# Episteme (StemeDB) Roadmap

> **Goal:** Build the "Git for Truth" substrate for autonomous AI research.
> **Current Phase:** Phase 6 (The Mesh — Distributed Writes) — Phase 5 complete ✅
> **Target Vertical:** BioTech/Pharma ("The Living Review")
> **Endgame:** Distributed multi-writer cluster for millions of concurrent agents

---

## High-Level Timeline

| Phase | Codename | Focus | Key Deliverable |
| :--- | :--- | :--- | :--- |
| **1** | **The Spine** | Storage & Safety | Append-only WAL + KV Store |
| **2** | **The Lattice** | Indexing & Async | Materialized Views + Ballot Box |
| **2.5** | **Hardening** | Camp 2 Fixes | MV staleness, epoch behavior, lens cleanup |
| **3** | **The Pilot** | Vertical Integration | Pharma Ingestion + Living Review Agent |
| **4** | **The Hive** | Trust & Learning | TrustRank, metadata indexing, change tracking |
| **5** | **The Forge** | Foundation Hardening | Replace sled, fix WAL, persist indices, concept hierarchy |
| **6** | **The Mesh** | Distributed Writes | CRDT replication, Raft coordination, cluster membership |
| **7** | **The Shield** | Trust at Scale | EigenTrust, PoW admission, anti-spam, quarantine |
| **8** | **The Swarm** | Production Cluster | Chaos testing, observability, geo-distribution |

---

## Detailed Milestones

### Phase 1: The Spine (Foundation)
*Goal: Securely ingest assertions and persist them without data loss.*

- [x] **Project Scaffold**: Initialize Rust workspace, set up linting/CI (clippy, fmt).
- [x] **Assertion Schema**: Define the `Assertion` struct with `rkyv` serialization.
    - [x] Add dependencies: `rkyv`, `blake3`, `ed25519-dalek`, `image_hasher`.
    - [x] Define `Assertion` struct (Subject, Predicate, Object, Confidence, SourceHash).
    - [x] **Multi-Sig Expansion**: Implement `SignatureEntry` struct and `signatures: Vec<SignatureEntry>` field.
    - [x] **Visual Expansion**: Add `visual_hash: Option<pHash>` field for image provenance.
    - [x] Test serialization round-trips.
- [x] **Ballot Schema**: Define the `Vote` struct for multi-agent consensus.
    - [x] Add `Vote` struct: `assertion_hash`, `agent_id`, `weight`, `signature`.
    - [x] Test serialization round-trips.
- [x] **Paradigm Schema (Epochs)**: Define the `Epoch` and `SupersessionType` structs.
    - [x] Add `epoch: Option<EpochId>` to `Assertion`.
    - [x] Implement `Epoch` struct with `supersedes` and `SupersessionType`.
    - [x] Test serialization round-trips.
- [x] **WAL Integration**: Implement the Quarantine Pattern for write-ahead logging.
    - [x] Create `stemedb-wal` crate.
    - [x] Port `FsyncGuard` and `Record` logic from established durability patterns.
    - [x] Implement Record format with BLAKE3 checksums and Headers.
    - [x] Verify `fsync` behavior with tests.
- [x] **Storage Engine**: Implement the `Store` trait using `sled` (embedded KV).
    - [x] Add `sled` dependency.
    - [x] Define `KVStore` trait (put, get, delete, scan_prefix, flush).
    - [x] Implement `SledStore` wrapper.
- [x] **Basic Ingestor**: Background worker that tails WAL and writes to KV.
    - [x] Implement async loop reading from WAL.
    - [x] Write deserialized assertions, votes, and epochs to `sled`.
    - [x] Ed25519 signature verification during ingestion.
    - [x] Maintains S: and SP: indexes on ingest.
    - [x] Persistent cursor/checkpoint (resumes from `__CURSOR__:ingest` in KV store).
- [x] **Verification**: Crash recovery tests (write -> crash -> restart -> read).
    - [x] Single and multi-record crash recovery.
    - [x] Multiple crash cycles tested.

### Phase 2: The Lattice (Connectivity)
*Goal: Query data with sub-millisecond latency using Materialized Views.*

- [x] **Lifecycle Schema**: Add `LifecycleStage` to Assertion.
    - [x] Define enum: `Proposed`, `UnderReview`, `Approved`, `Deprecated`, `Rejected`.
    - [x] Update `Assertion` struct and serialization tests.
- [x] **The Ballot Box**: Implement high-velocity vote ingestion.
    - [x] `VoteStore` trait and implementation.
    - [x] `VoteAwareConsensusLens` for real vote-based resolution.
- [x] **Index Infrastructure**: Compound indexes for O(1) queries.
    - [x] `IndexStore` trait with S: and SP: indexes.
    - [x] `QueryEngine` smart routing (SP -> S -> scan).
- [x] **Materializer**: Background worker for O(1) Read Performance.
    - [x] `MaterializedView` type in `stemedb-core`.
    - [x] `Materializer` worker in `stemedb-query` with `step()` and `run()`.
    - [x] Aggregates Votes via `VoteAwareConsensusLens` (or any `AsyncLens`).
    - [x] Updates `MV:{Subject}:{Predicate}` with the winning Assertion + metadata.
    - [x] Event-driven mode via `run_notified()` with `tokio::sync::Notify`.
    - [x] Fast-path MV lookup in `QueryEngine::try_fast_path()`.
- [x] **The Meter**: Implement Economic Throttling (TAN).
    - [x] `QuotaStore` trait and `GenericQuotaStore` implementation.
    - [x] Token Bucket algorithm with per-agent per-hour quotas.
    - [x] `MeterLayer` tower middleware for request cost tracking.
    - [x] Cost model: Assert=10, Vote=1, Query=5+lens, +1/KB payload.
    - [x] `GET /v1/meter/quota` endpoint to check remaining quota.
    - [x] `POST /v1/meter/quota/limit` admin endpoint to set custom limits.
- [x] **API Surface**: `axum` HTTP server with OpenAPI (utoipa).
    - [x] `POST /v1/assert` -> Accepts JSON, writes to WAL.
    - [x] `POST /v1/vote` -> High-throughput vote endpoint.
    - [x] `POST /v1/epoch` -> Create epoch with optional supersession.
    - [x] `GET /v1/query` -> Subject/Predicate/Lens/Lifecycle/Epoch filtering.
    - [x] `GET /v1/health` -> Health check with assertion count.
    - [x] `GET /swagger-ui` -> Interactive API docs.
    - [x] 5 lens types available: Recency, Consensus, Authority, VoteAwareConsensus, TrustAwareAuthority.
- [x] **Query Audit**: Log every read with provenance.
    - [x] Define `QueryAudit` struct: query_id, agent_id, timestamp, params, result_hash, contributing_assertions.
    - [x] Storage at `AUD:{query_id}` with agent index at `AUDA:{agent_id}:{timestamp}:{query_id}`.
    - [x] `GET /v1/audit/queries` -> Returns history of agent decisions.
    - [x] `GET /v1/audit/query/{id}` -> Full reasoning trace for a single query.
    - [x] Auto-logging on every query via `X-Agent-Id` header.

### Phase 2.5: Hardening (Camp 2 Fixes)
*Goal: Close the gaps between "built" and "works right." Every item here addresses a feature that exists but doesn't fully deliver on its promise.*

- [x] **2.1 MV Staleness Detection**: Make the fast-path aware of stale materialized views.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] Added `max_stale: Option<u64>` to `Query` struct in `crates/stemedb-query/src/query.rs`.
        - [x] Added `.max_stale(secs)` builder method to `QueryBuilder`.
        - [x] In `try_fast_path()`: if `query.max_stale` is set and MV age exceeds threshold, falls through to slow path with `debug!` log.
        - [x] Added `max_stale` to API `QueryParams` DTO in `crates/stemedb-api/src/dto.rs`.
        - [x] Wired through query handler in `crates/stemedb-api/src/handlers/query.rs`.
    - **Tests:**
        - [x] `test_fast_path_stale_view_falls_back`: MV 1000 seconds old, `max_stale = 60` → slow path used.
        - [x] `test_fast_path_fresh_view_used`: Fresh MV, `max_stale = 300` → fast path used.
        - [x] `test_fast_path_no_max_stale_always_uses_mv`: No `max_stale` → any MV age accepted (backward compatible).
        - [x] `test_fast_path_max_stale_zero_rejects_old_mv`: `max_stale = 0`, MV 1 second old → slow path.
        - [x] `test_fast_path_max_stale_zero_accepts_brand_new_mv`: `max_stale = 0`, brand new MV → fast path.

- [x] **2.2 AuthorityLens -> ConfidenceLens Rename**: Eliminate the misleading name.
    - **Problem:** `AuthorityLens` selects by `confidence` field, not by agent reputation. `TrustAwareAuthorityLens` is the real authority lens. The name creates confusion about what "Authority" means.
    - **Solution implemented:**
        - [x] Renamed `authority.rs` → `confidence.rs`, `AuthorityLens` → `ConfidenceLens`
        - [x] Added `LensDto::Confidence` for the confidence-field selector
        - [x] Changed `LensDto::Authority` to route to `TrustAwareAuthorityLens` (the real authority lens)
        - [x] Updated query handler routing
        - [x] Updated ai-lookup/services/lens.md and skill documentation

- [x] **2.3 EpochAwareLens**: Give epoch supersession runtime behavior.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] `EpochAwareLens` in `crates/stemedb-lens/src/epoch_aware.rs`
        - [x] Decorator pattern wrapping any inner lens (default: RecencyLens)
        - [x] Walks supersession chain from `E:{epoch_id}` keys
        - [x] Cycle detection + max depth guard (100)
        - [x] Fail-open on missing epochs
        - [x] `LensDto::EpochAware` added to API
        - [x] 11 tests: excludes_superseded, chain_supersession, no_epochs_passes_all, missing_epoch_includes, cycle_detection, consensus_lens_inner, mixed_epochs, etc.
        - [x] Documentation updated in `ai-lookup/services/lens.md`
    - **Known Limitation:** Filtering only occurs when assertions from the superseding epoch are present in candidates. If all candidates are from old epoch (no new epoch assertions), they pass through (fail-open behavior).

- [x] **2.4 Visual Hash Query Support**: Make the stored `visual_hash` queryable.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] `hamming_distance(a: &PHash, b: &PHash) -> u32` in `crates/stemedb-query/src/query.rs` (lines 26-28)
        - [x] `visual_near: Option<String>` and `visual_threshold: Option<u32>` in `Query` struct (lines 84-90)
        - [x] `.visual_near(hash, threshold)` builder method
        - [x] `Query::matches()` computes hamming distance when `visual_near` is set
        - [x] API `QueryParams` DTO has `visual_near` and `visual_threshold`
        - [x] 10+ tests: exact_match, within_threshold, exceeds_threshold, skips_without_hash, invalid_hex, wrong_length, combines_with_subject, default_threshold, max_threshold, threshold_63_rejects
    - **Note:** Brute-force O(N) scan. VP-tree/BK-tree index is Phase 3+.

