fix: make all templates runnable; clean CLI output; add smoke + sanity tests

[AdishAssain]

A hands-on UAT (scaffold → configure → run a 10-patch waning-immunity model) surfaced several issues. This fixes them and adds tests that would have caught each.

Bugs fixed

• init --template {sis,seir} + run was broken. The scaffold shipped one fixed S,I,R seed file, which mismatches SIS (S,I) and SEIR (S,E,I,R) compartments. init now generates a seed file matching the chosen template. (The getting-started walkthrough tells users to init --template seir then run — previously that errored.)
• run --json reported a non-existent plot path. It returned patch_timeseries_<model>_ode.png while viz saved all_patches_<model>_ode.png. viz now saves the reported name and plots the model's actual compartments (fixes an SIS KeyError: R_0 and SEIR dropping E).
• Noisy CLI output. list-models / validate / run routed user-facing text through the logger (timestamps + cli.py:NN). Now printed cleanly, matching the docs. --json output is unaffected.
• Dangling catalog entry. list-models advertised ka_fmd_sirsv_discrete, whose implementation file was removed. Dropped from the catalog.
• Column case. setup_simulation hardcoded Population; the docs say lowercase population. Now accepted case-insensitively.

Tests added

• tests/test_cli_e2e.py — every template scaffolds, runs, and the reported CSV/plot artifacts exist on disk; list-models output is clean and only lists implemented models.
• tests/test_simulation_sanity.py — multi-patch SIRS: population conservation, non-negativity, epidemic growth from a seed, network-driven spatial spread, and endemic persistence under waning immunity.

All 33 tests pass; ruff check and ruff format --check clean.

[coderabbitai]

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 2024f289-484e-4ec4-b40d-f4582a234f9a

📥 Commits

Reviewing files that changed from the base of the PR and between c82fe49 and 122b922.

📒 Files selected for processing (7)

• src/patchsim/cli.py
• src/patchsim/core/model_runner.py
• src/patchsim/core/simulation.py
• src/patchsim/utils/viz.py
• tests/test_cli_e2e.py
• tests/test_simulation_sanity.py
• tests/test_smoke.py

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix/templates-cli-and-tests

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