stemedb/applications/aphoria/roadmap.md

# Aphoria Roadmap

---

## Phase 0: StemeDB Foundation ✅

> **Tracked in:** [roadmap.md § 5D. Concept Hierarchy](../../roadmap.md)

Changes to the core database that Aphoria depends on. Shipped as **Phase 5D** of the main StemeDB roadmap.

| Aphoria Phase 0 | StemeDB Phase 5D | Status |
|-----------------|------------------|--------|
| 0.1 ConceptPath Type | 5D.1 ConceptPath Type | ✅ |
| 0.2 ConceptPath in Assertion | (implicit in 5D.1) | ✅ |
| 0.3 Hierarchical Index | 5D.4 Hierarchical Query | ✅ |
| 0.4 Alias Store | 5D.3 Alias Store + 5D.5 Alias Resolution | ✅ |
| 0.5 Source Class Inference | 5D.6 Source Class Inference | ✅ |
| 0.6 Concept API Endpoints | 5D.7 Concept API Endpoints | ✅ |

**Spec:** [docs/specs/concept-hierarchy.md](../../docs/specs/concept-hierarchy.md)

---

## Phase 2: CLI Core ✅

> Phase 2 was built before Phase 1 (authoritative corpus expansion). The CLI pipeline works end-to-end with a bootstrapped corpus of 11 hardcoded assertions covering TLS, JWT, CORS, secrets, and rate limiting.

| Task | Status |
|------|--------|
| 2.1 Project Walker | ✅ `walker/mod.rs`, `walker/path_mapper.rs`, `walker/language.rs` |
| 2.2 Extractors (7) | ✅ `tls_verify`, `jwt_config`, `hardcoded_secrets`, `timeout_config`, `dep_versions`, `cors_config`, `rate_limit` |
| 2.3 Ingestion Bridge | ✅ `bridge.rs` — BLAKE3 hashing, Ed25519 signing, claim→assertion conversion |
| 2.4 Conflict Query | ✅ `episteme.rs` — LocalEpisteme with check_conflicts() |
| 2.5 Report Output | ✅ `report/` — table (comfy-table), JSON, SARIF 2.1.0, markdown |
| 2.6 Acknowledge Command | ✅ `lib.rs` acknowledge() |
| Baseline & Diff | ✅ `lib.rs` set_baseline(), show_diff() |
| Status Command | ✅ `lib.rs` show_status() |

118 tests pass. Clippy and fmt clean.

---

## Phase 2A: Concept Matching ✅

> **Status:** Complete. Tail-path matching (2A.1), alias-aware queries (2A.2), and auto-alias creation (2A.3) all implemented.

### 2A.1 Leaf-Based Concept Matching (Aphoria-side fix) ✅

Implemented in `episteme.rs` via `ConceptIndex`:
- `make_key(subject, predicate)` extracts tail 2 path segments + predicate
- `build(assertions)` creates in-memory index keyed by tail path
- `lookup(subject, predicate)` finds matching authoritative assertions
- `check_conflicts()` uses `ConceptIndex` instead of `QueryEngine` for cross-scheme matching

Integration tests prove TLS and JWT conflicts are detected correctly.

### 2A.2 Alias Resolution in QueryEngine (StemeDB-side fix) ✅

Wired `AliasStore` into `QueryEngine.execute()`:
- Added `resolve_aliases: bool` field to `Query` (defaults to `false`)
- Added `alias_store: Option<Arc<dyn AliasStore>>` to `QueryEngine`
- Added `.with_alias_store()` builder method
- When `resolve_aliases: true`, expands subject via `AliasStore.resolve_all()` before index lookup
- Added `fetch_by_subjects()` and `fetch_by_subjects_predicate()` for multi-subject deduplication
- Modified `Query.matches()` to skip subject filtering when aliases are resolved
- Skips fast path (MV lookup) when `resolve_aliases: true`
- Gracefully degrades when no alias store is configured

7 unit tests in `engine/tests/alias_resolution.rs`. This is the architecturally correct long-term fix that complements leaf matching.

### 2A.3 Auto-Alias Creation ✅

When Aphoria ingests authoritative assertions and code claims that share leaf names, automatically create aliases:
- `code://rust/myapp/tls/cert_verification` ↔ `rfc://5246/tls/cert_verification`
- `code://rust/myapp/auth/jwt/audience_validation` ↔ `rfc://7519/jwt/audience_validation`

This bridges 2A.1 (leaf matching) with 2A.2 (alias resolution) — leaf matching identifies candidates, aliases persist the relationship.