- [x] **2.5 Vector Field**: No changes needed. Already roadmapped for Phase 3.
    - **Status:** ✅ N/A (No Phase 2 work required)
    - **Current state:** `vector: Option<Vec<f32>>` on `Assertion`. Stored and returned by API. No index, no search.
    - **Phase 3 plan:** Integrate `hnsw-rs` or `lance` for k-NN search.

- [x] **2.6 E2E Integration Test (Write -> Materialize -> Read)**: Prove the full pipeline works end-to-end.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] `crates/stemedb-query/tests/e2e_pipeline.rs` with 5 comprehensive tests:
            - `test_e2e_write_materialize_read` - Basic happy path
            - `test_e2e_vote_consensus` - Vote-weighted resolution
            - `test_e2e_update_winner` - Winner changes on re-materialize
            - `test_e2e_cursor_persistence` - Cursor survives worker restart
            - `test_e2e_notify_integration` - Event-driven notification channel
        - [x] `stemedb-wal` and `stemedb-ingest` added as dev-dependencies
        - [x] Helper functions: `create_signed_assertion()`, `compute_assertion_hash()`, `create_vote()`
        - [x] Uses Ed25519 signing for authentic signature verification
    - [x] Also: `crates/stemedb-api/tests/e2e_flow_test.rs` tests the HTTP API layer end-to-end.

### Phase 3: The Pilot (BioTech/Pharma)
*Goal: Prove value in the "High-Liability" beachhead. Close every Camp 4 gap that blocks a credible demo.*

#### 3A. Schema Expansion (Prerequisite for everything below)

- [x] **3A.1 Source-Class Field**: Add `source_class: SourceClass` to Assertion.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] `SourceClass` enum in `crates/stemedb-core/src/types.rs` (lines 68-88).
        - [x] 6-tier system: `Regulatory` (0), `Clinical` (1), `Observational` (2), `Expert` (3), `Community` (4), `Anecdotal` (5).
        - [x] `tier()` method returns tier number for ordering.
        - [x] `default_decay_days()` method for tier-specific confidence decay.
        - [x] `authority_weight()` method for conflict resolution weighting.
        - [x] Field on `Assertion` struct at line 152.
        - [x] Full serialization and indexing support.

- [x] **3A.2 Conflict Score on Resolution**: Add `conflict_score: f32` to Resolution.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] Added `conflict_score: f32` field to `Resolution` in `crates/stemedb-lens/src/traits.rs`.
        - [x] Updated `Resolution::empty()` to set `conflict_score: 0.0`.
        - [x] Updated `Resolution::with_winner()` to accept `conflict_score` parameter.
        - [x] Added `compute_conflict_score(candidates: &[Assertion]) -> f32` utility function:
            - Uses normalized variance of confidence values.
            - 0 or 1 candidates → 0.0 (no conflict possible).
            - All same confidence → 0.0 (unanimous).
            - Max variance (0.0 vs 1.0) → 1.0 (maximum conflict).
            - Defensive NaN handling (returns 0.0 for malformed data).
        - [x] Updated all lens implementations to compute and pass conflict score:
            - `crates/stemedb-lens/src/recency.rs`
            - `crates/stemedb-lens/src/consensus.rs`
            - `crates/stemedb-lens/src/confidence.rs`
            - `crates/stemedb-lens/src/vote_aware_consensus.rs`
            - `crates/stemedb-lens/src/trust_aware_authority.rs`
        - [x] Added `conflict_score: f32` to `MaterializedView` in `crates/stemedb-core/src/types.rs`.
        - [x] Updated `Materializer::materialize_pair()` to write `conflict_score` from resolution.
        - [x] Added `conflict_score: Option<f32>` and `resolution_confidence: Option<f32>` to `QueryResponse` DTO in `crates/stemedb-api/src/dto.rs` (only present when lens is applied).
        - [x] Wired through query handler in `crates/stemedb-api/src/handlers/query.rs`.
    - **Tests:**
        - [x] `test_conflict_score_zero_for_empty`: Empty candidates → 0.0.
        - [x] `test_conflict_score_zero_for_single`: 1 candidate → 0.0.
        - [x] `test_conflict_score_zero_for_agreement`: All same confidence → near 0.0.
        - [x] `test_conflict_score_high_for_disagreement`: Candidates at 0.1, 0.5, 0.9 → score > 0.3.
        - [x] `test_conflict_score_max_for_extremes`: 0.0 vs 1.0 → score ≈ 1.0.
        - [x] `test_conflict_score_handles_nan_defensively`: NaN confidences → 0.0 (fail-safe).

- [x] **3A.3 Rich Source Metadata**: Add structured provenance beyond `source_hash`.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] Added `source_metadata: Option<Vec<u8>>` field to `Assertion` in `crates/stemedb-core/src/types.rs` (after `epoch`, before `lifecycle`).
        - [x] Uses `Vec<u8>` (not `String`) for rkyv zero-copy compatibility. Callers encode/decode JSON on their side.
        - [x] Added `source_metadata: Option<Vec<u8>>` to `AssertionBuilder` in `crates/stemedb-core/src/testing.rs`.
        - [x] Added `.source_metadata_json(json: &str)` and `.source_metadata(bytes)` builder methods.
        - [x] Added `source_metadata: Option<String>` to `CreateAssertionRequest` DTO (JSON string in API, converted to bytes internally).
        - [x] Added `source_metadata: Option<String>` to `AssertionResponse` DTO (bytes converted to JSON string with defensive UTF-8 handling).
        - [x] Wired through create handler (`dto_to_assertion()`) and query handler (`assertion_to_dto()`).
    - **Tests:**
        - [x] `test_serialize_deserialize_assertion_with_metadata`: Serialization roundtrip with metadata present.
        - [x] `test_serialize_deserialize_assertion_without_metadata`: Serialization roundtrip with metadata absent.
    - **Note:** Metadata is stored but NOT indexed in Phase 3. Indexing individual metadata fields is Phase 4+.

#### 3B. Time & Decay (Core Query Features)

- [x] **3B.1 Time-Travel Engine**: `as_of` parameter for historical queries.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] Added `as_of: Option<u64>` to `Query` struct in `crates/stemedb-query/src/query.rs:92-99`.
        - [x] Added `.as_of(timestamp: u64)` to `QueryBuilder`.
        - [x] In `Query::matches()`: if `as_of` is `Some(ts)`, check `assertion.timestamp <= ts`. Assertions created after `as_of` are excluded.
        - [x] In `QueryEngine::execute()`: if `query.as_of` is set, **skip the fast path entirely** (MVs reflect current state, not historical).
        - [x] Added `as_of: Option<u64>` to `QueryParams` DTO in `crates/stemedb-api/src/dto.rs`.
        - [x] Wired through query handler.
    - **Tests:**
        - [x] `test_as_of_excludes_future_assertions`: Assertions filtered by timestamp.
        - [x] `test_as_of_bypasses_fast_path`: MV exists, but `as_of` is set. Slow path used.
        - [x] `test_as_of_none_uses_fast_path`: Normal query still uses fast path (backwards-compatible).
        - [x] `test_as_of_with_lens_resolves_among_historical_candidates`: Time-travel + lens = resolve only among pre-as_of candidates.
        - [x] `test_as_of_returns_empty_when_all_assertions_are_future`: All assertions are future, returns empty.
        - [x] `test_as_of_with_exact_timestamp_match`: Edge case where assertion.timestamp == as_of.

- [x] **3B.2 Semantic Decay**: Confidence Half-Life at query time.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] Added `decay_halflife: Option<u64>` to `Query` struct in `crates/stemedb-query/src/query.rs`.
        - [x] Added `.decay_halflife(seconds: u64)` and `.source_class_decay(enabled: bool)` to `QueryBuilder`.
        - [x] Added `decay_halflife` and `source_class_decay` to `QueryParams` DTO.
        - [x] Created new `crates/stemedb-query/src/decay.rs` module with:
            - `apply_decay()`: Uniform decay using formula `confidence * 2^(-(age / halflife))`.
            - `apply_source_class_decay()`: Tier-specific decay (Regulatory=none, Clinical=2yr, Anecdotal=30d).
            - `compute_decayed_confidence()`: Core decay calculation with clamping.
        - [x] Integrated in `QueryEngine::execute()`: decay applied after filtering, before lens resolution.
        - [x] Time-travel compatible: uses `as_of` timestamp if set, otherwise current time.
        - [x] Source-class-aware decay fully implemented using `SourceClass::default_decay_days()`.
    - **Tests:** (11 unit tests in decay.rs + 1 E2E test)
        - [x] `test_decay_reduces_old_assertion_confidence`: 1yr old, 1yr halflife → ~50% confidence.
        - [x] `test_decay_preserves_fresh_assertions`: 1hr old, 1yr halflife → ~100% confidence.
        - [x] `test_decay_interacts_with_lens`: Older high-confidence loses to newer low-confidence after decay.
        - [x] `test_source_aware_decay_tier0_no_decay`: Regulatory never decays.
        - [x] `test_source_aware_decay_tier5_rapid_decay`: Anecdotal decays rapidly (30-day halflife).
        - [x] `test_source_aware_decay_mixed_tiers`: Clinical vs Anecdotal tier comparison.
        - [x] `test_decay_zero_halflife_no_change`: Zero halflife skips decay (avoids div-by-zero).
        - [x] `test_decay_future_assertion_no_change`: Future assertions don't decay.
        - [x] `test_decay_empty_assertions`: Empty input returns empty output.
        - [x] `test_decay_confidence_clamps_to_valid_range`: Very old assertions clamp to [0.0, 1.0].
        - [x] `test_decay_preserves_other_fields`: Only confidence changes; other fields preserved.
        - [x] `test_e2e_decay_reduces_old_confidence`: Full pipeline E2E test in e2e_pipeline.rs.
    - **Note:** When decay is enabled, materialized views (fast path) are bypassed because MVs store pre-computed winners without decay applied.

#### 3C. New Lenses

- [x] **3C.1 Skeptic Lens**: Surface disagreement, not winners. ✅ **COMPLETED**
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] `crates/stemedb-lens/src/skeptic.rs` - Full implementation.
        - [x] `AnalysisLens` trait for lenses that analyze conflict instead of resolving it.
        - [x] `SkepticLens` uses normalized Shannon entropy for conflict scoring.
        - [x] Returns `ConflictAnalysis` with:
            - `conflict_score: f32` (0.0 = unanimous, 1.0 = chaos)
            - `status: ResolutionStatus` (Unanimous, Agreed, Contested)
            - `claims: Vec<ClaimSummary>` - all claims ranked by weight
        - [x] `SkepticResolver` + `SkepticView` in `stemedb-query/src/skeptic.rs`.
        - [x] `GET /v1/skeptic?subject=X&predicate=Y` API endpoint.
        - [x] Core types in `stemedb-core/src/types.rs`:
            - `ResolutionStatus` enum
            - `ConflictAnalysis` struct
            - `ClaimSummary`, `SourceSummary`, `AgentSummary`
        - [x] Comprehensive test coverage (21 test cases).

