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stemedb/docs/README.md
jml 9bfa626203 docs: reorganize documentation structure for clarity 
Major documentation restructure to improve discoverability and reduce duplication.

## Changes

**Deleted (Archived/Consolidated)**:
- Removed duplicate getting started guides
- Archived outdated planning documents
- Consolidated corpus and configuration docs
- Removed obsolete vision/spec files (superseded by vision.md)
- Cleaned up scrapyard and old PDFs

**New Structure**:
- docs/about/ - Project overview and introduction
- docs/guides/ - User guides (moved from root)
- docs/specs/ - Technical specifications
- docs/sdk/ - SDK documentation (Go)
- docs/references/ - API references
- docs/archive/ - Archived historical docs
- applications/aphoria/docs/advanced/ - Advanced topics
- applications/aphoria/docs/reference/ - CLI reference
- applications/aphoria/docs/archive/ - Archived aphoria docs

**Updated**:
- README.md - New root README with clear navigation
- CONTRIBUTING.md - Contribution guidelines
- CLAUDE.md - Updated paths to new structure
- roadmap.md - Added recent completions

## Files Changed
- 57 files changed
- 1,977 insertions(+)
- 961 deletions(-)

**Net change**: +1,016 lines (added CONTRIBUTING.md, README.md, reorganized content)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
2026-02-11 07:33:40 +00:00

