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goose 17efc4f656 docs: reconcile documentation with reality (P3) 
Make the project's documentation match the code and remove the sprawl. The docs
claimed Phase 2.8 (drug interactions) was 'planning/0%' and the backend '~91%
complete' — both wrong: 2.8 is implemented and live, plus the P0/P1 security
and test work is done. Five root CI/CD docs described a 'docker-build' CI job
that was removed; ~18 backend/ status snapshots and ~24 docs/implementation
duplicates cluttered the tree.

Deletions (85 files):
- Root: 4 stale CI/CD reports (CI-CD-{COMPLETION-REPORT,IMPLEMENTATION-SUMMARY,
  STATUS-REPORT,FINAL-STATUS}.md) — all describe the removed docker-build job.
- backend/: 18 phase/build/fix snapshots and code-dump .txt files.
- docs/: the 3 one-time reorg reports; ~17 docs/implementation duplicates and
  process artifacts; 4 stale docs/development CI docs + git snapshots;
  redundant deployment/testing files.
- thoughts/: STATUS.md (said Phase 2.4 in-progress), superseded phase notes and
  duplicative research inputs. tmp/ (928KB of CI debug logs, gitignored).

Moves (18 files):
- 9 genuine decision records -> docs/adr/ (Architecture Decision Records),
  date-prefixes stripped, with an index README.
- 8 historical-but-valuable phase plans/specs + the old CI-CD-FINAL-SOLUTION ->
  docs/archive/ (now-populated, with a README explaining it's superseded
  material). thoughts/ tree removed.

Rewrites (13 files) to match reality:
- Drop the fake '% complete' figures everywhere in favor of Implemented /
  In-Progress / Planned with concrete endpoint/feature lists.
- Phase 2.8 -> Implemented; add /api/interactions/* and /api/auth/{refresh,
  logout} to the endpoint lists; fix 'Rust 1.93' -> edition 2021.
- Add a Security section (token_version validation, hashed refresh-token
  persistence, fail-fast config, real-IP audit) and correct the test-coverage
  and deployment claims to reality.
- New canonical docs/development/CI-CD.md (4 jobs: format/clippy/build/test,
  mongo service, no docker-build + why).
- README, docs/README, product/{STATUS,ROADMAP,PROGRESS,README,introduction},
  implementation/README, development/README, testing/README, AI_AGENT_GUIDE,
  .cursorrules, .gooserules all updated.

Verified: greps for 'Phase 2.8 (Planning)', 'PLANNING (0%)', 'Rust 1.93',
'91%/10%/85% complete', and 'docker-build' return nothing outside docs/archive;
all internal doc links resolve; backend/src untouched (cargo build clean).
2026-06-27 16:02:16 -03:00
..
ANALYSIS_RECOMMENDATIONS.md docs(ai): reorganize documentation and update product docs 2026-03-09 11:04:44 -03:00
encryption.md docs(ai): reorganize documentation and update product docs 2026-03-09 11:04:44 -03:00
ENCRYPTION_UPDATE_SUMMARY.md docs(ai): reorganize documentation and update product docs 2026-03-09 11:04:44 -03:00
introduction.md docs: reconcile documentation with reality (P3) 2026-06-27 16:02:16 -03:00
PERSONA_AND_FAMILY_MANAGEMENT.md fix(clippy): resolve all clippy warnings 2026-03-12 09:03:38 -03:00
PROGRESS.md docs: reconcile documentation with reality (P3) 2026-06-27 16:02:16 -03:00
README.md docs: reconcile documentation with reality (P3) 2026-06-27 16:02:16 -03:00
ROADMAP.md docs: reconcile documentation with reality (P3) 2026-06-27 16:02:16 -03:00
STATUS.md docs: reconcile documentation with reality (P3) 2026-06-27 16:02:16 -03:00

README.md

Normogen - Product Documentation

Welcome to the Normogen product documentation. Normogen (Mapudungun for "Balanced Life") is an open-source health data platform for private, secure health data management.