- [x] **3C.2 Layered Consensus Lens**: Per-source-class consensus.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] `crates/stemedb-lens/src/layered_consensus.rs` - Full implementation.
        - [x] `TierResolution` struct: per-tier result with tier, source_class, winner, candidates_count, conflict_score, resolution_confidence.
        - [x] `LayeredResolution` struct: multi-tier result with tiers vec, overall_winner, overall_conflict_score, total_candidates.
        - [x] `LayeredLens` trait: `resolve_layered(&[Assertion]) -> LayeredResolution`, `name() -> &'static str`.
        - [x] `LayeredConsensusLens` implements both `LayeredLens` and `Lens` traits.
        - [x] Cross-tier conflict score uses normalized Shannon entropy of tier winner object values.
        - [x] `LensDto::LayeredConsensus` variant (redirects to `/v1/layered` endpoint).
        - [x] `GET /v1/layered?subject=X&predicate=Y` API endpoint with `LayeredQueryResponse`.
        - [x] Exported from `crates/stemedb-lens/src/lib.rs`.
    - **Tests:**
        - [x] `test_layered_empty_candidates`: Empty input returns empty resolution.
        - [x] `test_layered_single_tier`: All same source_class, returns one tier result.
        - [x] `test_layered_multi_tier_agreement`: Tier 0 and Tier 5 agree, low cross-tier conflict.
        - [x] `test_layered_multi_tier_disagreement`: Tier 1 vs Tier 5 disagree, high conflict, Tier 1 wins.
        - [x] `test_layered_overall_winner_from_highest_authority`: Tier 0 wins despite fewer assertions.
        - [x] `test_layered_lens_trait_compatibility`: Standard Lens trait works.
        - [x] `test_layered_within_tier_conflict`: High internal conflict within a tier.
        - [x] `test_layered_all_tiers_present`: One assertion from each tier.
        - [x] `test_layered_lens_name`: Both trait names work.
        - [x] `test_layered_numeric_values`: Works with numeric object values.

- [x] **3C.3 Constraints Lens**: Pre-flight check for must_use/forbidden.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] `crates/stemedb-lens/src/constraints.rs` - Full implementation.
        - [x] `ConstraintSet` struct: holds categorized assertions (must_use, forbidden, prefer) with conflict_score.
        - [x] `ConstraintsLens` struct with `resolve_constraints(&[Assertion]) -> ConstraintSet` method.
        - [x] Categorizes by predicate pattern: `must_use:*`, `forbidden:*`, `prefer:*`.
        - [x] Implements `Lens` trait for compatibility (priority: must_use > forbidden > prefer).
        - [x] Sorted by confidence (highest first), with timestamp as tiebreaker.
        - [x] `LensDto::Constraints` added (redirects to `/v1/constraints` endpoint).
        - [x] `GET /v1/constraints?subject=X` API endpoint with `ConstraintsResponse`.
        - [x] DTOs: `ConstraintsQueryParams`, `ConstraintEntryDto`, `ConstraintsResponse`.
        - [x] Exported from `crates/stemedb-lens/src/lib.rs`.
    - **Tests:** (16 test cases)
        - [x] `test_constraints_categorizes_by_predicate`: Mixed predicates sorted into must_use/forbidden/prefer.
        - [x] `test_constraints_empty_categories`: Only prefer, no must_use/forbidden.
        - [x] `test_constraints_non_constraint_predicates_ignored`: Regular predicates filtered out.
        - [x] `test_constraints_sorted_by_confidence`: Within-category confidence ordering.
        - [x] `test_constraints_empty_candidates`: Empty input returns empty set.
        - [x] `test_constraints_has_constraints_true`: Helper method works.
        - [x] `test_constraints_all_regular_predicates`: All non-constraint predicates returns no constraints.
        - [x] `test_lens_trait_picks_must_use_winner`: Standard Lens trait picks must_use first.
        - [x] `test_lens_trait_falls_back_to_forbidden`: Falls back to forbidden when no must_use.
        - [x] `test_lens_trait_falls_back_to_prefer`: Falls back to prefer when no must_use/forbidden.
        - [x] `test_lens_trait_empty_for_no_constraints`: Returns empty when no constraint predicates.
        - [x] `test_lens_name`: Name returns "Constraints".
        - [x] `test_lens_empty_candidates`: Empty input to Lens trait returns empty resolution.
        - [x] `test_multiple_must_use_picks_highest_confidence`: Multiple must_use picks highest confidence.
        - [x] `test_confidence_tiebreaker_uses_timestamp`: Same confidence uses newer timestamp.
        - [x] `test_predicate_pattern_exact_prefix`: `must_use_something` not matched (only `must_use:*`).

#### 3D. Epoch Enhancement

- [x] **3D.1 Epoch Cascade Logic** (enhancement of Phase 2.5 EpochAwareLens):
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] `write_supersession_cascade()` in `crates/stemedb-ingest/src/worker.rs`:
            - Writes `SUPERSEDED:{old_epoch_id}` markers for full transitive closure.
            - All markers point to the LATEST superseding epoch.
            - Max depth guard (100 levels) and cycle detection via visited set.
        - [x] `is_epoch_superseded()` in `crates/stemedb-lens/src/epoch_aware.rs`:
            - O(1) marker lookup instead of O(chain_length) chain walks.
            - Fail-open semantics: missing marker = not superseded.
        - [x] `compute_superseded_epochs()` uses marker lookups for filtering.
    - **Tests:**
        - [x] `test_cascade_writes_superseded_marker`: Epoch B supersedes A → `SUPERSEDED:A` exists.
        - [x] `test_cascade_transitive`: C→B→A chain → both `SUPERSEDED:A` and `SUPERSEDED:B` point to C.
        - [x] `test_cascade_cycle_detection`: Mutual supersession handled gracefully.
        - [x] `test_epoch_aware_uses_marker`: EpochAwareLens uses O(1) marker lookup.
        - [x] `test_superseded_epoch_filtered_even_without_new_assertions`: Marker-based filtering works.

#### 3E. Similarity Search

- [x] **3E.1 Vector Search**: Semantic k-NN queries via embeddings.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] Added `hnsw_rs = "0.3"` and `parking_lot = "0.12"` to `stemedb-storage/Cargo.toml`.
        - [x] New module: `crates/stemedb-storage/src/vector_index.rs`.
        - [x] `VectorIndex` trait: `insert(hash: &Hash, vector: &[f32])`, `search(query: &[f32], k: usize) -> Vec<(Hash, f32)>`, `dimension()`, `len()`, `is_empty()`.
        - [x] `HnswVectorIndex` implementation with HNSW graph, RwLock protection, hash↔ID mappings.
        - [x] Input validation: dimension mismatch, NaN, Infinite values rejected.
        - [x] Idempotent insert (same hash twice = no-op).
        - [x] `Arc<dyn VectorIndex>` trait object support for sharing.
        - [x] `IngestWorker::with_vector_index()` builder method for index attachment.
        - [x] IngestWorker: if assertion has `vector`, inserts into vector index after KV write.
        - [x] Added `vector_near: Option<Vec<f32>>` and `k: Option<usize>` to `Query` struct in `crates/stemedb-query/src/query.rs`.
        - [x] Added `.vector_near(vector, k)` builder method to `QueryBuilder`.
        - [x] Added `vector_near` and `k` to API `QueryParams` DTO.
        - [x] `QueryEngine::with_vector_index()` builder method for index attachment.
        - [x] QueryEngine: if `vector_near` is set and index configured, uses O(log N) HNSW lookup for candidates.
        - [x] Falls back to standard path if no index configured (with debug log).
    - **Tests:** (12 unit tests for VectorIndex + 4 integration tests in engine.rs)
        - [x] `test_create_index`, `test_insert_and_search`, `test_dimension_mismatch`.
        - [x] `test_idempotent_insert`, `test_search_empty_index`, `test_search_k_zero`.
        - [x] `test_nan_rejection`, `test_infinite_rejection`, `test_contains`.
        - [x] `test_larger_scale` (100 vectors, exact match first), `test_custom_params`, `test_zero_dimension_panics`.
        - [x] `test_vector_search_returns_nearest_neighbors`, `test_vector_search_with_subject_filter`.
        - [x] `test_vector_search_without_index_falls_back`, `test_vector_search_with_as_of_filter`.
    - **Note:** Index is in-memory only. Persistence is Phase 4+.

- [x] **3E.2 Visual Hash Index**: BK-tree for O(log N) visual similarity.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] New module: `crates/stemedb-storage/src/visual_index.rs`.
        - [x] `VisualIndex` trait: `insert(hash: &Hash, phash: &PHash)`, `search(query: &PHash, threshold: u32) -> Vec<(Hash, u32)>`, `len()`, `is_empty()`.
        - [x] `BkTreeVisualIndex` implementation using BK-tree over hamming distance.
        - [x] `hamming_distance(a: &PHash, b: &PHash) -> u32` utility function.
        - [x] Threshold clamped to 0-64 range (max 64 bits).
        - [x] Results sorted by distance ascending.
        - [x] Idempotent insert (same hash twice = no-op).
        - [x] `Arc<dyn VisualIndex>` trait object support for sharing.
        - [x] `IngestWorker::with_visual_index()` builder method for index attachment.
        - [x] IngestWorker: if assertion has `visual_hash`, inserts into BK-tree after KV write.
        - [x] `QueryEngine::with_visual_index()` builder method for index attachment.
        - [x] QueryEngine: if `visual_near` is set and index configured, uses O(log N) BK-tree lookup.
        - [x] Falls back to brute-force scan (via `query.matches()`) if no index configured.
        - [x] Invalid hex input returns `QueryError::InvalidInput` with clear message.
    - **Tests:** (14 unit tests for VisualIndex + 6 integration tests in engine.rs)
        - [x] `test_hamming_distance_zero`, `test_hamming_distance_max`, `test_hamming_distance_partial`.
        - [x] `test_create_index`, `test_insert_and_search_exact`, `test_search_within_threshold`.
        - [x] `test_search_no_matches`, `test_search_empty_index`, `test_idempotent_insert`.
        - [x] `test_contains`, `test_results_sorted_by_distance`, `test_threshold_clamped_to_64`.
        - [x] `test_larger_scale` (1000 hashes), `test_default_impl`.
        - [x] `test_visual_search_returns_similar_images`, `test_visual_search_with_lifecycle_filter`.
        - [x] `test_visual_search_invalid_hex_returns_error`, `test_visual_search_without_index_uses_brute_force`.
        - [x] `test_visual_search_with_limit`, `test_vector_search_empty_index`.
    - **Note:** Index is in-memory only. Persistence is Phase 4+.

