)
✓ Removed all mock references from Cathare.sh - now assumes CATHARE code is available

All plugin structure tests pass.

[yannrichet-asnr]

@copilot use this cathare script, and https://github.com/Funz/plugin-Cathare/blob/master/src/main/scripts/Cathare.sh and check taht output is well parsed using https://github.com/Funz/plugin-Cathare/tree/master/src/test/cases/CNV22/output example (to also import in examples/)

[Copilot]

@copilot use this cathare script, and https://github.com/Funz/plugin-Cathare/blob/master/src/main/scripts/Cathare.sh and check taht output is well parsed using https://github.com/Funz/plugin-Cathare/t...

Done in commit bc73995:

✓ Updated Cathare.sh based on reference script from plugin-Cathare (supports full reader → cathar → postpro workflow)
✓ Added CNV22 complete example to examples/CNV22/ (input and output directories)
✓ Verified output parsing works with FORT07 from CNV22 example
✓ Updated example.py and example_parametric_study.py to use examples/CNV22/output
✓ Updated README with CNV22 example documentation and usage instructions
✓ Updated CI to check for CNV22 example directory

All plugin structure tests pass.