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8f6506b70a
stemedb/CLAUDE.md
jordan 8f6506b70a feat: Aphoria scan modes + stemedb-ontology crate + consumer health UAT 
Major additions:
- Staged scanning modes (working tree, staged, committed) with git integration
- Drift detection for baseline vs current state comparisons
- Hosted API handlers for policy CRUD operations via StemeDB API
- stemedb-ontology crate with domain definitions and medical extractors
- Consumer health vertical UAT scenarios (GLP-1, gastroparesis, etc.)
- Aphoria development skill documentation

Code organization:
- Split large files into focused modules to stay under 500-line limit
- Extracted config tests, episteme helpers/drift/aliases, API helpers

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2026-02-04 21:57:33 -07:00

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# Episteme (StemeDB)
A probabilistic knowledge graph database that stores Claims, not Facts. Append-only Merkle DAG with read-time resolution via Lenses.
**Core Concept:** "Git for Truth" - conflicting assertions coexist, resolved at query time through Consensus, Recency, Authority, or custom Lenses.
## Find Your Guide
| If you need to... | Read this |
|-------------------|-----------|
| **Get started fast** | [quickstart.md](./quickstart.md) |
| **Understand what Episteme is** | [what-is-episteme.md](./what-is-episteme.md) |
| **Understand the technical vision** | [vision.md](./vision.md) |
| **See use cases** | [use-cases/README.md](./use-cases/README.md) |
| **Understand architecture** | [architecture.md](./architecture.md) |
| **Learn data structures** | [docs/data-structures.md](./docs/data-structures.md) |
| **See the roadmap** | [roadmap.md](./roadmap.md) |
| **Build apps on Episteme** | [docs/app-concepts/index.md](./docs/app-concepts/index.md) |
| **Consumer Health vertical** | [docs/app-concepts/consumer-health.md](./docs/app-concepts/consumer-health.md) |
| **Use Go SDK** | [ai-lookup/services/sdk.md](ai-lookup/services/sdk.md) |
| **Write Rust code** | [.claude/guides/backend/rust-guidelines.md](.claude/guides/backend/rust-guidelines.md) |
| **Set up local dev** | [.claude/guides/local/setup.md](.claude/guides/local/setup.md) |
| **Run tests** | [.claude/guides/local/testing.md](.claude/guides/local/testing.md) |
| **Understand quality checks** | [.claude/guides/local/quality-checks.md](.claude/guides/local/quality-checks.md) |
| **Learn about simulation** | [ai-lookup/features/simulation.md](ai-lookup/features/simulation.md) |
| **Advance the simulator** | [arena-roadmap.md](./arena-roadmap.md) |
| **Work on storage/DAG** | Load skill: `stemedb-core` |
| **Implement a Lens** | Load skill: `stemedb-lens` |
| **Work on domain ontology** | `crates/stemedb-ontology/` |
| **Consumer Health UAT** | [uat/consumer-health/README.md](./uat/consumer-health/README.md) |
| **Plan a milestone** | `/plan-milestone` command |
| **Analyze use case gaps** | `/analyze-gaps` command |
| **Add an API endpoint** | [.claude/guides/backend/api-endpoints.md](.claude/guides/backend/api-endpoints.md) |
| **Integrate with AI tools** | [.claude/guides/integrations/ai-coding-assistant-integration.md](.claude/guides/integrations/ai-coding-assistant-integration.md) |
| **ADK-Go + Episteme** | [.claude/guides/integrations/adk-go-episteme.md](.claude/guides/integrations/adk-go-episteme.md) |
| **Distributed architecture** | [docs/research/distributed-write-path.md](docs/research/distributed-write-path.md) |
| **Write UAT reports** | [.claude/guides/local/uat-reports.md](.claude/guides/local/uat-reports.md) |
| **Phase 6 UAT results** | [ai-lookup/features/phase6-uat.md](ai-lookup/features/phase6-uat.md) |
## Critical Rules
- **Append-Only:** NEVER mutate existing Assertions. Create new ones.
- **Content-Addressed:** Assertion ID = BLAKE3 hash of content.
- **No Unwrap:** NEVER use `unwrap()` or `expect()` in production code. CI enforces via `clippy::unwrap_used` and `clippy::expect_used` at deny level.
- **Defensive Writes:** All writes go through WAL with fsync.
- **Zero-Copy:** Use `rkyv` for serialization. ALWAYS use `stemedb_core::serde::{serialize, deserialize}` — NEVER use raw `AllocSerializer` in production code.
- **Instrument Critical Paths:** Use `#[instrument]` on public methods in WAL, storage, ingestion, and lens code. Include meaningful fields (key_len, payload_len, offset, candidates_count, lens).