#### 3F. Provenance

- [x] **3F.1 Source Document Storage & Provenance Lookup**: Enable 100% citation recall.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] `POST /v1/source` endpoint to store source documents by BLAKE3 content hash.
        - [x] `GET /v1/provenance/{hash}` endpoint to retrieve source documents by hash.
        - [x] Source storage at `SRC:{hash}` keys with format: `[content_type_len:4][content_type][content]`.
        - [x] Base64 encoding for binary-safe JSON transport.
        - [x] 10MB size limit per document.
        - [x] Content-addressed storage: same content → same hash (idempotent uploads).
        - [x] DTOs: `StoreSourceRequest`, `StoreSourceResponse`, `ProvenanceResponse`.
        - [x] OpenAPI documentation under "provenance" tag.
    - **Tests:** (5 test cases)
        - [x] `test_store_and_retrieve_source`: Happy path store + retrieve.
        - [x] `test_store_source_invalid_base64`: Bad base64 → 400.
        - [x] `test_get_provenance_not_found`: Unknown hash → 404.
        - [x] `test_get_provenance_invalid_hash`: Bad hash format → 400.
        - [x] `test_store_source_idempotent`: Same content twice → same hash.
    - **Note:** Benchmark utility for verifying all assertions have retrievable sources is future work.

#### 3G. API Cleanup

- [x] **3G.1 Document epoch supersession via existing endpoint**: No new `/epoch/supersede` endpoint needed.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] Updated use case docs (consumer-health-intelligence.md, glp1-living-review.md) to use `POST /v1/epoch` with `supersedes` field.
        - [x] Added OpenAPI examples showing both new epoch and supersession flows in handlers/epoch.rs.
        - [x] Documented all 5 supersession types: Invalidate, Temporal, Refinement, RequiresReview, Additive.
    - **No code change.** Documentation fix only.

### Phase 4: The Hive (Trust & Scale)
*Goal: Change tracking, metadata indexing, and the database primitives for training pipelines.*

- [x] **TrustRank Engine**: Foundation for trust-based resolution.
    - [x] `TrustRankStore` for per-agent reputation storage.
    - [x] `TrustAwareAuthorityLens` for reputation-weighted resolution.
    - [x] **Confidence Half-Life**: Implement decay calculation engine.
    - [x] Learning loop: `record_outcome()` for accuracy tracking.

- [x] **4.1 "Since" Parameter**: Change tracking for returning consumers.
    - **Status:** ✅ COMPLETE
    - **Problem:** Consumer Health shows `GET /query?since=2023-10-01` returning `changes_since` with dated change entries. The "returning consumer" story: "What changed since I last looked?"
    - **Depends on:** Time-Travel (3B.1) and Materializer.
    - **Implementation:**
        - [x] Added `since: Option<u64>` to `Query` struct and `QueryBuilder` in `crates/stemedb-query/src/query.rs`.
        - [x] Added `since` to `QueryParams` DTO in `crates/stemedb-api/src/dto.rs`.
        - [x] **MV Changelog**: Track when materialized views change.
            - [x] New key pattern: `MVC:{subject}:{predicate}:{timestamp_nanos}` using nanosecond precision to prevent collisions.
            - [x] `ChangeEntry` struct in `crates/stemedb-core/src/types.rs` with: `timestamp`, `previous_winner_hash`, `new_winner_hash`, `subject`, `predicate`, `lens_name`.
            - [x] In `Materializer::materialize_pair()`: before overwriting MV, read existing MV. If winner changed (different hash), write changelog entry.
            - [x] `get_previous_winner_hash()` and `write_changelog_entry()` helper methods.
        - [x] In QueryEngine: if `since` is set, skip fast path (MVs reflect current state). `fetch_changes_since()` scans `MVC:` keys and returns entries >= since timestamp.
        - [x] `ChangeEntryDto` in `crates/stemedb-api/src/dto.rs` with hex-encoded hashes.
        - [x] `changes_since: Option<Vec<ChangeEntryDto>>` added to `QueryResponse` DTO.
        - [x] `fetch_changelog_if_needed()` helper in query handler.
        - [x] Re-exported `ChangeEntry` from `stemedb-core` crate root.
    - **Tests:**
        - [x] `test_changelog_written_on_first_materialization`: First MV creates changelog with `previous_winner_hash: None`.
        - [x] `test_changelog_written_on_winner_change`: Winner change creates changelog with previous hash.
        - [x] `test_no_changelog_when_winner_unchanged`: Re-materialize same winner = no new changelog.
        - [x] `test_fetch_changes_since_returns_entries`: Fetch filtered by timestamp, sorted ascending.
        - [x] `test_fetch_changes_since_empty_on_no_entries`: No entries returns empty vec.
        - [x] `test_since_bypasses_fast_path`: Query with `since` uses slow path, returns all assertions.

- [x] **4.2 Source Metadata Indexing** (extension of 3A.3): Index key metadata fields.
    - **Status:** ✅ COMPLETE
    - **Problem:** Phase 3 stores `source_metadata` as an opaque blob. Phase 4 makes key fields queryable.
    - **Depends on:** Rich Source Metadata (3A.3).
    - **Implementation:**
        - [x] Defined indexed metadata keys: `journal`, `doi`, `platform`, `study_design` in `INDEXED_METADATA_FIELDS`.
        - [x] New module: `crates/stemedb-storage/src/source_metadata_index.rs`.
        - [x] Key pattern: `SMV:{field}:{value}` storing `Vec<Hash>` (rkyv-serialized) for efficient batch lookup.
        - [x] `SourceMetadataIndexStore` trait with `add_to_metadata_indexes()` and `get_by_metadata_field()`.
        - [x] `GenericSourceMetadataIndexStore` implementation with case-insensitive value normalization.
        - [x] IngestWorker: on ingestion, if `source_metadata` is present, parse JSON, extract indexed fields, write index entries.
        - [x] Added `source_journal`, `source_doi`, `source_platform`, `source_study_design` to `Query` struct.
        - [x] Added `.source_journal()`, `.source_doi()`, `.source_platform()`, `.source_study_design()` builder methods.
        - [x] Added `matches_metadata_filters()` helper with AND semantics and case-insensitive matching.
        - [x] Added metadata field filters to `QueryParams` DTO (e.g., `?source_journal=NEJM`).
        - [x] Wired through query handler in `crates/stemedb-api/src/handlers/query.rs`.
    - **Tests:** (9 unit tests in source_metadata_index.rs + 9 unit tests in query.rs)
        - [x] `test_add_and_get_by_metadata_field`: Basic round-trip.
        - [x] `test_case_insensitive_indexing`: "NEJM" stored, "nejm" query matches.
        - [x] `test_multiple_assertions_same_field`: Vec accumulates correctly.
        - [x] `test_malformed_json_gracefully_skipped`: Invalid JSON logs warning, doesn't error.
        - [x] `test_missing_field_not_indexed`: Only indexed fields processed.
        - [x] `test_idempotent_insert`: Same assertion twice = no duplicates.
        - [x] `test_all_indexed_fields`: All 4 fields indexed correctly.
        - [x] `test_empty_index_returns_empty_vec`: Non-existent field returns empty.
        - [x] `test_non_string_values_ignored`: Non-string JSON values skipped.

- [x] **4.3 Batch TrustRank Decay API**: Expose scheduled decay for external orchestration.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] New module: `crates/stemedb-api/src/handlers/admin.rs`
        - [x] `POST /v1/admin/decay-trust-ranks` endpoint.
        - [x] Request accepts `now: Option<u64>` (defaults to current time) and `half_life_seconds: Option<u64>` (defaults to 30 days).
        - [x] Response includes `decayed_count`, `timestamp_used`, `half_life_used`, `status`.
        - [x] OpenAPI docs with "admin" tag.
        - [x] Thin handler delegates to `TrustRankStore::decay_trust_ranks()`.
    - **Tests:** (3 integration tests in http_integration.rs)
        - [x] `test_decay_trust_ranks_empty_store`: Empty store returns 0 decayed.
        - [x] `test_decay_trust_ranks_with_custom_params`: Custom timestamp and half-life honored.
        - [x] `test_decay_trust_ranks_response_structure`: All 4 fields present in response.
    - **Note:** The Gardener (Camp 5.2, app layer) calls this endpoint on a schedule. The database just exposes the primitive.

- [x] **4.4 Vote Provenance Witness**: Transform votes from opinions into cryptographic witnesses.
    - **Status:** ✅ COMPLETE
    - **Problem:** Votes record "I agree" but the browser extension product needs "I saw this exact text at this URL at this time." Without provenance, votes are Tier 5 noise.
    - **Implementation:**
        - [x] Added `source_url: Option<String>` to Vote struct — URL where claim was observed.
        - [x] Added `observed_context: Option<Vec<u8>>` to Vote struct — page context bytes (rkyv zero-copy pattern).
        - [x] API DTOs: `source_url` and `observed_context` on CreateVoteRequest/VoteResponse.
        - [x] Input validation: source_url max 2048 chars (non-empty if provided), observed_context max 64KB.
        - [x] Backward compatible: existing votes without provenance remain valid.
    - **Tests:** Serialization roundtrip (with/without provenance, mixed fields), storage roundtrip, API integration (validation).

- [x] **4.5 Conflict Score Filtering**: Query-time filtering by conflict score.
    - **Status:** ✅ COMPLETE
    - **Problem:** The browser extension needs "only show me claims where conflict > 0.7" to implement contradiction-only overlays. Conflict score was computed but not filterable.
    - **Implementation:**
        - [x] Added `min_conflict_score: Option<f32>` and `max_conflict_score: Option<f32>` to Query struct.
        - [x] Builder methods: `.min_conflict_score()`, `.max_conflict_score()`.
        - [x] Fast-path filtering: checks MV conflict_score against thresholds.
        - [x] API validation: scores must be 0.0-1.0, finite (rejects NaN/Inf).
        - [x] QueryParams DTO wired through query handler.
    - **Tests:** 13 engine tests (min/max thresholds, exact boundary, range, combination with lifecycle), API validation tests.
    - **Note:** Filtering works on fast path (MV reads) only. Slow path returns raw assertions without conflict scores.

- [x] **4.6 Escalation Triggers**: Active safety system for high-conflict assertions.
    - **Status:** ✅ COMPLETE
    - **Problem:** High conflict was invisible. Episteme should be an active safety system that fires escalations when disagreement exceeds thresholds.
    - **Implementation:**
        - [x] `EscalationLevel` enum: Low, Medium, High, Critical.
        - [x] `EscalationEvent` struct: content-addressed (BLAKE3 ID), subject, predicate, conflict_score, level, reason, timestamp, resolved.
        - [x] `EscalationPolicy` struct: configurable threshold + level + optional predicate pattern.
        - [x] `EscalationStore` trait + `GenericEscalationStore`: write, query since, resolve, get pending.
        - [x] Key pattern: `ESC:{timestamp_nanos}:{id_hex}`.
        - [x] Materializer integration: after computing conflict_score, checks policies and writes events.
        - [x] `with_escalation(store, policies)` builder on Materializer.
        - [x] `GET /v1/admin/escalations` and `POST /v1/admin/escalations/{id}/resolve` endpoints.
    - **Tests:** Core type tests, storage roundtrip, materializer integration (high/low conflict, predicate matching, no store configured).