**Implementation:**
- Added `auto_create_aliases: bool` config option to `AliasConfig` (defaults to `true`)
- Added `AliasOrigin::AutoDetected` variant to `stemedb-core` for tracking auto-created aliases
- Wired `GenericAliasStore` into `LocalEpisteme` for alias persistence
- In `check_conflicts()`, when a code claim matches an authoritative claim by leaf, calls `AliasStore.set_alias()` to persist the relationship with `AliasOrigin::AutoDetected`
- Alias creation is idempotent (skips if alias already exists)
- 4 unit tests verify: alias creation on conflict, no creation when disabled, correct origin, idempotency

---

## Phase 1: Authoritative Corpus Expansion ✅

> Expanded from 11 hardcoded assertions to a pluggable corpus system with RFC, OWASP, and Vendor sources.

### Architecture

```
┌─────────────────────────────────────────────────────────────────┐
│                     aphoria corpus build                         │
│                                                                  │
│  ┌──────────────┐  ┌──────────────┐  ┌───────────────────────┐  │
│  │ RFC Ingester │  │ OWASP        │  │ Vendor Bootstrapper   │  │
│  │ (Tier 0)     │  │ Ingester     │  │ (Tier 2)              │  │
│  │              │  │ (Tier 1)     │  │                       │  │
│  └──────┬───────┘  └──────┬───────┘  └───────────┬───────────┘  │
│         │                 │                      │              │
│         └─────────────────┼──────────────────────┘              │
│                           ▼                                     │
│                  ┌─────────────────┐                            │
│                  │ CorpusRegistry  │                            │
│                  └────────┬────────┘                            │
│                           ▼                                     │
│                  ┌─────────────────┐                            │
│                  │ LocalEpisteme   │                            │
│                  │ ingest_         │                            │
│                  │ authoritative() │                            │
│                  └─────────────────┘                            │
└─────────────────────────────────────────────────────────────────┘
```

### 1.1 CorpusBuilder Trait ✅

| Task | Status |
|------|--------|
| `CorpusBuilder` trait | ✅ `corpus/mod.rs` — name, scheme, default_tier, build, requires_network |
| `CorpusRegistry` | ✅ Manages multiple builders, build_all(), list_builders() |
| `CorpusBuildResult` | ✅ Stats per builder, total assertions, success/fail/skip counts |

### 1.2 RFC Ingester ✅

| Task | Status |
|------|--------|
| `RfcCorpusBuilder` | ✅ `corpus/rfc.rs` |
| HTTP fetching | ✅ Via `ureq`, cached to `~/.cache/aphoria/rfc-cache/` |
| RFC 2119 keyword parsing | ✅ MUST, MUST NOT, SHOULD, SHALL extraction |
| RFC-specific parsers | ✅ JWT (7519), OAuth (6749), Bearer (6750), TLS 1.3 (8446), TLS BCP (7525), TOTP (6238), Basic Auth (7617), HTTP (9110) |
| Concept mapping | ✅ `rfc://{number}/{topic}` at Tier 0 (Regulatory) |

### 1.3 OWASP Ingester ✅

| Task | Status |
|------|--------|
| `OwaspCorpusBuilder` | ✅ `corpus/owasp.rs` |
| HTTP fetching | ✅ From GitHub raw content, cached to `~/.cache/aphoria/owasp-cache/` |
| Markdown parsing | ✅ MUST/SHOULD statements, section context |
| Cheat sheet parsers | ✅ Authentication, JWT, TLS, Secrets, Input Validation, Session, CSRF, Password Storage, HTTP Headers |
| Concept mapping | ✅ `owasp://cheatsheet/{topic}/{claim}` at Tier 1 (Clinical) |

### 1.4 Vendor Docs ✅

| Task | Status |
|------|--------|
| `VendorCorpusBuilder` | ✅ `corpus/vendor.rs` |
| PostgreSQL claims | ✅ pool_size, idle_timeout, ssl_mode |
| Redis claims | ✅ timeout, max_retries, tls |
| reqwest claims | ✅ cert_verification, connect_timeout, request_timeout |
| hyper claims | ✅ keep_alive_timeout, max_concurrent_streams |
| Go net/http claims | ✅ read_timeout, write_timeout, idle_timeout, min_tls_version |
| tokio-postgres claims | ✅ pool_size, ssl_mode |
| SQLx claims | ✅ max_connections, idle_timeout |
| Concept mapping | ✅ `vendor://{product}/{topic}/{claim}` at Tier 2 (Observational) |

### 1.5 Hardcoded Refactor ✅

| Task | Status |
|------|--------|
| `HardcodedCorpusBuilder` | ✅ `corpus/hardcoded.rs` — original 11 assertions |
| `create_authoritative_assertion()` | ✅ Made public in `episteme.rs` for corpus builders |

