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@ericelliott ericelliott commented Jan 20, 2026

Add comprehensive task epic for building RLM skill that applies MIT's
Recursive Language Model strategies to AI agent codebase exploration.
Epic includes 7 tasks covering research, design, implementation of
fan-out search, SQLite indexing, and SudoLang skill specification.


Note

Lays groundwork for the RLM skill with a SQLite indexing schema and planning docs, plus project setup updates.

  • Adds ai/tools/create-schema.js (with CLI) and comprehensive tests to create SQLite schema: documents + FTS5, dependencies, and ProductManager tables (personas, journeys, steps, pain_points, stories, functional_requirements), with indexes and triggers
  • Introduces RLM planning docs under plan/rlm/ (spec, architecture, database design, research summary)
  • Updates package.json (adds better-sqlite3, new test:bun, adjusts unit test filters) and adds .gitattributes
  • Updates indexes (ai/index.md, ai/rules/index.md) and adds ai/rules/sudolang/index.md and ai/tools/index.md

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Add comprehensive task epic for building RLM skill that applies MIT's
Recursive Language Model strategies to AI agent codebase exploration.
Epic includes 7 tasks covering research, design, implementation of
fan-out search, SQLite indexing, and SudoLang skill specification.
Research findings include:
- Agent Skills specification from agentskills.io
- MIT RLM paper analysis (arXiv 2512.24601)
- Implementation architecture for aidd framework
- Complete SQLite database design with FTS5

Documents recursive language model strategies for deep codebase
exploration through hierarchical task decomposition.
Replace single RLM epic with comprehensive phase-based approach:

Phase 1: SQLite Foundation + Indexing + Fan-out Search
- Database schema for documents, dependencies, productmanager
- Frontmatter and dependency indexers with TDD
- Fan-out search combining keyword, semantic, structured
- CLI query and indexing tools

Phase 2: Jiron DB API Skill
- Generic skill for SudoLang → Jiron API generation
- SQLite query bridge and middleware integration
- Fan-out search exposed via Jiron endpoints
- Includes ai/skills/jiron skill to teach agents Jiron protocol

Phase 3: Frontmatter Index Jiron API
- Apply Jiron DB API skill to frontmatter/codebase index
- Self-documenting API with progressive discovery
- Search and traversal endpoints with rich queries

Phase 4: ProductManager Skill Conversion
- Convert ai/rules/productmanager.mdc to full skill
- Jiron API for story maps with SQLite as source of truth
- Import existing YAML, export on demand
- Database-backed workflows

Phase 5: RLM Skill
- Recursive exploration through hierarchical decomposition
- Orchestrates all previous phases
- User journey documented with pain points
- Always-surfaced skill with agent self-direction

Archived original RLM epic for reference.
Analyzed 2026-01-20-claude-code-skills branch to check for conflicts
with our Phase 1-5 RLM + DB + Jiron epic plans.

Key findings:
- No blocking conflicts (.claude/ vs ai/ directories)
- janhesters built YAML-based skills for Claude Code
- Our approach adds SQLite + Jiron APIs + RLM on top
- Different problem spaces that complement each other
- Both can coexist and potentially converge later

Recommendation: Proceed with all 5 phases as planned.
Created comprehensive overview document that provides:
- Executive summary and big picture
- Visual phase dependencies and implementation order
- Concise summary of each phase with deliverables
- Architecture decisions with rationale
- Value proposition and quantified benefits
- Success metrics for each phase
- Implementation strategy and risk mitigation
- Links to detailed phase epics and research docs
- Relationship to janhesters' work

Makes it easy to absorb the entire 5-phase epic structure at a glance
before diving into detailed task lists.
Creates database-backed indexing system with FTS5 full-text search, dependency tracking, and ProductManager entities. Replaces YAML as source of truth for project metadata. Implements Phase 1 foundation for Recursive Language Model skill.
Auto-formatting from pre-commit hook.
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cursor bot commented Jan 26, 2026

🔬 Code Review: Recursive Language Model Skill Epic

🎯 Review Context

Reviewing PR #84 which adds comprehensive RLM skill groundwork including SQLite schema creation, planning documentation, and project configuration updates. The CI is failing with bun:sqlite import errors.


🚨 CI Failure Diagnosis

Root Cause

Issue: The test suite uses bun:sqlite imports, but CI runs on Node.js with Vitest.

import { Database } from "bun:sqlite";
import { createSchema } from "./create-schema.js";

Failure Flow:

  1. CI executes npm test (runs all tests via Vitest)
  2. Vitest attempts to load create-schema.test.js
  3. Node.js cannot resolve bun:sqlite (Bun-only module)
  4. Test fails: Cannot find package 'bun:sqlite'

Current Mitigation (Incomplete):

  • test:unit excludes this test
  • test:bun runs with Bun
  • npm test still includes it (what CI runs)

Solution Options

Option 1: Make Code Runtime-Agnostic (Recommended)

// Detect runtime and use appropriate SQLite library
const Database = globalThis.Bun 
  ? (await import('bun:sqlite')).Database
  : (await import('better-sqlite3')).default;

Pros: Works everywhere, uses optimal library per runtime
Cons: Adds conditional logic, slight complexity

Option 2: Update CI to Run Bun Tests Separately

- name: Run Node tests
  run: npm run test:unit
  
- name: Install Bun
  uses: oven-sh/setup-bun@v1
  
- name: Run Bun tests
  run: npm run test:bun

Pros: Clean separation, tests real Bun environment
Cons: CI complexity, longer run time

Option 3: Exclude from Main Test Script

"test": "vitest run --exclude '**/*-e2e.test.js' --exclude '**/create-schema.test.js' && npm run -s lint && npm run -s typecheck"

Pros: Quick fix, mirrors test:unit
Cons: Test doesn't run in default CI, easy to forget

Recommendation: Implement Option 1 for maximum compatibility, then add Option 2 to CI for comprehensive testing.


