# 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.

**ZERO TOLERANCE FOR MEDIOCRITY: We build enterprise-grade products that must survive in production. Panics are UNACCEPTABLE. Broken pipe errors are UNACCEPTABLE. Sloppy testing is UNACCEPTABLE. Every line of code ships to paying customers who depend on it. Test everything. Handle every error. No shortcuts. No excuses.**

**API Docs:** OpenAPI spec includes conceptual guide (`crates/stemedb-api/docs/api-intro.md`) with semaglutide examples showing claims vs facts, authority tiers, time-travel queries, and conflict resolution.

## 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) |
| **Understand governance models** | [docs/specs/governance-models.md](./docs/specs/governance-models.md) |
| **See the roadmap** | [roadmap.md](./roadmap.md) |
| **See completed phases** | [roadmap-archive.md](./roadmap-archive.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** | [roadmap.md#arena-simulation-roadmap](./roadmap.md#arena-simulation-roadmap) |
| **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) |
| **Verify production readiness** | [uat/production-readiness/README.md](./uat/production-readiness/README.md) |
| **Deploy to production** | [docs/operations/README.md](./docs/operations/README.md) |
| **Manage cluster nodes** | [docs/operations/node-lifecycle.md](./docs/operations/node-lifecycle.md) |
| **Install admin CLI** | [docs/operations/deployment/install-admin-cli.md](./docs/operations/deployment/install-admin-cli.md) |
| **Troubleshoot incidents** | [docs/operations/runbooks/](./docs/operations/runbooks/) |
| **Size your deployment** | [docs/operations/reference-architecture/resource-sizing.md](./docs/operations/reference-architecture/resource-sizing.md) |
| **Validate pilot success** | [docs/operations/pilot-success-criteria.md](./docs/operations/pilot-success-criteria.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) |
| **Configure Aphoria hosted mode** | [.claude/guides/services/aphoria-hosted-mode.md](.claude/guides/services/aphoria-hosted-mode.md) |
| **Aphoria config reference** | [ai-lookup/features/aphoria-config.md](ai-lookup/features/aphoria-config.md) |
| **Work on Admin Dashboard** | `applications/stemedb-dashboard/` (Next.js + shadcn/ui) |
| **Work on Disputed app** | `applications/disputed/` |
| **Understand repo structure** | [ai-lookup/repo-structure.md](ai-lookup/repo-structure.md) |
| **Understand Aphoria flywheel** | [ai-lookup/features/aphoria-flywheel.md](ai-lookup/features/aphoria-flywheel.md) |
| **Aphoria LLM eval** | Load skill: `aphoria-llm-optimization` |
| **General LLM optimization** | Load skill: `llm-optimization` |
| **Install Aphoria** | Load skill: `aphoria-install` |
| **Run Aphoria self-review** | Load skill: `aphoria-self-review` |
| **Author claims from diffs** | Load skill: `aphoria-claims` |
| **Suggest new claims** | Load skill: `aphoria-suggest` |
| **Automate post-commit analysis** | Load skill: `aphoria-post-commit-hook` |
| **Set up CI/CD automation** | Load skill: `aphoria-ci-setup` |
| **Create declarative extractors** | [applications/aphoria/docs/extractors/declarative-extractors.md](applications/aphoria/docs/extractors/declarative-extractors.md) |
| **Learn extractor examples** | [applications/aphoria/docs/examples/extractors/](applications/aphoria/docs/examples/extractors/) |
| **Avoid dogfooding mistakes** | [applications/aphoria/docs/dogfooding-common-mistakes.md](applications/aphoria/docs/dogfooding-common-mistakes.md) |

## Roadmap Maintenance

Two files, strict separation:

| File | Contains | When to modify |
|------|----------|----------------|
| `roadmap.md` | Current + future work only | Add new phases, update task status |
| `roadmap-archive.md` | Completed phases (1-7, 8A, MVP) | Move items when phase completes |

**Rules:**
- When a phase completes: Move entire phase section to archive, update status table in both files
- When adding tasks: Add to current phase in `roadmap.md` with `- [ ]` checkbox format
- When completing tasks: Change `- [ ]` to `- [x]`, add brief implementation notes
- Keep `roadmap.md` under 500 lines — if it grows, archive more aggressively
- Current phase always has "🎯" marker in status table

