TASK-041: Fluid Configuration Section

[AdamClemens]

Summary

Stage 5's first task: gives the simulated fluid's physical properties (viscosity, diffusion_coefficient) their own fluid: config section, separate from numerics: (which selects numerical schemes, not fluid properties). This is the project's first breaking configuration change -- a config still setting the retired numerics.diffusion_coefficient is rejected with a named error pointing at its new home, not silently defaulted.

• FluidConfig dataclass (viscosity, diffusion_coefficient, both default 1.0) added to PyFlowConfig, wired into load_config.
• numerics.diffusion_coefficient removed from NumericsConfig; a config still setting it fails loudly (loader.py's _numerics_config_from_raw).
• tests/features/fluid_configuration.feature (4 scenarios) bound by tests/integration/test_fluid_configuration.py -- lives in integration/, not unit/, since one scenario needs a real CLI subprocess run.
• Regenerated docs/implementation/config-template.yaml; migrated the Passive Scalar Transport golden demo's own config.

A real gap found while implementing, not predicted by the roadmap's own drafting: TASK-041's Dependencies section claimed "no engine dependency at all," but engine/numerics/assembly.py's assemble_numerics already read NumericsConfig.diffusion_coefficient directly (TASK-024). Moving the field required a real signature change -- assemble_numerics gained its own diffusion_coefficient: float = 1.0 parameter (default preserves every existing scheme-selection-only caller), and bootstrap.py's call site now threads config.fluid.diffusion_coefficient through explicitly. Recorded honestly in the roadmap (a Status note plus a correction in the Dependencies section itself) rather than fixed silently, per this repo's Integrity rule.

Blast radius also covers: tests/unit/numerics/test_assembly.py, tests/unit/test_main.py, tests/unit/test_generator.py, tests/integration/test_cli.py (key-order/field assertions), two architecture diagrams (sequences.md), an ICD signature line (icds.md), an ADR pointer (ADR-002), CLAUDE.md entries in configuration/ and engine/, and the roadmap's own live test/scenario-count paragraph (614→622 tests, 54→58 scenarios) plus regenerated status.md/repository-inventory.md.

Test plan

• make ci green: 622 tests passing, mypy --strict clean, all doc/graph/scenario/status/config-template checks pass.
• TDD: tests/features/fluid_configuration.feature scenarios and test_configuration.py's new viscosity tests written and confirmed red before implementation.
• make check-references/make check-manifest/make check-scenarios all clean against the new files.
• Golden demo (passive_scalar_transport.yaml) still runs through the real CLI and produces its already-tested quantitative result after migration.

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