Reorganize tests and improve coverage

[Presmanes3]

Problem

Tests are flat and minimal: 4 test files, basic structure, low coverage. No test organization mirrors the source structure.

Current:

tests/
├── conftest.py
├── test_api.py
├── test_models.py
├── test_pipeline.py
└── workers/test_alert_delivery.py

Proposed solution

Reorganize tests to mirror src/ structure and add comprehensive coverage:

tests/
├── conftest.py              # Shared fixtures
├── api/
│   ├── conftest.py          # TestClient fixture
│   ├── test_health.py
│   ├── test_runs.py
│   ├── test_predict.py
│   └── test_organizations.py
├── repositories/
│   ├── conftest.py      # Test DB (in-memory SQLite)
│   └── test_run_repository.py
├── analysis/
│   └── test_analysis_types.py
└── workers/test_alert_delivery.py

Tasks

• [ ] Restructure test directory to mirror src/ layout
• [ ] Add database fixtures (in-memory SQLite) for repository tests
• [ ] Add tests for each route group (health, runs, predict, orgs, alerts)
• [ ] Add tests for analysis type registry
• [ ] Add tests for repositories (CRUD operations)
• [ ] Achieve minimum 70% code coverage
• [ ] Add pytest-cov to CI workflow
• [ ] Add test documentation in CONTRIBUTING.md