**Task format:**
```markdown
- [ ] **P1.2 Feature Name**: Brief description
    - [ ] Subtask one
    - [ ] Subtask two
```

**Phase completion checklist:**
1. All tasks marked `[x]` in `roadmap.md`
2. Cut entire phase section, paste into `roadmap-archive.md`
3. Update status tables in both files
4. Update "Current Focus" in `roadmap.md` header

## Aphoria: The Autonomous Flywheel

**Aphoria is a continuous learning system that runs on EVERY commit, NOT a CLI tool you invoke manually.**

### The Commit-Time Loop (Runs Automatically):

```
Developer commits code
    ↓
1. SCAN: Extractors → observations
    ↓
2. CHECK: Compare observations against claims → violations
    ↓
3. FIX: Developer fixes violations
    ↓
4. GET REMAINING CLAIMS: Identify claims without extractors
    ↓
5. CREATE EXTRACTORS: Dynamically generate extractors for uncovered claims
    ↓
6. SUGGEST NEW CLAIMS: LLM analyzes patterns → suggests new claims
    ↓
7. CREATE NEW EXTRACTORS: Generate extractors for new claims
    ↓
(Loop repeats, knowledge compounds)
```

**Knowledge Compounding:** Each commit benefits from all previous commits' learning - not through ML training, but through accumulated structured decisions.

> **Remote vs Local:** In remote mode, all claims are stored in the remote StemeDB instance (no local TOML files). Developers query remote claims to discover org patterns (specs at Tier 1, popular patterns at Tier 3), then manually decide whether to align their code. Convergence is inspection-driven, not automatic. Promotion to higher tiers is manual.

### LLM Workflows ARE the Core Product

**CRITICAL:** Aphoria's autonomous operation REQUIRES LLM-driven automation:
- **Claude Code skills** (`/aphoria-claims`, `/aphoria-suggest`, `/aphoria-custom-extractor-creator`)
- **Go ADK agents** (custom agent implementations)
- **Other LLM methodology** (API-driven workflows)

**Manual CLI** (`aphoria scan`, `aphoria claims create`) is **debug interface** for when LLM automation is unavailable. It is NOT the primary workflow.

**Manual fallbacks to CLI operations are unacceptable in production workflows — if LLM automation is unavailable, the system is broken, not in "fallback mode."**

### Three Main Workflows:

1. **Commit-time (PRIMARY):** Developer commits → Aphoria scans → checks policies → dynamically creates extractors for uncovered existing claims → LLM suggests new claims from patterns → LLM creates extractors for new claims
2. **Onboarding:** New dev codes → Aphoria guides with team conventions + linked context (who, why, when)
3. **Graduation:** Patterns with frequency + authority → auto-promote to conventions (shadow mode → promotion)

**Critical:** The commit-time workflow has TWO extractor creation phases:
- **Phase 1:** Dynamic creation for existing claims without extractors (ensures all authored claims are verifiable)
- **Phase 2:** Creation for new claims suggested by pattern analysis (expands coverage)

### Skills That Drive the Flywheel:

| Skill | Purpose | When Used |
|-------|---------|-----------|
| `/aphoria-claims` | Analyze diffs, author/update claims | Every commit with code changes |
| `/aphoria-suggest` | Suggest new claims from patterns | When growing coverage |
| `/aphoria-custom-extractor-creator` | Generate extractors (for both existing uncovered claims AND new claims) | Continuous - both phases of loop |
| `/aphoria-corpus-import` | Import docs → create claims + extractors | Bootstrap from external sources |
| `/aphoria-post-commit-hook` | Automate all loop steps with post-commit hooks | One-time setup per project |
| `/aphoria-ci-setup` | Automate via CI/CD instead of local hooks | One-time setup per repo |

### Dogfooding Day 3: The Extractor Creation Phase

**Day 3 is where the flywheel validates.** This is the step that separates Aphoria from static linters.

**Why Day 3 is Critical:**
- Day 3 IS Steps 4-5 of the commit-time loop (identify gaps → create extractors)
- Without Day 3 extractor creation, NO knowledge is captured
- This is the CORE validation of autonomous learning