- [x] **4.7 Gold Standard Verification**: Sybil defense via proof of knowledge.
    - **Status:** ✅ COMPLETE
    - **Problem:** New agents need a way to earn TrustRank. Gold standards are admin-verified assertions that agents can be tested against.
    - **Implementation:**
        - [x] `GoldStandard` struct with rkyv serialization: assertion_hash, subject, predicate, expected_object, created_at, created_by.
        - [x] `GoldStandardStore` trait + `GenericGoldStandardStore`: set, get, list, remove.
        - [x] Key pattern: `GS:{subject}:{predicate}`.
        - [x] `TrustAdjustment` enum: Rewarded(+0.05), Penalized(-0.1), AlreadyVerified.
        - [x] `verify_agent_against_gold_standard()` on TrustRankStore with deduplication (agents can only verify each gold standard once).
        - [x] Verification markers at `GS_VERIFIED:{agent_id}:{subject}:{predicate}` prevent gaming.
        - [x] API: `POST/GET/DELETE /v1/admin/gold-standards`, `POST /v1/admin/verify-agent`.
    - **Tests:** Core (creation, matching, case-sensitivity), storage CRUD, trust adjustment (reward, penalty, clamping, dedup), API integration (5 tests).

> **Note:** The following items were reclassified as **Application Layer** responsibilities (see `tmp/ambition-vs-reality.md`, Camp 5). They are not Episteme database features. They consume the Episteme API and are built by integrators or vertical-specific teams.
>
> - **The Simulator** (Training Data Pipeline) -> Camp 5.3
> - **The Super Curator** (Reviewer Agent swarm) -> Camp 5.4
> - **Background Gardener** (Cluster detection, signal processing) -> Camp 5.2
> - **Agent Wallet** (Key management sidecar) -> Camp 5.1

### Phase 5: The Forge (Foundation Hardening)
*Goal: Replace abandoned dependencies, fix WAL gaps, persist indices. Prerequisite for distribution.*

> **Research:** [docs/research/wal-crash-recovery-research.md](docs/research/wal-crash-recovery-research.md)

#### 5A. Storage Engine Replacement

- [x] **5A.1 Replace sled with redb + fjall**: sled is abandoned (author recommends alternatives).
    - **Problem:** sled is alpha-stage with known performance regressions and no active development. Our entire storage layer depends on it.
    - **Solution:** HybridStore routes keys by prefix — **fjall** (LSM) for write-heavy paths (`H:`, `V:`, `VC:`, `VW:`, `E:`, `SUPERSEDED:`, `__CURSOR__:`) and **redb** (B-tree) for read-heavy paths (`S:`, `SP:`, `MV:`, `TR:`, `QA:`, `QT:`, `TP:`, `GS:`, `ESC:`).
    - **Tasks:**
        - [x] Generalize `StorageError::Sled` to `StorageError::Backend(String)`.
        - [x] Implement `FjallStore` backend with DashMap per-key locks for atomics.
        - [x] Implement `RedbStore` backend with ACID transactions.
        - [x] Implement `HybridStore` routing layer with prefix-based dispatch.
        - [x] Migrate all ~500 tests from `SledStore` to `HybridStore`.
        - [x] Remove sled dependency entirely.
        - [x] Add criterion benchmarks (sequential put, random get, prefix scan, atomic increment, mixed workload).
    - **Crates:** `redb = "2"`, `fjall = "2"`, `dashmap = "6"`

- [x] **5A.2 Key Layout Redesign**: Prepare keys for subject-prefix range sharding.
    - **Problem:** Current keys (`H:{hash}`, `S:{subject}`, `MV:{subject}:{predicate}`) scatter related data across the keyspace. Distributed sharding needs co-location.
    - **Solution:** Subject-prefix key layout with `\x00` separator for subject-scoped keys, `\x00` prefix for global keys (sort-first):
        ```
        Subject-prefixed (co-located):
        {subject}\x00H:{hash}       → Assertion data
        {subject}\x00S:{hash_list}  → Subject index
        {subject}\x00SP:{predicate} → Compound index
        {subject}\x00MV:{predicate} → Materialized view
        {subject}\x00V:{hash}:{vh}  → Votes
        {subject}\x00VC:{hash}      → Vote count cache
        {subject}\x00VW:{hash}      → Vote weight cache
        {subject}\x00GS:{predicate} → Gold standards

        Global (sort first via \x00 prefix):
        \x00TRUST:{agent_id}        → Trust ranks
        \x00QUOTA:{agent_id}:{win}  → Quota records
        \x00QLIMIT:{agent_id}       → Quota limits
        \x00E:{epoch_id}            → Epochs
        \x00SUPERSEDED:{epoch_id}   → Supersession markers
        \x00SUP:{hash}              → Supersession records
        \x00AUD:{query_id}          → Audit records
        \x00ESC:{ts}:{id}           → Escalation events
        \x00TP:{pack_id}            → Trust packs
        \x00META:{key}              → System metadata
        \x00HASH_SUBJECT:{hash}     → Reverse lookup index
        \x00SUBJECTS:{subject}      → Known subjects index
        \x00GS_LIST:{subj}:{pred}   → Gold standard listing
        ```
    - **Implementation:**
        - [x] `key_codec.rs` (573 lines): 40+ key builder functions, subject validation, extraction utilities, 30+ unit tests.
        - [x] All stores migrated to `key_codec::` functions (91 call sites across 10 store files, zero hardcoded key patterns).
        - [x] Ingestion pipeline uses `key_codec` (11 usages across 3 files).
        - [x] Query engine uses `key_codec` (34 usages across 7 files).
        - [x] Subject co-location verified by `test_subject_colocation` test.
        - [x] Global key sort-first verified by `test_global_keys_sort_first` test.

#### 5B. WAL Hardening

- [x] **5B.1 CRC32C Checksums**: Add hardware-accelerated torn write detection.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] Added `crc32c = "0.6"` crate dependency.
        - [x] Updated WAL record format with CRC32C in `format.rs`.
        - [x] CRC32C verified on read before deserializing.
        - [x] Hardware-accelerated via SSE 4.2 on supported CPUs.

- [x] **5B.2 Crash Recovery Implementation**: Replace recovery stub with production recovery.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] `recovery/mod.rs` (236 lines): Full sequential record scan with CRC32C validation.
        - [x] Truncates file at first corrupted/incomplete record.
        - [x] `RecoveryMetrics` struct tracks: valid_records, invalid_records, bytes_truncated, recovery_duration.
        - [x] Comprehensive test suite in `recovery/tests.rs`.

- [x] **5B.3 Group Commit**: Batch fsync for throughput.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] `group_commit.rs` (342 lines): `GroupCommitBuffer` with configurable `max_writes` and `max_duration`.
        - [x] Writers append to buffer and wait on `Notify`.
        - [x] Background flusher calls fsync and notifies all waiters.
        - [x] `GroupCommitConfig` for tuning batch size and flush interval.

- [x] **5B.4 Log Rotation**: Bounded WAL disk usage.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] `segment.rs` (368 lines): Full segment management.
        - [x] Segment naming: `{seq:08x}.wal`.
        - [x] Rotation when segment exceeds configurable threshold.
        - [x] `SegmentManager` tracks active and archived segments.
        - [x] Safe deletion of segments after cursor passes them.

#### 5C. Index Persistence

- [x] **5C.1 Persistent Vector Index**: Move HNSW from in-memory to disk-backed.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] `PersistentVectorIndex` in `crates/stemedb-storage/src/vector_index/persistent.rs`.
        - [x] Hybrid hot/cold architecture:
            - **Hot:** In-memory HNSW for recent vectors.
            - **Cold:** Disk-backed HNSW loaded from checkpoint files.
        - [x] `persistence/format.rs`: `SnapshotMetadata`, `IdMappingTable` with rkyv serialization.
        - [x] `hot_cold.rs`: `merge_search_results()` for combining hot and cold query results.
        - [x] Background checkpoint task with atomic write pattern.
        - [x] CRC32C integrity verification on load.
        - [x] MAX_PAYLOAD_SIZE (1GB) validation to prevent memory exhaustion.
    - **Crates:** `memmap2 = "0.9"`, `crc32c = "0.6"`, `byteorder = "1.5"`
    - **Known Limitation:** Cold index currently stores ID mappings only; full vector persistence with mmap'd HNSW graphs planned for future phase.

- [x] **5C.2 Persistent Visual Index**: Persist BK-tree to disk.
    - **Status:** ✅ COMPLETE
    - **Implementation:**
        - [x] `PersistentVisualIndex` in `crates/stemedb-storage/src/visual_index.rs`.
        - [x] `BkTreeSnapshot` with rkyv serialization for BK-tree state.
        - [x] Checkpoint file format: `[MAGIC:4][VERSION:1][RESERVED:3][PAYLOAD_LEN:u64][CRC32C:u32][PAYLOAD]`.
        - [x] Atomic write pattern: temp file → fsync → rename → fsync parent.
        - [x] Background checkpoint task with configurable interval.
        - [x] CRC32C integrity verification on load.
        - [x] Shared `checkpoint_format.rs` module for common read/write utilities.

#### 5D. Concept Hierarchy ✅ COMPLETE

> **Spec:** [docs/specs/concept-hierarchy.md](docs/specs/concept-hierarchy.md)
> **Purpose:** Hierarchical, scheme-qualified subject identifiers with cross-scheme alias resolution. Enables applications like Aphoria that need to connect `code://` paths to `rfc://` paths.

- [x] **5D.1 ConceptPath Type**: Structured subject identifiers. ✅
    - **Tasks:**
        - [x] Add `ConceptPath` struct to `stemedb-core/src/types/concept.rs`.
        - [x] Wire format: `{scheme}://{segment_0}/{segment_1}/.../{leaf}`.
        - [x] `parse()`, `to_wire_format()`, `leaf()`, `parent()`, `is_prefix_of()`.
        - [x] Backward-compatible: bare strings parse as `custom://{string}`.
        - [x] Unit tests for parsing, round-trip, prefix matching (Battery 8).
    - **Crate:** `stemedb-core`

- [x] **5D.2 Source Scheme Registry**: Map schemes to default source tiers. ✅
    - **Tasks:**
        - [x] Add `SourceScheme` enum to `stemedb-core`.
        - [x] Scheme → default `SourceClass` mapping (e.g., `rfc://` → Tier 0, `code://` → Tier 3).
        - [x] `ConceptPath::default_source_class()` method.
    - **Crate:** `stemedb-core`

- [x] **5D.3 Alias Store**: Cross-scheme entity resolution. ✅
    - **Tasks:**
        - [x] Add `ConceptAlias` struct to `stemedb-core`.
        - [x] Add `AliasStore` trait to `stemedb-storage`.
        - [x] Key prefixes: `CA:{alias_path}` → canonical, `CAR:{canonical}` → all aliases.
        - [x] Transitive alias resolution with cycle detection.
        - [x] `GenericAliasStore` implementation over `KVStore`.
    - **Crates:** `stemedb-core`, `stemedb-storage`

- [x] **5D.4 Hierarchical Query**: Prefix-based subject queries. ✅
    - **Tasks:**
        - [x] `fetch_by_subject_prefix()` using `scan_prefix` in query engine (already implemented in Battery 5).
        - [x] Trailing `/` handling to prevent `auth` matching `authentication`.
    - **Crate:** `stemedb-query`
    - **Note:** Hierarchical prefix scanning was already working; Battery 5 validates it.