🚀 Quick Start

For Users

1. Quick Setup (Docker)

# Clone the repository
git clone <repository-url>
cd normogen

# Start the backend with Docker
cd backend
docker compose up -d

# Check health
curl http://localhost:8000/health

2. Access the API

The backend API will be available at http://localhost:8000

For Developers

1. Prerequisites

  • Backend: Rust (edition 2021 toolchain), Docker
  • Frontend: Node.js 18+, npm

2. Backend Development

cd backend
cargo build              # Build
cargo test               # Run tests
cargo run                # Run locally

3. Frontend Development

cd web/normogen-web
npm install              # Install dependencies
npm start                # Start dev server
npm test                 # Run tests

4. Learn the Project

  1. Read introduction.md - Project background and purpose
  2. Check STATUS.md - Current development status
  3. Review ROADMAP.md - Development phases and timeline
  4. Understand encryption.md - Security architecture

📊 Current Status

Backend: ✅ Phase 2.x feature-complete (through drug interactions); security-hardened; deployed on Solaria. Frontend: 🚧 Early (Login/Register + API/store layer; router not yet wired). Deployment: Docker on Solaria (image built manually — not in CI). Tests: 18 unit + 13 integration (auth + medication), CI-gated with MongoDB.

See STATUS.md for detailed progress tracking.

📚 Documentation Files

Core Documentation

README.md

This file - Product documentation overview and quick start.

STATUS.md

Current project status and progress tracking

  • Overall status (Backend feature-complete through Phase 2.8; Frontend early stage)
  • Phase-by-phase completion status
  • Recently completed features
  • Next milestones

Last Updated: 2026-03-09
Updates: Real-time progress tracking

ROADMAP.md

Development phases and milestones

  • Phase breakdown (1-5)
  • Timeline estimates
  • Feature planning
  • Technology stack

Last Updated: 2026-03-09
Scope: Complete project timeline through 2027

Background & Context

introduction.md

Project introduction, motivation, and background

  • Naming origin (Mapudungun)
  • Purpose and vision
  • Business model (subscriptions, not data selling)
  • Architecture overview
  • Feature list

Last Updated: 2026-01-04
Length: 82 lines

encryption.md

Security architecture and encryption design

  • Zero-knowledge encryption for MongoDB
  • Shareable links with embedded passwords
  • Security best practices
  • Advanced features (recovery, revocation)
  • Code examples (currently JavaScript, needs Rust)

Size: 32KB (1,248 lines)
Last Updated: 2026-01-10
Note: Comprehensive security documentation

🔑 Key Information

Project Overview

  • Name: Normogen (Balanced Life in Mapudungun)
  • Goal: Open-source health data platform for private, secure health data management
  • Current Phase: 2.8 (drug interactions) implemented; open work is the frontend (Phase 3)
  • Backend: Rust + Axum + MongoDB (Phase 2.x feature-complete, security-hardened)
  • Frontend: React + TypeScript + Material-UI (early stage — Login/Register + API/store layer)

Technology Stack

Backend:

  • Rust (edition 2021), Axum 0.7
  • MongoDB 7.0
  • JWT authentication (15min access, 30day refresh)
  • PBKDF2 password hashing (100K iterations)

Frontend:

  • React 19.2.4, TypeScript 4.9.5
  • Material-UI (MUI) 7.3.9
  • Zustand 5.0.11 (state management)
  • Axios 1.13.6 (HTTP client)

🎯 Key Features

Implemented ✅

  • JWT authentication with token rotation
  • User management and profiles
  • Permission-based access control
  • Share management (share resources with others)
  • Security hardening (rate limiting, audit logging)
  • Medication management (CRUD, adherence tracking)
  • Health statistics tracking
  • Lab results storage
  • OpenFDA integration

In Progress 🚧

  • Drug interaction checking (Phase 2.8)
  • Automated reminder system
  • Advanced health analytics

Planned 🔮

  • Healthcare data export (FHIR, HL7)
  • Medication refill tracking
  • Caregiver access
  • Frontend dashboard
  • Mobile apps (iOS, Android)
  • AI/ML features

🔒 Security

Normogen implements enterprise-grade security:

  • Zero-knowledge encryption: Data encrypted at rest
  • PBKDF2: Password hashing with 100K iterations
  • JWT: Secure authentication with token rotation
  • Rate limiting: Protection against brute force
  • Audit logging: Track all security events

See encryption.md for comprehensive security documentation.