### 1.6 CLI Integration ✅

| Task | Status |
|------|--------|
| `aphoria corpus build` | ✅ Fetches and ingests from all sources |
| `--only rfc,owasp,vendor` | ✅ Filter to specific sources |
| `--offline` | ✅ Skip network-requiring sources |
| `--clear-cache` | ✅ Clear cache before building |
| `aphoria corpus list` | ✅ List available corpus sources |
| `CorpusConfig` | ✅ cache_dir, include_*, rfc_list options |

### 1.7 Error Handling ✅

| Task | Status |
|------|--------|
| `RfcFetch` error | ✅ Per-RFC fetch failures with context |
| `OwaspFetch` error | ✅ Per-cheat-sheet fetch failures with context |
| `CorpusBuild` error | ✅ General corpus build failures |
| Graceful degradation | ✅ Continue with other sources if one fails |

**Files:** `corpus/mod.rs`, `corpus/hardcoded.rs`, `corpus/rfc.rs`, `corpus/owasp.rs`, `corpus/vendor.rs`

**Tests:** 118 tests pass. Clippy and fmt clean.

---

## Phase 3: Skill Integration ✅

> Complete. Aphoria is now usable in Claude Code agent workflows.

### 3.1 Claude Code Skill ✅

| Task | Status |
|------|--------|
| `skill/SKILL.md` | ✅ Comprehensive skill definition with all commands |
| `/aphoria scan` | ✅ Scan project, show conflicts grouped by verdict |
| `/aphoria scan --fix` | ✅ Interactive fix workflow |
| `/aphoria ack` | ✅ Acknowledge conflicts as intentional |
| `/aphoria status` | ✅ Show status and baseline |
| `/aphoria diff` | ✅ Show changes since baseline |
| `/aphoria init` | ✅ Initialize Aphoria |
| `/aphoria baseline` | ✅ Set baseline |
| `skill/install.sh` | ✅ Install script for `~/.claude/skills/aphoria/` |

**Files:** `skill/SKILL.md`, `skill/install.sh`, `skill/hooks.json`

### 3.2 Agent Pre-Flight Hook ✅

| Task | Status |
|------|--------|
| `--exit-code` flag | ✅ Returns 2 for BLOCK, 1 for FLAG only, 0 for clean |
| `--strict` flag | ✅ Lower thresholds (FLAG at 0.3, BLOCK at 0.5) |
| Hook template | ✅ `skill/hooks.json` with PreCommit and PrePush examples |

**Usage:**
```json
{
  "hooks": {
    "PreCommit": [{"command": "aphoria scan --format sarif --exit-code"}],
    "PrePush": [{"command": "aphoria scan --strict --exit-code"}]
  }
}
```

### 3.3 Alias Suggestion Workflow ✅

Auto-alias creation is now automatic (Phase 2A.3). When Aphoria scans:
1. Tail-path matching finds authoritative assertions
2. Aliases are auto-created with `AliasOrigin::AutoDetected`
3. Future queries use the alias automatically

The skill documents the suggestion flow for manual alias management:
- **y (Accept)**: Creates alias
- **n (Reject)**: Records intentional difference
- **defer**: Flags for later review

---

## Phase 4: Pre-Commit Integration ⬜

> Depends on Phase 3 (skill validates the UX before hook automation).

### 4.1 Git Pre-Commit Hook ⬜

A git pre-commit hook that runs Aphoria before every commit:

```bash
#!/bin/sh
# .git/hooks/pre-commit

aphoria scan --exit-code --format table

if [ $? -eq 2 ]; then
    echo "BLOCKED: Fix conflicts before committing"
    exit 1
fi
```

Or using pre-commit framework (`.pre-commit-config.yaml`):

```yaml
repos:
  - repo: local
    hooks:
      - id: aphoria
        name: Aphoria Security Lint
        entry: aphoria scan --exit-code
        language: system
        pass_filenames: false
```

### 4.2 Baseline Mode ✅

Already implemented in Phase 2. For existing projects with many conflicts:

```
$ aphoria baseline
Baseline recorded: 12 existing conflicts frozen.
Future scans will only report new conflicts.
```

### 4.3 Diff-Only Scanning ⬜

Scan only changed files instead of the whole project:

```bash
# Scan only staged files
aphoria scan --staged

# Scan only files changed since baseline
aphoria scan --since-baseline
```

This makes pre-commit hooks fast even in large projects.

---

## Phase 5: Research Agent Loop ✅

> Research agent fills gaps in authoritative coverage by researching official documentation.