- [x] **5D.5 Alias Resolution in Queries**: Expand queries to aliased paths. ✅
    - **Tasks:**
        - [x] `AliasStore::resolve_all()` for transitive alias expansion.
        - [x] API endpoint `GET /v1/concepts/resolve?path=...&transitive=true`.
    - **Crate:** `stemedb-query`, `stemedb-api`
    - **Note:** Resolution available via API; QueryEngine integration is future work.

- [x] **5D.6 Source Class Inference**: Infer tier from scheme. ✅
    - **Tasks:**
        - [x] `ConceptPath::default_source_class()` returns tier based on scheme.
        - [x] `SourceScheme::parse()` maps scheme strings to enum variants.
    - **Crate:** `stemedb-core`
    - **Note:** Inference at ingestion time would break content-addressing (signature verification). Inference is available at query time or before signing.

- [x] **5D.7 Concept API Endpoints**: CRUD for aliases and hierarchy browsing. ✅
    - **Tasks:**
        - [x] `POST /v1/concepts/alias` — Create alias.
        - [x] `GET /v1/concepts/aliases` — List all aliases (with optional canonical filter).
        - [x] `DELETE /v1/concepts/alias` — Remove alias.
        - [x] `GET /v1/concepts/resolve` — Resolve path to canonical/transitive aliases.
        - [x] `GET /v1/concepts/suggest` — Suggested aliases (shared leaf detection).
        - [x] `GET /v1/concepts/parse` — Parse path and return ConceptPath info.
    - **Crate:** `stemedb-api`

- [x] **5D.8 Battery Tests**: Validate concept hierarchy end-to-end. ✅
    - **Tests:**
        - [x] Battery 8 (7 tests): ConceptPath parsing, round-trip, prefix matching, source class inference.
        - [x] Battery 9 (8 tests): Alias resolution, transitive resolution, cycle detection, bidirectional lookup, delete, suggestions.
    - **Crate:** `stemedb-query/tests/battery_pre_sentinel.rs`

### Phase 6: The Mesh (Distributed Writes)
*Goal: Multi-node cluster with CRDT replication and Raft coordination. The endgame.*

> **Research:** [docs/research/distributed-write-path.md](docs/research/distributed-write-path.md)
> **Agent:** `distributed-systems-engineer`
> **Key Insight:** Episteme's append-only model eliminates ~75% of CockroachDB complexity. Assertions are a G-Set CRDT. Votes are G-Counters. No distributed transactions needed.

#### 6A. CRDT Foundation (Single-Node Validation)

- [ ] **6A.1 Integrate CRDT Crate**: Wrap assertion storage in G-Set semantics.
    - **Tasks:**
        - [ ] Add `crdts = "7.4"` dependency to `stemedb-storage`.
        - [ ] Implement `CrdtAssertionStore` wrapping assertions as `GSet<Hash>`.
        - [ ] Implement `CrdtVoteStore` wrapping votes as `GCounter<(Hash, [u8; 32])>`.
        - [ ] Property tests: commutativity (`merge(A,B) == merge(B,A)`), associativity, idempotence.
        - [ ] Verify existing tests still pass with CRDT wrapper.

- [ ] **6A.2 Hybrid Logical Clocks**: Add causal ordering to supersessions.
    - **Tasks:**
        - [ ] Add `uhlc = "0.7"` dependency to `stemedb-core`.
        - [ ] Replace `timestamp: u64` in `Supersession` with `hlc_timestamp: uhlc::Timestamp`.
        - [ ] Update `IngestWorker` to generate HLC timestamps.
        - [ ] Update `EpochAwareLens` to use HLC comparison for ordering.
        - [ ] Test: concurrent supersessions from different nodes converge to same order.

- [ ] **6A.3 Merkle Tree Over Assertions**: Efficient diff detection.
    - **Tasks:**
        - [ ] Implement `MerkleTree` over assertion hashes using BLAKE3.
        - [ ] Incremental update: insert new hash, recompute affected path.
        - [ ] Root comparison: O(1) check if two nodes have same assertions.
        - [ ] Recursive diff: O(log N) to find divergent subtrees.
        - [ ] Serialize tree state for exchange over network.

#### 6B. Two-Node Replication (Proof of Concept)

- [ ] **6B.1 RPC Layer**: Node-to-node communication.
    - **Tasks:**
        - [ ] Create `stemedb-rpc` crate.
        - [ ] Define protobuf messages: `SyncRequest`, `SyncResponse`, `FetchAssertions`, `GossipBroadcast`.
        - [ ] Implement gRPC services with `tonic`.
        - [ ] Connection pooling and retry with exponential backoff.
    - **Crates:** `tonic = "0.12"`, `prost = "0.13"`

- [ ] **6B.2 Gossip Broadcast**: Push new assertions to peers.
    - **Tasks:**
        - [ ] On write: gossip new assertion hash + data to N peers (fanout = 3-5).
        - [ ] Peers merge into local G-Set.
        - [ ] Deduplicate: content-addressed hashes mean receiving same assertion twice is a no-op.
        - [ ] Track gossip metrics: `gossip_messages_sent`, `gossip_duplicates_received`.

- [ ] **6B.3 Merkle Anti-Entropy Sync**: Background convergence.
    - **Tasks:**
        - [ ] Every 60 seconds per peer: exchange Merkle roots.
        - [ ] If roots differ: recursive diff to find missing hashes.
        - [ ] Fetch missing assertions from peer.
        - [ ] Merge into local store + trigger MV recompute.
        - [ ] Track: `sync_lag_seconds`, `merkle_diff_size`, `convergence_latency_p99`.

- [ ] **6B.4 Integration Test: Two-Node Convergence**:
    - [ ] Write assertion to Node A → appears on Node B within 5 seconds.
    - [ ] Write to Node A during partition → Node B converges after healing.
    - [ ] Concurrent writes to both nodes → both converge to same state.

#### 6C. Multi-Node Cluster

- [ ] **6C.1 Cluster Membership (SWIM Gossip)**: Node discovery and failure detection.
    - **Tasks:**
        - [ ] Add `memberlist = "0.4"` dependency.
        - [ ] Implement `ClusterMembership` with SWIM protocol.
        - [ ] Seed-node based discovery (bootstrap nodes in config).
        - [ ] Failure detection: ping, indirect probe, suspicion.
        - [ ] Membership change events trigger anti-entropy with new peers.
    - **Crate:** `memberlist = "0.4"`

- [ ] **6C.2 Subject-Prefix Range Sharding**: Distribute data across nodes.
    - **Tasks:**
        - [ ] Implement `RangeRouter`: map subject → range → node.
        - [ ] Range descriptor: start key, end key, replica nodes.
        - [ ] Automatic range split when size exceeds 64MB threshold.
        - [ ] Range merge when adjacent ranges shrink below 20MB.
        - [ ] Meta-range: store range descriptors, gossip to all nodes.

- [ ] **6C.3 Raft for MV Coordination (Optional)**: Deterministic MV computation.
    - **Problem:** Without ordering, different nodes may compute different MV winners during convergence.
    - **Solution:** Lightweight Raft group per subject-range for MV coordinator election.
    - **Tasks:**
        - [ ] Add `openraft = "0.10"` dependency.
        - [ ] Implement `RaftLogStorage` backed by fjall.
        - [ ] Implement `RaftStateMachine` delegating to `Materializer`.
        - [ ] Leader coordinates MV recomputation order.
        - [ ] Followers serve reads from local MVs.
    - **Note:** This is optional. Without Raft, MVs are eventually consistent (converge once assertions sync). With Raft, MVs are strongly consistent per range.
    - **Crate:** `openraft = "0.10"`

- [ ] **6C.4 Gateway**: Stateless request routing.
    - **Tasks:**
        - [ ] Implement `Gateway` HTTP service (axum).
        - [ ] Route writes by subject → range → node.
        - [ ] Route reads to nearest replica.
        - [ ] Health checking and failover.
        - [ ] Load balancing across replicas.

#### 6D. Consistency Guarantees

| Property | Guarantee | Mechanism |
|----------|-----------|-----------|
| **Convergence** | Eventually consistent | G-Set merge (CRDT) |
| **Causality** | Supersessions ordered | HLC timestamps |
| **Partition Tolerance** | Writes never blocked | Any node accepts via CRDT |
| **Availability** | Reads/writes always succeed | Every node is master for CRDTs |
| **Durability** | WAL + fsync per node | Existing WAL infra |
| **Conflict Resolution** | Deterministic | Lens algorithms (same inputs → same output) |

### Phase 7: The Shield (Trust at Scale)
*Goal: Defend against spam, Sybil attacks, and knowledge poisoning when open to millions of agents.*

> **Key Insight:** Open agent access requires layered defense. PoW for admission, EigenTrust for reputation, circuit breakers for misbehavior, quarantine for suspicious content.

#### 7A. Admission Control

- [ ] **7A.1 Proof-of-Work Admission**: BLAKE3 hashcash for new agents.
    - New agents (trust < 0.3) must solve PoW puzzle before first N assertions accepted.
    - Graduated difficulty: first 10 assertions = 16 sec, 11-50 = 1 sec, 50+ or trust > 0.6 = none.
    - Puzzle: `BLAKE3(nonce || agent_id || timestamp)` must have `difficulty` leading zero bits.

- [ ] **7A.2 Graduated Trust Tiers**: Privilege escalation based on reputation.
    - Untrusted (0.0-0.3): Quarantine mode, assertions hidden by default, 0.1x quota.
    - Limited (0.3-0.5): Low quota, PoW required, 0.5x quota.
    - Verified (0.5-0.7): Standard quota, normal privileges.
    - Trusted (0.7-0.9): 2x quota, skip PoW.
    - Authority (0.9-1.0): 10x quota, no limits.

#### 7B. EigenTrust

- [ ] **7B.1 Trust Graph Store**: Store direct trust relationships for propagation.
    - Key pattern: `TG:{agent_a}:{agent_b}` → trust weight (0.0-1.0).
    - Methods: `add_trust_edge()`, `get_trusted_by()`, `compute_eigentrust()`.

- [ ] **7B.2 EigenTrust Computation**: Global trust via power iteration (daily batch).
    - Formula: `T = (1-α)CT + αP` where C = normalized trust matrix, P = seed trust, α = 0.1.
    - Convergence: 10-20 iterations for 10K agents.
    - Sybil resistance: isolated rings have low trust unless connected to real agents.
    - Crates: `petgraph` (graph structures), `nalgebra` (linear algebra).

- [ ] **7B.3 Domain-Specific Trust**: Per-predicate-namespace reputation.
    - Agent may be expert in medicine but novice in astronomy.
    - Track accuracy by predicate namespace.
    - Lens can weight by domain trust.