**Workflow:**
1. **Baseline scan** → Detect X violations (often 0-20% on new domains)
2. **Gap analysis** → Identify claims with no extractors (MISSING verdicts)
3. **Extractor creation** → Use `/aphoria-custom-extractor-creator` to generate extractors (REQUIRED)
4. **Verification scan** → Detect Y violations (target: ≥90%)
5. **Document** → Record detection rate improvement (X% → Y%)

**Success Criteria:**
- Detection rate ≥90% after extractor creation
- All extractors produce correct observations (concept_path matches claim)
- Learning documented (which patterns were added to corpus)
- Time ≤2 hours (including all 5 phases)

**Evidence of Correct Execution:**
```bash
ls .aphoria/extractors/*.toml | wc -l  # Should be: 8+ (number of violations)
ls scan-v2.json                        # Must exist (verification scan)
ls DAY3-SUMMARY.md                     # Must exist (daily summary)
```

**If ANY of these are missing, Day 3 was NOT completed correctly.**

**Common Mistake:** Running scan once, seeing low detection rate, and moving on without creating extractors. This breaks the entire flywheel. See `applications/aphoria/docs/dogfooding-common-mistakes.md` for full details.

---

### CRITICAL PROHIBITION:

**NEVER describe Aphoria as:**
- ❌ "CLI tool with LLM features"
- ❌ "Static scanner with optional automation"
- ❌ "Tool you run when you want"

**ALWAYS describe Aphoria as:**
- ✅ "Autonomous continuous learning system"
- ✅ "LLM-driven commit-time flywheel"
- ✅ "System that runs on every commit"

**For questions about "what is the flywheel?" or "main use cases", read:**
`/home/jml/Workspace/stemedb/applications/aphoria/vision.md`

---

## Aphoria: What Is a Claim?

A **claim** is a human-authored statement about what code MUST do and WHY, with provenance and consequences.

> **Storage today:** Claims live in `.aphoria/claims.toml` (a flat mutable file), NOT in StemeDB. Observations flow through StemeDB (WAL, append-only, content-addressed). Claims do not. Closing this gap is tracked in `tmp/aphoria-stemedb-gap-closure.md`.

### Claims vs Observations

| Type | What it is | Who creates it | Example |
|------|-----------|----------------|---------|
| **Observation** | Grep result: "this code does X" | Extractors (automated) | `imports/tokio: true` |
| **Claim** | Rule: "code MUST do X because Y, or Z breaks" | Humans (via skill) | "Core MUST NOT import tokio because it creates runtime coupling. If tokio appears in core imports, the library becomes async-only and breaks sync users." |

**Observations are garbage.** They're indexed facts with no meaning. Nobody cares that `imports/format: true` — that's just grep output.

**Claims are the product.** They encode architectural decisions, safety invariants, and spec compliance with full context: provenance (where the rule came from), invariant (what must stay true), and consequence (what breaks if violated).

### Structure of a Claim

```toml
[[claim]]
id = "core-no-tokio-001"
concept_path = "stemedb/core/imports/tokio"
predicate = "imported"
value = false
comparison = "absent"  # Code MUST NOT have this
provenance = "Architecture decision by jml 2024-12-15"
invariant = "Core modules MUST remain sync-only"
consequence = "Importing tokio makes core async-only, breaking sync library users"
authority_tier = "expert"
category = "architecture"
evidence = ["ADR-003", "design review notes"]
status = "active"
```

### Aphoria Workflows (Primary Use Cases)

**Day-to-day (commit-time claim authoring):**
1. Look at the entire diff
2. Use `aphoria-claims` skill to identify "claimable" patterns (spec constants, ordering changes, boundary violations, derive changes on wire types)
3. Skill does lookups: `aphoria claims list` to check what exists
4. If alignment needed, skill uses `aphoria claims update` or `supersede`
5. Skill crafts and submits new claims via `aphoria claims create`
6. If needed for audit, create paired extractor

**Audit (scan-time claim verification):**
1. **Direction 1**: `aphoria scan` runs extractors → observations, compares against authored claims → PASS/CONFLICT/MISSING
2. **Direction 2**: `aphoria verify run` walks all claims, verifies each one's pattern exists in code → PASS/CONFLICT/MISSING

The skill drives the CLI. The CLI doesn't know about the skill. They connect via skill calling `aphoria claims` commands in a loop.