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# Episteme Documentation
Complete documentation for Episteme (StemeDB) - a probabilistic knowledge graph database.
---
## Getting Started
### First Steps
- **[Quick Start](../quickstart.md)** - Get running in 5 minutes
- **[What is Episteme?](../what-is-episteme.md)** - Core concepts and examples
- **[Architecture Overview](../architecture.md)** - Technical design
- **[Vision](../vision.md)** - Product philosophy
### Use Cases
- **[Use Cases Index](../use-cases/README.md)** - All scenarios
- **[Consumer Health Intelligence](../use-cases/consumer-health-intelligence.md)** - Drug safety tracking
- **[Financial Due Diligence](../use-cases/financial-due-diligence.md)** - M&A analysis
- **[Agile Agent Team](../use-cases/agile-agent-team.md)** - AI collaboration
- **[GLP-1 Living Review](../use-cases/glp1-living-review.md)** - Real-world example
---
## Application Development
### Building on Episteme
- **[App Concepts Index](./app-concepts/index.md)** - Application layer patterns
- **[Consumer Health Vertical](./app-concepts/consumer-health.md)** - Healthcare application design
- **[Boundary Principles](./app-concepts/index.md#the-boundary-principle)** - What Episteme does vs. what your app does
### SDKs & Integration
- **[Go SDK Guide](./sdk/go-sdk.md)** - HTTP client with Ed25519 signing
- **[Go Usage Examples](./sdk/go-usage-guide.md)** - Fluent builders and patterns
- **[ADK-Go Reference](./references/go-adk/reference-guide.md)** - AI agent integration
- **[ADK-Go Examples](./references/go-adk/)** - Agent patterns (chatbot, researcher, etc.)
---
## Technical References
### Core Architecture
- **[Data Structures](./data-structures.md)** - Assertion, Vote, Epoch, MaterializedView
- **[Consistency Model](./consistency-model.md)** - Conflict resolution and convergence
- **[Governance Models](./specs/governance-models.md)** - Authority hierarchies
### Advanced Topics
- **[Distributed Write Path](./research/distributed-write-path.md)** - Clustering and sharding
- **[WAL Crash Recovery](./research/wal-crash-recovery-research.md)** - Storage durability
- **[Concept Hierarchy](./specs/concept-hierarchy.md)** - Subject/predicate organization
- **[Visual Hash Query](./specs/visual-hash-query.md)** - Screenshot-based retrieval
### Specifications
- **[RFCs Index](./rfcs/README.md)** - All RFCs
- **[RFC-001: Enterprise Policy Aliases](./rfcs/rfc-001-enterprise-policy-aliases.md)** - Multi-tenant policy
---
## Development Guides
### Setting Up
- **[Local Development Setup](../.claude/guides/local/setup.md)** - Environment configuration
- **[Testing Guide](../.claude/guides/local/testing.md)** - Running test suites
- **[Quality Checks](../.claude/guides/local/quality-checks.md)** - Pre-commit hooks
- **[Coding Guidelines](../.claude/guides/coding-guidelines.md)** - Rust standards
### How-To Guides
- **[Adding a Domain](./guides/adding-a-domain.md)** - Extend ontology for new verticals
- **[Implementation Audit Checklist](./guides/implementation-audit-checklist.md)** - Production readiness
- **[Writing UAT Reports](../.claude/guides/local/uat-reports.md)** - User acceptance testing
### Integration Guides
- **[AI Coding Assistant Integration](../.claude/guides/integrations/ai-coding-assistant-integration.md)** - Claude/Cursor setup
- **[ADK-Go + Episteme](../.claude/guides/integrations/adk-go-episteme.md)** - Building agents
---
## Demos & Examples
- **[VulnBank Demo](./demo/vulnbank/README.md)** - Security vulnerability tracking example
---
## Project Planning
### Current Work
- **[Roadmap](../roadmap.md)** - Current and planned features
- **[Roadmap Archive](../roadmap-archive.md)** - Completed phases
### Specifications & Planning
- **[Aphoria Claims API](./specs/aphoria-claims-api.md)** - Claims management design
- **[Ontology Layer: Medical Vertical](./specs/ontology-layer-medical-vertical.md)** - Healthcare domain modeling
---
## About Episteme
### Vision & Strategy
- **[Market Position](./about/market-position.md)** - Competitive landscape and thesis
- **[Simulation Vision](./about/simulation-vision.md)** - Agent-based validation
### Legal
- **[Patent Disclosure](./legal/patent-disclosure.md)** - IP documentation
- **[Patent Figures](./legal/patent-figures.md)** - Visual diagrams
- **[Patent Specification](./legal/patent-specification.md)** - Technical claims
---
## Tools & Infrastructure
- **[Grafana Dashboard](../tools/grafana/)** - Metrics visualization
- **[Presentations](./presentations/README.md)** - Slide decks and demos
---
## Archive
Historical documentation and snapshots:
- **[Documentation Updates Summary](./archive/DOCUMENTATION_UPDATES.md)** - 2026-02-08 audit
- **[Corpus Quick Start](./archive/CORPUS-QUICK-START.md)** - Legacy setup guide
---
## Quick Reference: What Goes Where
| If you need to... | Episteme provides... | You build... |
|-------------------|---------------------|--------------|
| Store conflicting facts | Assertion type, append-only DAG | Nothing - just POST assertions |
| Resolve conflicts | Lenses (Recency, Consensus, Skeptic) | Lens selection logic |
| Query historical state | `as_of` parameter | Time-travel UI |
| Track changes | `since` parameter + MV changelog | Notification system |
| Weight by source authority | `source_class` field + decay | Tier classifier |
| Detect emerging signals | Skeptic Lens + conflict_score | Gardener (threshold logic) |
| Show per-tier consensus | Layered Consensus Lens | Dashboard UI |
| Extract claims from papers | Nothing - pre-assertion transform | NLP pipeline |
| Sign assertions | Signature verification | Agent wallet / key management |
| Generate summaries | Structured query responses | LLM summarizer |
---
## Contributing
See **[CONTRIBUTING.md](../CONTRIBUTING.md)** for:
- Documentation standards
- File organization principles
- How to add new guides
- Review process
---
## Navigation Tips
- **Breadth-first**: Start with [What is Episteme?](../what-is-episteme.md) → [Use Cases](../use-cases/README.md) → [Quick Start](../quickstart.md)
- **Depth-first**: Start with [Architecture](../architecture.md) → [Data Structures](./data-structures.md) → [Distributed Write Path](./research/distributed-write-path.md)
- **Hands-on**: Start with [Quick Start](../quickstart.md) → [Go SDK](./sdk/go-sdk.md) → [App Concepts](./app-concepts/index.md)
---
**[← Back to Main README](../README.md)**
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