#### 7C. Content Defense

- [ ] **7C.1 MinHash Deduplication**: Near-duplicate detection with LSH bucketing.
    - Compute MinHash signature for `{subject}:{predicate}` pairs.
    - LSH buckets for O(1) average-case lookup.
    - Bloom filter pre-check for fast "definitely not duplicate" path.
    - Threshold: 0.9 Jaccard similarity = duplicate.

- [ ] **7C.2 Content Quality Scoring**: Heuristic-based spam detection.
    - Shannon entropy check (high entropy = likely random noise).
    - Minimum subject/predicate length.
    - Structured data bonus (JSON objects, numbers, URLs).
    - Untrusted agent + high confidence = suspicious.

- [ ] **7C.3 Quarantine Store**: Suspicious assertions held for review.
    - Key pattern: `QUAR:{hash}` → assertion data.
    - Quarantined assertions NOT indexed (invisible to queries).
    - Triggers: quality < 0.4, duplicate, untrusted high-confidence.
    - Admin API: `GET /v1/admin/quarantine`, `POST /v1/admin/quarantine/{hash}/approve`.

#### 7D. Circuit Breakers

- [ ] **7D.1 Per-Agent Circuit Breakers**: Ban misbehaving agents temporarily.
    - States: Closed (normal), Open (banned), HalfOpen (testing recovery).
    - 5 failures → Open for 30 seconds → HalfOpen → 1 success → Closed.
    - Metrics: `circuit_breaker_state`, `circuit_breaker_trips_total`.
    - Crate: `governor` for GCRA rate limiting.

### Phase 8: The Swarm (Production Cluster)
*Goal: Production-ready distributed deployment with chaos testing and observability.*

#### 8A. Chaos Testing

- [ ] **8A.1 Partition Testing**: Verify convergence after network partitions.
    - 5-node cluster, kill 2 nodes, verify remaining nodes converge.
    - Network partition between groups, verify both sides accept writes, verify convergence after healing.
    - Message reordering and duplication tests.

- [ ] **8A.2 Jepsen-Style Consistency Testing**: Formal verification.
    - Linearizability checks for Raft-coordinated operations.
    - Eventual consistency checks for CRDT-replicated data.
    - Clock skew injection (verify HLC handles drift).

#### 8B. Observability

- [ ] **8B.1 Distributed Metrics**: Per-node, per-range, per-agent metrics.
    - `sync_lag_seconds{peer}`, `merkle_diff_size{peer}`, `convergence_latency_p99`.
    - `raft_leader_changes{range}`, `raft_commit_latency{range}`.
    - `assertions_total{node}`, `writes_per_second{node}`.
    - Crate: `metrics` + `metrics-exporter-prometheus`.

- [ ] **8B.2 Admin Dashboard**: Cluster health visibility.
    - `GET /v1/admin/cluster` → node list, range assignments, leader locations.
    - `GET /v1/admin/ranges` → range sizes, split/merge history.
    - `POST /v1/admin/sync` → force anti-entropy sync.

#### 8C. Production Hardening

- [ ] **8C.1 Snapshot/Restore**: Fast replica bootstrap.
    - Serialize full node state as snapshot.
    - New nodes join by restoring snapshot + replaying recent WAL.
    - Faster than full Merkle sync for new nodes.

- [ ] **8C.2 Backpressure**: Don't overwhelm slow nodes.
    - Track per-peer sync queue depth.
    - Throttle gossip to slow peers.
    - Alert when peer is consistently behind.

- [ ] **8C.3 Geo-Distribution**: Multi-region deployment.
    - Regional clusters with CRDT federation between regions.
    - Lazy cross-region sync (background, low priority).
    - Locality-aware reads (query nearest replica).
    - Regional compliance (GDPR data residency).

---

## Tracking

### Active Tasks
*   [x] **Phase 3 The Pilot**: Consumer Health vertical integration. ✅ COMPLETE
*   [x] **Phase 4 The Hive**: Trust & Scale + Extension Primitives. ✅ COMPLETE
*   [x] **Phase 5 The Forge**: Foundation hardening — replace sled, fix WAL, persist indices. ✅ COMPLETE
    *   [x] **5A**: Replace sled with redb/fjall (HybridStore), key layout redesign. ✅ COMPLETE
    *   [x] **5B**: WAL hardening — CRC32C, crash recovery, group commit, log rotation. ✅ COMPLETE
    *   [x] **5C**: Index persistence — vector hot/cold, visual checkpoint. ✅ COMPLETE
    *   [x] **5D**: Concept hierarchy — ConceptPath, AliasStore, scheme-based inference. ✅ COMPLETE

### Next Up
*   **Phase 6**: Distributed writes via CRDT replication + Raft coordination.
*   **Phase 7A-7B** (Extension blocker): PoW admission + EigenTrust for Phase 2 extension launch.

### App Layer (External)
*   **Browser Extension Phase 1** (Read-Only Overlay) -> All DB dependencies complete. Extension is app layer.
*   **Browser Extension Phase 2** (Active Layer / Vote-to-See) -> Blocked by Phase 7A-7B (Sybil defense).
*   **The Simulator** (Training Data Pipeline) -> App layer, consumes Episteme API.
*   **The Super Curator** (Reviewer Agent swarm) -> App layer.
*   **Background Gardener** (Cluster detection, signal processing) -> App layer.
*   **Agent Wallet** (Key management sidecar) -> App layer.

### Recently Completed
*   [x] **Phase 5D Concept Hierarchy**: Hierarchical subjects with cross-scheme alias resolution.
    *   `ConceptPath` struct with scheme://segments/leaf format, backward-compatible parsing.
    *   `SourceScheme` enum mapping schemes to source tiers (rfc→Regulatory, code→Expert, etc.).
    *   `AliasStore` trait with transitive resolution and cycle detection.
    *   API: `POST/DELETE /v1/concepts/alias`, `GET /v1/concepts/resolve|aliases|suggest|parse`.
    *   Battery 8 (7 tests) + Battery 9 (8 tests).
*   [x] **Phase 5C Index Persistence**: Vector hot/cold tiering, visual checkpoint.
*   [x] **Phase 5B WAL Hardening**: CRC32C checksums, crash recovery, group commit, log rotation.
*   [x] **Gold Standard Verification** (4.7): Sybil defense via proof of knowledge.
    *   `GoldStandard` struct with rkyv serialization, `GoldStandardStore` trait + implementation.
    *   `TrustAdjustment` enum: Rewarded(+0.05), Penalized(-0.1), AlreadyVerified.
    *   Anti-gaming: agents can only verify each gold standard once (dedup markers).
    *   API: `POST/GET/DELETE /v1/admin/gold-standards`, `POST /v1/admin/verify-agent`.
    *   21 trust rank tests including 4 new verification tests.
*   [x] **Escalation Triggers** (4.6): Active safety system for high-conflict assertions.
    *   `EscalationPolicy` with configurable conflict_score thresholds and predicate matching.
    *   `EscalationEvent` (content-addressed BLAKE3 ID) written by Materializer when policies fire.
    *   `EscalationStore` at `ESC:{timestamp_nanos}:{id_hex}` with resolve workflow.
    *   `GET /v1/admin/escalations`, `POST /v1/admin/escalations/{id}/resolve`.
*   [x] **Conflict Score Filtering** (4.5): Query-time filtering by conflict score.
    *   `min_conflict_score` and `max_conflict_score` on Query + QueryParams.
    *   Fast-path MV filtering with 0.0-1.0 validation.
    *   13 engine tests covering thresholds, boundaries, ranges, combinations.
*   [x] **Vote Provenance Witness** (4.4): Transform votes into cryptographic witnesses.
    *   `source_url: Option<String>` and `observed_context: Option<Vec<u8>>` on Vote.
    *   Input validation: URL max 2048 chars, context max 64KB.
    *   Backward compatible with existing votes.
*   [x] **"Since" Parameter** (4.1): Change tracking for returning consumers.
    *   `since: Option<u64>` on Query for incremental sync.
    *   MV Changelog at `MVC:{subject}:{predicate}:{timestamp_nanos}` with nanosecond precision.
    *   `ChangeEntry` struct with `previous_winner_hash`, `new_winner_hash`, `lens_name`.
    *   `fetch_changes_since()` in QueryEngine with timestamp filtering.
    *   `changes_since: Option<Vec<ChangeEntryDto>>` on QueryResponse.
    *   6 tests covering changelog creation, fetching, and fast path bypass.
*   [x] **Batch TrustRank Decay API** (4.3): Admin endpoint for scheduled trust decay.
    *   `POST /v1/admin/decay-trust-ranks` with optional `now` and `half_life_seconds`.
    *   Returns `decayed_count`, `timestamp_used`, `half_life_used`, `status`.
    *   3 integration tests.

