feat: reliability refactor — core/services layout, conformal UQ, MCDM…

[Rafalexandre-code]

…, safe serialization, manifest, CI

Reorganizes the project around reusable modules and adds the reliability, traceability, and security infrastructure referenced by the new help tab:

Core (CSTRChemIA/core/)

• safe_serialization: JSON + SHA-256 persistence for scalers, removes pickle from the happy path (mitigates CWE-502)
• data_validation: ValidationReport dataclass, clean_dataset, explicit bounds/flag checks; replaces silent median imputation with reporting
• model_manifest: ModelManifest dataclass + build/read/write + verify_integrity for end-to-end artifact auditability (models.json)
• uncertainty: SplitConformalCalibrator (Vovk 2005), MC Dropout (Gal & Ghahramani 2016), deep ensemble (Lakshminarayanan 2017), predict_with_interval helper
• feature_engineering: 11 derived features with safe_div / log_clip
• constants, exceptions, i18n, logging, settings, types, units, utils

Optimization

• decision_methods: TOPSIS, VIKOR, PROMETHEE II, knee-point (L1-ASF), consensus_ranking
• problem_v2: NSGA-II / NSGA-III problem with n_ieq_constr=5 native constraint handling

Training

• train_xgboost_baseline: per-target XGBoost baseline on engineered features
• train_surrogate: ReduceLROnPlateau + ModelCheckpoint + --seed CLI, writes manifest entries on completion

Services (CSTRChemIA/services/)

• model_registry (models.json precedence, verify_integrity)
• simulation_service, optimization_service, training_service, data_file_service

API skeleton (CSTRChemIA/api/): FastAPI app + pydantic schemas for a future headless deployment mode.

Tests

• CSTRChemIA/tests/: 46 pytest cases over the new core modules
• tests/: service and integration tests (mypy-typed, no TF required)

Tooling & deploy

• pyproject.toml (ruff, mypy, pytest config)
• .github/workflows/ci.yml (lint, typecheck, matrix tests, docker build)
• .pre-commit-config.yaml, .editorconfig, .dockerignore
• Dockerfile + Dockerfile.api + docker-compose.yml
• docs/ARCHITECTURE.md, docs/CONTRIBUTING.md, docs/DEPLOYMENT.md
• Makefile, README.md at repo root

UI

• assets/html_help/index.html rewritten: 20 sections, ~2000 lines, full coverage of the modules above (sidebar, CSS tokens, callouts)
• layout_TAB.py: dashboard upgrade (Analytics tab, K-means, Hypervolume)
• custom.css: purple-theme refinements

Other

• requirements.txt: add keras-tuner>=1.4.0
• .gitignore: exclude .claude/ working directory