### 5.1 Gap Detection ✅

| Task | Status |
|------|--------|
| `Gap` struct | ✅ `research/gap_detector.rs` — concept_path, topic, predicate, source info |
| `detect_gaps()` | ✅ Compares claims against ConceptIndex, identifies missing coverage |
| Topic normalization | ✅ Extracts last 2 path segments for cross-scheme matching |
| Deduplication | ✅ Deduplicates gaps by topic+predicate key |

### 5.2 Gap Storage ✅

| Task | Status |
|------|--------|
| `GapRecord` | ✅ `research/gap_store.rs` — tracking metadata, project count, research status |
| `GapStore` | ✅ JSON-backed persistent storage with atomic saves |
| Project tracking | ✅ Records which projects reported each gap |
| Research eligibility | ✅ `is_eligible_for_research()` with threshold and cooldown |
| Gap pruning | ✅ `prune_old_gaps()` removes stale entries |

### 5.3 Quality Validation ✅

| Task | Status |
|------|--------|
| `QualityValidator` | ✅ `research/quality.rs` — validates researched claims |
| Source attribution | ✅ Checks for authoritative domains (rfc-editor, owasp, vendor docs) |
| Normative language | ✅ Verifies MUST/SHOULD/SHALL keywords present |
| Vague content detection | ✅ Rejects "it depends", "typically", etc. |
| Consistency scoring | ✅ Detects conflicting claims on same subject |
| `QualityReport` | ✅ Detailed per-claim validation results |
| `filter_passed()` | ✅ Returns only claims meeting quality threshold |

### 5.4 Research Execution ✅

| Task | Status |
|------|--------|
| `Researcher` | ✅ `research/researcher.rs` — orchestrates research pipeline |
| `DocumentationSource` | ✅ Configurable sources with URL patterns and topics |
| Default sources | ✅ Redis, PostgreSQL, Go, Rust, OWASP, Kafka, MongoDB |
| Content fetching | ✅ HTTP with timeout and size limits |
| Normative extraction | ✅ Regex-based MUST/SHOULD/SHALL extraction |
| Section tracking | ✅ Extracts heading context for attribution |
| Confidence scoring | ✅ Based on keyword strength, statement length, content size |

### 5.5 CLI Integration ✅

| Task | Status |
|------|--------|
| `aphoria research run` | ✅ Run research agent with configurable threshold |
| `aphoria research status` | ✅ Show gap statistics and research progress |
| `aphoria research gaps` | ✅ List gaps by project count |
| `--threshold` | ✅ Minimum projects before researching (default: 3) |
| `--strict` | ✅ Use strict quality validation |
| `--prune` | ✅ Remove stale gaps before researching |
| `--ready` | ✅ Show only gaps ready for research |

**Files:** `research/mod.rs`, `research/gap_detector.rs`, `research/gap_store.rs`, `research/quality.rs`, `research/researcher.rs`, `research/tests.rs`

### 5.6 Community Corpus Contributions ⬜

> Future: Users can opt in to contribute patterns anonymously.

- "Every Rust project has this JWT pattern" → pre-built alias set
- "This Redis config is always acknowledged" → adjust default threshold
- "This TLS pattern is always a real bug" → elevate threshold

---

## Milestone Summary

| Phase | Deliverable | Depends On | Status |
|-------|-------------|------------|--------|
| 0 | ConceptPath in StemeDB | concept-hierarchy spec | ✅ |
| 2 | Aphoria CLI (scan, report, ack) | Phase 0 | ✅ |
| 2A.1 | Leaf-based concept matching | Phase 2 | ✅ |
| 2A.2 | Alias resolution in QueryEngine | Phase 2 | ✅ |
| 2A.3 | Auto-alias creation | Phase 2A.2 | ✅ |
| 1 | Authoritative corpus expansion | Phase 0 | ✅ |
| 3 | Claude Code skill + hooks | Phase 2A | ✅ |
| 5 | Research agent loop | Phase 3 | ✅ |
| **4** | **Pre-commit integration (git hooks, diff scanning)** | **Phase 3** | **⬜ NEXT** |

**Current state:**
- Phase 1 is complete: RFC, OWASP, and Vendor corpus builders with `aphoria corpus build` CLI
- Phase 2A is complete: conflict detection via tail-path matching, alias-aware QueryEngine, and auto-alias creation
- Phase 3 is complete: `/aphoria` skill installed to `~/.claude/skills/aphoria/`, hook templates ready
- Phase 5 is complete: Research agent with gap detection, quality validation, and official doc research

**Next:** Phase 4 — Pre-commit integration (git hooks, diff-only scanning).