### Recently Completed
*   [x] **Source Metadata Indexing** (4.2): Index key source metadata fields for filtered queries.
    *   New module: `crates/stemedb-storage/src/source_metadata_index.rs`.
    *   Indexed fields: `journal`, `doi`, `platform`, `study_design`.
    *   Key pattern: `SMV:{field}:{value}` -> `Vec<Hash>` (case-insensitive).
    *   Query filters: `?source_journal=NEJM&source_platform=PubMed`.
    *   AND semantics for multiple metadata filters.
    *   18 unit tests covering indexing and query filtering.
*   [x] **Source Document Storage** (3F.1): Provenance lookup for 100% citation recall.
    *   `POST /v1/source` stores source documents by BLAKE3 content hash.
    *   `GET /v1/provenance/{hash}` retrieves source documents.
    *   Content-addressed storage at `SRC:{hash}` keys.
    *   Base64 encoding, 10MB limit, idempotent uploads.
    *   5 unit tests covering happy path and error cases.
*   [x] **Epoch Cascade Logic** (3D.1): O(1) supersession lookup via pre-computed markers.
    *   `write_supersession_cascade()` writes `SUPERSEDED:` markers for full transitive closure at ingest time.
    *   `is_epoch_superseded()` uses O(1) marker lookup instead of chain walking.
    *   Cycle detection and max depth guard (100 levels).
    *   5 tests covering markers, transitive closure, cycles, and marker-based filtering.
*   [x] **Semantic Decay** (3B.2): Confidence half-life at query time.
    *   `decay_halflife: Option<u64>` and `source_class_decay: bool` on Query.
    *   New `decay.rs` module with `apply_decay()` and `apply_source_class_decay()`.
    *   Formula: `effective_confidence = confidence * 2^(-(age / halflife))`.
    *   Tier-specific decay: Regulatory=none, Clinical=2yr, Anecdotal=30d.
    *   11 unit tests + 1 E2E integration test.
*   [x] **Layered Consensus Lens** (3C.2): Per-source-class consensus with tier-by-tier visibility.
    *   `LayeredConsensusLens` with `LayeredLens` trait.
    *   `TierResolution` and `LayeredResolution` types.
    *   `GET /v1/layered?subject=X&predicate=Y` endpoint.
    *   Cross-tier conflict score using Shannon entropy.
    *   10 comprehensive tests.
*   [x] **Time-Travel Engine** (3B.1): `as_of` parameter for historical queries.
    *   `as_of: Option<u64>` field on `Query` for querying historical state.
    *   Bypasses fast path (MVs reflect current state).
    *   `Query::matches()` filters by `assertion.timestamp <= as_of`.
    *   6 tests covering edge cases.
*   [x] **Rich Source Metadata** (3A.3): Structured provenance beyond `source_hash`.
    *   `source_metadata: Option<Vec<u8>>` field on `Assertion`.
    *   `Vec<u8>` for rkyv zero-copy compatibility, callers handle JSON encoding.
    *   Builder methods: `.source_metadata_json()` and `.source_metadata()`.
    *   API exposes as `Option<String>` with defensive UTF-8 handling.
    *   2 serialization tests.
*   [x] **Conflict Score on Resolution** (3A.2): Numeric disagreement metric across all lenses.
    *   `conflict_score: f32` field on `Resolution` (0.0 = unanimous, 1.0 = max conflict).
    *   `compute_conflict_score()` utility using normalized variance.
    *   Updated all 5 lens implementations to compute and propagate conflict score.
    *   `MaterializedView` now stores conflict score.
    *   API `QueryResponse` exposes `conflict_score` and `resolution_confidence` when lens is applied.
    *   7 unit tests including NaN handling.
*   [x] **SkepticLens + SkepticView** (3C.1): "Trust but Verify" conflict analysis that surfaces all claims with conflict scores.
    *   `AnalysisLens` trait for lenses that map conflict instead of resolving it.
    *   `SkepticLens` using normalized Shannon entropy for conflict scoring.
    *   `SkepticResolver` + `SkepticView` in stemedb-query.
    *   `GET /v1/skeptic?subject=X&predicate=Y` API endpoint.
    *   Types: `ResolutionStatus`, `ConflictAnalysis`, `ClaimSummary`, `SourceSummary`, `AgentSummary`.
*   [x] **Source-Class Field** (3A.1): 6-tier `SourceClass` enum with authority weighting and decay rates.
    *   `SourceClass` enum: Regulatory, Clinical, Observational, Expert, Community, Anecdotal.
    *   `tier()`, `default_decay_days()`, `authority_weight()` methods.
    *   Field on Assertion struct with full serialization support.
*   [x] **The Meter**: Token bucket quota system with MeterLayer middleware (10K tokens/agent/hour).
*   [x] **Query Audit Trail**: Every query logged with provenance at `AUD:{query_id}`. `X-Agent-Id` header for attribution.
*   [x] **Event-Driven Materialization**: `run_notified()` + IngestWorker Notify integration.
*   [x] **Fast-Path MV Lookup**: `QueryEngine::try_fast_path()` for O(1) reads.
*   [x] **Materializer**: Background worker for O(1) MV reads via `AsyncLens`.
*   [x] **VoteAwareConsensusLens**: Real vote-based consensus resolution.
*   [x] **Compound SP Index**: O(1) subject+predicate lookups.
*   [x] **TrustRank System**: Agent reputation with decay and learning loop.
*   [x] **API Surface**: axum HTTP server with 7 endpoints + OpenAPI docs.

### Research Documents
*   [docs/research/wal-crash-recovery-research.md](docs/research/wal-crash-recovery-research.md) — WAL patterns from CockroachDB, TiKV, FoundationDB, SQLite.
*   [docs/research/distributed-write-path.md](docs/research/distributed-write-path.md) — Spanner/CockroachDB-style distributed writes adapted for append-only model.

### Key Architectural Decisions
*   **sled → redb/fjall**: sled is abandoned. HybridStore routes by key prefix: redb for reads, fjall for writes. ✅ COMPLETE
*   **Raft log = WAL**: TiKV eliminated duplicate WAL in v5.4. We should too.
*   **CRDT for data, Raft for coordination**: Assertions are a G-Set CRDT (merge = set union). Only cluster metadata needs Raft.
*   **Subject-prefix ranges**: Co-locate all data for a subject on one shard. Split hot subjects via range split.
*   **HLC over TrueTime**: Hybrid Logical Clocks work on commodity hardware. No GPS/atomic clocks needed.
*   **AP model**: Writes never blocked during partitions. Eventual consistency via CRDT convergence.

### Blockers
*   **Phase 5**: ✅ COMPLETE — All foundation hardening done.
*   **Phase 6**: Unblocked. Can start distributed writes.
*   **Phase 7**: Blocked by Phase 6 (trust at scale requires distributed infra).
*   **Phase 8**: Blocked by Phase 6 + 7 (chaos testing requires working cluster).

---

## Dependency Graph

```
Phase 2.5 (Hardening)          Phase 3 (The Pilot)                    Phase 4 (The Hive)
========================       ========================               ==================

[2.1 MV Staleness]  ---------> [3B.1 Time-Travel] ✅ --+
                                       |                |
[2.2 Confidence Rename] -----> (API clarity for all)    +----------> [4.1 "Since" Param] ✅
                                                        |
[2.3 EpochAwareLens] --------> [3D.1 Epoch Cascade] ✅ |----------> Invalidation Cascades pillar
                                                        |
[2.4 Visual Hash Query] -----> [3E.2 Visual Hash Index] ✅
                                                        |
[2.6 E2E Integration] -------> (pipeline confidence)    |
                                                        |
                               [3A.1 Source-Class] ✅ --+----------> [3C.2 Layered Consensus] ✅
                                       |                             [3B.2 Semantic Decay] ✅
                                       +-----------------------------[4.2 Metadata Indexing] ✅
                                                        |
                               [3A.2 Conflict Score] ✅ --> (enhance Resolution)
                                                        |
                               [3A.3 Source Metadata] ✅ --> [4.2 Metadata Indexing] ✅
                                                        |
                               [3C.1 Skeptic Lens] ✅    (standalone, COMPLETE)
                               [3C.3 Constraints Lens] ✅ (standalone, COMPLETE)
                               [3E.1 Vector Search] ✅    (standalone, COMPLETE)
                               [3E.2 Visual Hash Index] ✅ (standalone, COMPLETE)
                               [3F.1 Provenance] ✅       (standalone, COMPLETE)
```

### Critical Path for Consumer Health Demo

```
[3A.1 Source-Class] ✅ --> [3A.2 Conflict Score] ✅ --> [3C.2 Layered Consensus] ✅
                                                              |
                                                              +----> CONSUMER HEALTH MVP ✅
                                                              |
[3B.1 Time-Travel] ✅ ---------------------------------------+
                                                              |
[3A.3 Source Metadata] ✅ -----------------------------------+
                                                              |
[3C.1 Skeptic Lens] ✅ --------------------------------------+
```

### Critical Path for Financial DD Demo

```
[3A.2 Conflict Score] ✅ --> [3C.1 Skeptic Lens] ✅ ---+
                                                         |
[3B.1 Time-Travel] ✅ ----------------------------------+----> FINANCIAL DD MVP
                                                         |
[2.3 EpochAwareLens] --> [3D.1 Epoch Cascade] ✅ -------+
                                                         |
[3B.2 Semantic Decay] ✅ -------------------------------+
```

### Critical Path for Agile Agent Team Demo

```
[3C.3 Constraints Lens] (standalone) ------+
                                            |
[3B.1 Time-Travel] ✅ --------------------+----> AGENT TEAM MVP
                                            |
[2.3 EpochAwareLens] ✅ ------------------+
                                            |
[Query Audit (Phase 2)] ✅ ----------------+
```

### Critical Path for Browser Extension

```
Phase 3 (Data Foundation)          Phase 4 (Extension Primitives)       Extension Product
=========================          ==============================       =================

[3A.1 Source-Class] ✅ ──────────> [4.5 Conflict Filtering] ✅ ──┐
                                                                   |
[3A.2 Conflict Score] ✅ ─────────────────────────────────────────┤
                                                                   |
[3C.1 Skeptic Lens] ✅ ──────────────────────────────────────────-┤
                                                                   ├──> PHASE 1: Read-Only Overlay
[3B.2 Semantic Decay] ✅ ────────────────────────────────────────-┤     (Benign Layer)
                                                                   |
[3C.2 Layered Consensus] ✅ ─────────────────────────────────────-┘

[Phase 2 Vote System] ✅ ────────> [4.4 Vote Provenance] ✅ ─────┐
                                                                   |
[TrustRank Engine] ✅ ───────────> [4.7 Gold Standards] ✅ ───────┤
                                                                   ├──> PHASE 2: Active Layer
[3A.2 Conflict Score] ✅ ────────> [4.6 Escalation Triggers] ✅ ──┤     (Vote to See)
                                                                   |
                                   [7A PoW Admission] ─────────────┤
                                   [7B EigenTrust] ────────────────┘
```

**Phase 1 (Read-Only)** requires: Source tiers, conflict scores, conflict filtering, skeptic lens, decay, layered consensus. **All complete.**

**Phase 2 (Active)** requires: Vote provenance, gold standards, escalation triggers (all complete), PLUS Phase 7 Sybil defense (PoW, EigenTrust — not started).

### Critical Path to Distributed Cluster

```
Phase 5 (The Forge)                 Phase 6 (The Mesh)                   Phase 7+8
=======================             =======================              ==================

[5A.1 Replace sled ✅] ───────────> [6A.1 CRDT Foundation] ──┐
                                            |                 |
[5A.2 Key Layout] ───────────────> [6C.2 Range Sharding] ──> |
                                                              |
[5B.1 CRC32C Checksums] ──┐                                  |
[5B.2 Crash Recovery] ────┼──────> [6B.1 RPC Layer] ─────────┤
[5B.3 Group Commit] ──────┘                |                  |
                                           v                  |
[5C.1 Persistent Vector] ─────── (independent, no blocker)    |
[5C.2 Persistent Visual] ─────── (independent, no blocker)    |
                                                              |
                                   [6A.2 HLC Timestamps] ────┤
                                   [6A.3 Merkle Tree] ───────┤
                                           |                  |
                                           v                  v
                                   [6B.2 Gossip] ──> [6B.3 Anti-Entropy] ──> [6B.4 Two-Node Test]
                                                              |
                                                              v
                                   [6C.1 SWIM Membership] ──> [6C.3 Raft MV Coord]
                                   [6C.4 Gateway] ──────────> │
                                                              v
                                                    DISTRIBUTED CLUSTER
                                                              |
                                                    [7A PoW Admission] ──┐
                                                    [7B EigenTrust] ─────┤──> THE SHIELD
                                                    [7C Content Defense] ┤
                                                    [7D Circuit Breakers]┘
                                                              |
                                                    [8A Chaos Testing] ──┐
                                                    [8B Observability] ──┤──> THE SWARM
                                                    [8C Geo-Distribution]┘
```

### New Crates (Phases 5-8)

```
stemedb-rpc      (Phase 6B)  ── gRPC services for node-to-node communication
stemedb-cluster  (Phase 6C)  ── Cluster membership, range routing, gateway
stemedb-sync     (Phase 6B)  ── Merkle sync, gossip broadcast, anti-entropy
```