📡 API Endpoints

Authentication

  • POST /api/auth/register - User registration
  • POST /api/auth/login - User login
  • POST /api/auth/logout - User logout
  • POST /api/auth/refresh - Refresh access token
  • POST /api/auth/recover-password - Password recovery

User Management

  • GET /api/users/me - Get current user profile
  • PUT /api/users/me - Update profile
  • DELETE /api/users/me - Delete account
  • POST /api/users/me/change-password - Change password
  • GET/PUT /api/users/me/settings - User settings

Medications

  • POST /api/medications - Create medication
  • GET /api/medications - List medications
  • GET /api/medications/:id - Get medication
  • POST /api/medications/:id - Update medication
  • POST /api/medications/:id/delete - Delete medication
  • POST /api/medications/:id/log - Log dose
  • GET /api/medications/:id/adherence - Get adherence

Health Statistics

  • POST /api/health-stats - Create health stat
  • GET /api/health-stats - List health stats
  • GET /api/health-stats/:id - Get health stat
  • PUT /api/health-stats/:id - Update health stat
  • DELETE /api/health-stats/:id - Delete health stat
  • GET /api/health-stats/trends - Get trends

Shares & Permissions

  • POST /api/shares - Create share
  • GET /api/shares - List shares
  • PUT /api/shares/:id - Update share
  • DELETE /api/shares/:id - Delete share
  • POST /api/permissions/check - Check permissions

Sessions

  • GET /api/sessions - List sessions
  • DELETE /api/sessions/:id - Revoke session
  • DELETE /api/sessions/all - Revoke all sessions

Health Check

  • GET /health - Health check endpoint

🛠️ Development

Backend Development

cd backend
cargo build              # Build backend
cargo test               # Run tests
cargo clippy             # Lint
cargo run                # Run locally
docker compose up -d     # Run with Docker

Frontend Development

cd web/normogen-web
npm install              # Install dependencies
npm start                # Start dev server
npm test                 # Run tests

Testing

# Backend tests
cd backend && cargo test

# Frontend tests
cd web/normogen-web && npm test

# Integration tests
./docs/testing/quick-test.sh
./docs/testing/test-api-endpoints.sh

📈 Project Progress

Backend: Phase 2.x feature-complete ✅

  • ✅ Authentication & authorization (JWT, refresh-token rotation, token_version invalidation)
  • ✅ User management
  • ✅ Medication management
  • ✅ Health statistics
  • ✅ Lab results
  • ✅ Security features (audit logging, account lockout, fail-fast config, real-IP audit)
  • ✅ Drug interactions (Phase 2.8)

Frontend: Early stage 🚧

  • 🚧 Login/register pages + API/store layer
  • 📋 Router wiring, dashboard (planned)
  • 📋 Medication UI (planned)

See STATUS.md for detailed progress.

🗺️ Roadmap

Phase 2.8 follow-ups (not started)

  • Automated reminders
  • Advanced analytics
  • Data export (FHIR, HL7)

Phase 3 (Planned - Q2 2026)

  • Complete frontend app
  • Dashboard and visualization
  • Medication management UI

Phase 4 (Future - 2027)

  • Mobile apps (iOS, Android)
  • AI/ML features
  • Third-party integrations

See ROADMAP.md for complete roadmap.

🤝 Contributing

We welcome contributions! See:

📞 Support & Resources

Documentation

External Resources

📝 License

TBD (not yet decided)

Last Updated: 2026-03-09
Maintained By: Project maintainers
For Questions: Create an issue or discussion