[M0-R][DOCS] Establish the canonical source-of-truth documentation baseline

[andreazedda]

Scope

Addresses #14 by establishing the canonical documentation/source-of-truth baseline on the supported dependency and framework state.

base master = a33418fb8ae9cb9fd05832dd9bc1cb0778e08533
branch head = e9441e175466131d1184e8a8b74425822407fc09
intended use = E1_research_prototype

What this PR changes

Mission and project identity

• defines bmyCure4MM as a virtual and reproducible Multiple Myeloma research laboratory;
• makes virtual patients, established and experimental therapy hypotheses, falsification, reproducible protocols and the Knowledge Commons explicit;
• derives the target architecture from that mission;
• preserves current E1 limits and rejects prescriptive/causal overclaim.

Current versus target architecture

• publishes a verified current-system architecture;
• publishes a separately labelled target virtual-laboratory architecture;
• converts the former architecture guide into a compatibility pointer;
• prevents target models and research hypotheses from being presented as current implementation.

Current mathematical models

• maps each twin_engine/model_registry.json model to version, entry point and maturity status;
• documents current ODE/PK/PD, observation, exposure, toxicity-signal and counterfactual utility equations;
• defines variables, units/evidence status, numerical examples, limitations, code mapping and falsification criteria;
• marks the therapy-design model as a hypothetical toy model.

Source-of-truth and corpus governance

• adds the GitHub/Notion/DOCX precedence hierarchy and conflict protocol;
• adds documentation status/metadata/formula/diagram standards;
• adds a machine-readable documentation inventory plus a navigable explanation;
• separates current, target, hypothesis, deferred and historical material.

Research and operations contracts

• documents Twin/computational-input lineage;
• documents comparability and append-only invalidation;
• documents the target M1 Research Loop and valid negative outcomes;
• documents authentication/access boundaries and the smoke-user limitation;
• documents testing, numerical identity, dependency audit and CI boundaries.

Public documentation repair

• rewrites README and documentation landing page;
• rebuilds MkDocs navigation;
• updates CHANGELOG through the current M0-R state;
• replaces obsolete security/version/authentication claims in SECURITY.md;
• removes root RELEASE_PREPARATION.md and retains a clearly invalidated historical archive record;
• adds strict MkDocs validation to documentation pull requests without deploying PR content.

Supported baseline now documented

Merged PRs #71 and #72 established:

Django 5.2.17 LTS
sqlparse 0.6.0
dependency audit = PASS
ordinary and synthetic deploy checks = PASS
migration drift = zero
disposable migrations = PASS
Python 3.11/3.12 core suites = PASS
authorization-sensitive compatibility subset = PASS
numerical baseline = unchanged
Secret Scan = PASS
Docker locked build = PASS
protected required result = PASS

The remaining exact development-only pytest advisory decision is documented and is not a Django/runtime exception.

Source-of-truth boundary

code/schemas/registries/machine-readable governance
> current GitHub documentation at a verified SHA
> GitHub issues, PRs and validation evidence
> Notion dashboard and decisions
> architecture DOCX proposals
> historical archives

The architecture DOCX remains a target proposal and will be revised only after this repository baseline becomes canonical.

Change classification

runtime/scientific code = no
scientific numerical outputs = no
DB schema/migrations = no
private data = no
documentation/governance = yes
security wording = yes
MkDocs PR validation = yes
historical archive = yes
intended-use expansion = no

Required validation before ready/merge

strict MkDocs build
Secret Scan
uv lock --check and frozen sync
Ruff and format
mypy
repository hygiene
numerical baseline unchanged
dependency audit
Django checks and migration drift
Python 3.11/3.12 core suites
Docker locked build
protected required result

Also inspect Mermaid rendering and the current/target labels on key pages.

Non-goals

• no full [M0-R][CI] Consolidate existing workflows into mandatory scientific quality gates and protected PR governance #13 CI rationalization beyond PR-time docs validation;
• no [M0-R][QA] Enforce the minimum scientific invariants and define the extended test architecture #23 QA expansion;
• no product-auth/RBAC change;
• no production runtime change;
• no new Patient Twin calibration, patient-specific what-if or biological model;
• no DOCX rewrite in this PR.

Rollback

Revert this documentation PR. No database, dependency or numerical rollback is required.

Next

After merge, complete #14 evidence, update Notion to the final merge SHA, then unblock #13. #23 Phase A remains blocked until the final aggregate CI and PR-governance contract exists.