- **Structured Logging:** Use `tracing` (info!, warn!, error!) instead of `println!`/`eprintln!`. Clippy enforces via `print_stdout`/`print_stderr` at warn level. CLI binaries (e.g., `stemedb-sim`) may use `#![allow()]` for user-facing output.
- **Document Changes:** Update `ai-lookup/` when adding new types/concepts. Keep skills in sync with code.
- **No Git Operations:** NEVER use git stash, git branch, git checkout, or any git operations unless the user explicitly tells you to.
## Quick Reference
```bash
# Build
cargo build --workspace
# Test
cargo test --workspace
# Lint (must pass before commit)
cargo clippy --workspace -- -D warnings
cargo fmt --check
```
## Port Scheme (181XX)
| Offset | Service | Default | Env Var |
|--------|---------|---------|---------|
| +0 | HTTP API | 18180 | `STEMEDB_BIND_ADDR` |
| +1 | Cluster Gateway | 18181 | `STEMEDB_NODE_API_ADDR` |
| +2 | Cluster RPC | 18182 | `STEMEDB_NODE_RPC_ADDR` |
| +3 | SWIM Gossip | 18183 | via `SwimConfig` |
| +4 | Metrics | 18184 | (reserved) |
| +5 | Admin | 18185 | (reserved) |
| +6 | Latent Signal | 18186 | — |
| +7 | Community App | 18187 | — |
## Specialized Agents
| Domain | Agent | When to use |
|--------|-------|-------------|
| **Product Vision** | `episteme-product-visionary` | Use cases, "why not Postgres?", product-market fit |
| General Rust | `primary-developer` | Feature implementation, refactoring |
| Code Quality | `rust-quality-engineer` | Reviews, test coverage, clippy |
| Storage | `storage-engine-architect` | WAL, LSM, crash recovery |
| Graph Engine | `rust-graph-engine-architect` | Lock-free structures, cache optimization |
| Defensive | `defensive-systems-architect` | Rate limiting, circuit breakers, hostile input |
| Distributed | `distributed-systems-engineer` | CRDT replication, Raft coordination, Merkle sync, clustering |
| Lenses | `stemedb-lens-architect` | Query resolution, ranking algorithms |
| Planning | `stemedb-planner` | Milestone planning, roadmap |
## Architecture Overview
```
Write Path (Spine): Read Path (Cortex):
[Agent] -> [Ingestion] [Agent] <- [Lens Engine]
| |
v |
[WAL/Fsync] [Index Lookup]
| |
v |
[KV Store] <--------------------+
```
## Crates
| Crate | Purpose | Status |
|-------|---------|--------|
| `stemedb-core` | Assertion, LifecycleStage, MaterializedView, types | ✅ Implemented |
| `stemedb-wal` | Write-ahead log with crash recovery | ✅ Implemented |
| `stemedb-storage` | KVStore, VoteStore, IndexStore, TrustRankStore, QuarantineStore, SimilarityIndex | ✅ Implemented |
| `stemedb-ingest` | Ingestion pipeline, signature verification, ContentDefenseLayer | ✅ Implemented |
| `stemedb-query` | Query engine, Materializer for O(1) MV: reads | ✅ Implemented |
| `stemedb-lens` | Lenses (Recency, Consensus, Authority, Vote/Trust-aware) | ✅ Implemented |
| `stemedb-api` | HTTP API with axum + utoipa OpenAPI docs | ✅ Implemented |
| `stemedb-sim` | Simulation for testing the pipeline | ✅ Implemented |
| `stemedb-merkle` | BLAKE3 Merkle tree for diff detection | ✅ Implemented |
| `stemedb-rpc` | gRPC services for node-to-node communication | ✅ Implemented |
| `stemedb-sync` | Merkle sync, gossip broadcast, anti-entropy | ✅ Implemented |
| `stemedb-cluster` | Cluster membership (SWIM), sharding, gateway | ✅ Implemented |
| `stemedb-ontology` | Domain definitions (Pharma), subject builders, medical extractors | ✅ Implemented |
## SDKs
| SDK | Purpose | Status |
|-----|---------|--------|
| `sdk/go/steme` | Go HTTP client with Ed25519 signing and fluent builders | ✅ Implemented |
| `sdk/go/adk` | ADK-Go tools and callbacks for AI agents | ✅ Implemented |
## Latent Signal (latent/)
Python CLI tools for adverse event signal detection. Different rules from Rust crates:
**Allowed:**
- `print()` for user-facing CLI output (these are scripts, not libraries)
- `except Exception as e:` for CLI error handling (log and continue)
**Required:**
- **Environment Variables for URLs:** NEVER hardcode `localhost` URLs without env fallback
- Use `os.getenv("VAR", "http://localhost:...")` in Python
- Use `process.env.VAR || 'http://localhost:...'` in TypeScript
- **StemeDB Integration:** New ingestors should use `StemeDBClient` pattern from `adk-agent/`, not write to JSONL files
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