### Inline Claim Markers (`@aphoria:claim`)

Capture claim intent while writing code with inline markers:

**1. Add marker in comment:**
```rust
// @aphoria:claim[safety] Pool size MUST NOT exceed 50 -- OOM under sustained load
const MAX_POOL_SIZE: u32 = 50;
```

**2. Enable in config** (`.aphoria/config.toml`):
```toml
[extractors.inline_markers]
enabled = true
sync_to_pending = true  # Auto-sync during scan (default)
```

**3. Scan detects markers:**
```bash
aphoria scan
# Output: ℹ Detected 1 new claim marker(s). Run 'aphoria claims list-markers' to review.
```

**4. Review pending markers:**
```bash
aphoria claims list-markers --format table
# Shows: ID, file, line, category, invariant

aphoria claims list-markers --format json
# JSON output for skills to process
```

**5. Formalize via CLI:**
```bash
aphoria claims formalize-marker marker-abc123 \
  --id myapp-pool-max-001 \
  --tier expert \
  --evidence "tests/pool_tests.rs load test" \
  --by jml
# Creates full claim in .aphoria/claims.toml
# Updates marker status to "formalized"
```

**Or reject if not worth a claim:**
```bash
aphoria claims reject-marker marker-abc123 --reason "Implementation detail, not architecture"
```

**6. Update comment after formalization:**
```rust
// @aphoria:claimed myapp-pool-max-001
const MAX_POOL_SIZE: u32 = 50;
```

**Supported comment styles:**
- `// @aphoria:claim` (Rust, Go, C, TypeScript, JavaScript)
- `# @aphoria:claim` (Python, Ruby, Shell, YAML)
- `-- @aphoria:claim` (SQL)
- `/* @aphoria:claim */` (CSS, C-style blocks)
- `<!-- @aphoria:claim -->` (HTML, XML)

**Optional fields:**
- Category in brackets: `@aphoria:claim[category]`
- Consequence after ` -- `: `invariant -- consequence`

**Storage:**
- Detected markers → `.aphoria/pending_markers.toml` (auto-synced during scan)
- Formalized claims → `.aphoria/claims.toml`
- Already formalized → `@aphoria:claimed <claim-id>` (skipped by extractor)

## Critical Rules

- **No Random Summaries:** Do not create summary documents (like `*-SUMMARY.md`) unless explicitly requested.
- **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.
- **Query Parameter Arrays:** In API handlers, use `QsQuery` extractor (not standard `Query`) for any DTO with `Vec<T>` or `Option<Vec<T>>` fields. Dashboard uses bracket notation (`?sources[]=a&sources[]=b`) which requires `serde_qs`. Standard `Query` silently fails on array params. See `crates/stemedb-api/src/extractors.rs` for details.
- **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.
- **No GitHub Workflows:** We use pre-commit hooks, not GitHub Actions CI.

## Quick Reference

```bash
# Build
cargo build --workspace

# Test (choose based on need)
cargo test -p stemedb-core        # Fast: single crate (~30s)
cargo test --workspace --lib      # Medium: all unit tests (~3min)
cargo nextest run                 # Full: parallel runner (~5min)
cargo test --workspace            # Legacy: sequential (~15min)

# 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 | — |
| +8 | StemeDB Dashboard | 18188 | — |
| +9 | Aphoria Dashboard | 18189 | — |

## Specialized Agents

| Domain | Agent | When to use |
|--------|-------|-------------|
| **Product Vision** | `episteme-product-visionary` | Use cases, "why not Postgres?", product-market fit |
| **Pilot Prep** | `enterprise-skeptic-buyer` | Pressure-test demos, find gaps, prepare for tough questions |
| **Aphoria Pitch** | `aphoria-skeptic-buyer` | Pressure-test Aphoria demos, security tool buyer objections |
| **Aphoria Phase 7** | `declarative-extractor-skeptic` | Pressure-test declarative extractors, LLM extraction, pattern learning |
| **Aphoria Phase 9** | `autonomous-learning-skeptic` | Pressure-test autonomous promotion, shadow mode, cross-project learning |
| 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, signing utilities | ✅ 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