1. Code Structure and Organization

🎯 What I'm Reviewing

Code organization, file placement, and architectural decisions for the SQLite schema foundation.

💡 Observations

Strengths:

  • ✅ Clear separation of concerns: schema creation vs tests
  • ✅ CLI-friendly design with #!/usr/bin/env bun shebang
  • ✅ Proper export of core function for testing
  • ✅ Planning docs well-organized in plan/rlm/
  • ✅ Follows existing project structure conventions

Issues:

  • Outdated index files: ai/tools/index.md says "This directory is empty" but contains files
  • Missing TypeScript definitions: No create-schema.d.ts file
  • ⚠️ Inconsistent naming: File is create-schema.js but could be schema.js (simpler)

🪞 Critical Reflection

The planning documentation is thorough and well-researched. However, the implementation shows signs of rushing - index files weren't updated, type definitions are missing, and runtime compatibility wasn't considered.

🔭 Broader Context

This is foundational code for Phase 1 of a 5-phase epic. Any compatibility issues here will cascade to future phases. Getting the foundation right is critical.

⚖️ Score: 7/10

Good structure, but missing polish and completeness checks.


2. Adherence to Coding Standards

🎯 Checking Against

  • javascript/javascript.mdc - JavaScript best practices
  • tdd.mdc - Test-driven development patterns
  • Project conventions

💡 Observations

Follows Project Standards: ✅

  • Uses ESM imports
  • Functional programming style
  • Riteway + Vitest for tests
  • Proper use of beforeEach/afterEach
  • Named exports over default exports

JavaScript Best Practices: ✅

export function createSchema(db) {
  • Clear, self-describing function name ✅
  • Single responsibility ✅
  • Pure function (no side effects beyond db mutation) ✅

Test Quality: ✅

  test("should return version and success status", async () => {
    const result = createSchema(db);

    assert({
      given: "schema creation",
      should: "return version 1",
      actual: result.version,
      expected: 1,
    });
  • Answers the 5 questions (unit, behavior, actual, expected, debugging) ✅
  • Isolated tests with fresh db per test ✅
  • Explicit assertions ✅

Issues:

  • ⚠️ Uses async in test functions but doesn't await anything (unnecessary)
  • ⚠️ Date.now() for timestamps (not mockable for deterministic tests)
  • ❌ Missing JSDoc for public API function

🪞 Critical Reflection

The code follows FP principles well. Tests are thorough and isolated. However, some async/await usage is cosmetic, and the lack of JSDoc hurts discoverability.

⚖️ Score: 8/10

Strong adherence to standards, minor improvements needed.


3. Test Coverage and Quality

🎯 Evaluating

Test comprehensiveness, edge cases, and TDD compliance.

💡 Analysis

Coverage: Excellent ✅

  • Schema creation verification
  • Table existence checks
  • Column validation
  • FTS5 virtual table
  • Indexes verification
  • Foreign key constraints
  • Triggers
  • CHECK constraints
  • Idempotency

Test Quality: Strong ✅

  test("should enforce foreign key constraints", async () => {
    createSchema(db);

    let errorThrown = false;
    let errorMessage = "";

    try {
      db.prepare(
        `
        INSERT INTO stories (
          id, step_id, name, priority, status, created_at, updated_at
        ) VALUES (
          'story1', 'nonexistent', 'Test Story', 50, 'backlog', ?, ?
        )
      `,
      ).run(Date.now(), Date.now());
    } catch (error) {
      errorThrown = true;
      errorMessage = error.message;
    }

    assert({
      given: "invalid foreign key",
      should: "throw foreign key constraint error",
      actual: errorThrown && errorMessage.includes("FOREIGN KEY"),
      expected: true,
    });

Tests verify both happy paths and constraints. Good coverage of SQL semantics.

Missing Tests:

  • ❌ No tests for CLI execution path (lines 266-290)
  • ❌ No integration tests with real file system
  • ❌ No performance benchmarks (important per design doc)
  • ⚠️ No tests for concurrent access (SQLite locking)

🔭 Expansion

The design doc mentions "TDD-friendly in-memory tests" and this delivers. However, missing integration tests for the CLI path and performance validation against stated goals (100 files in <1s).

⚖️ Score: 8.5/10

Excellent unit test coverage, missing integration and performance tests.


4. Performance Considerations

🎯 Evaluating

Implementation efficiency against stated performance goals.

💡 Analysis

Design Goals (from database-design.md):

  • 100 files: ~100ms ✓ (stated goal)
  • Simple query: <10ms ✓ (stated goal)
  • FTS5 search: <200ms ✓ (stated goal)

Implementation: Good Foundation ✅

  // Enable foreign keys
  db.exec("PRAGMA foreign_keys = ON");

  // Schema version tracking
  db.exec(`
    CREATE TABLE IF NOT EXISTS schema_version (
      version INTEGER PRIMARY KEY,
      applied_at INTEGER NOT NULL
    )
  `);

Efficient Patterns:

  • ✅ Uses IF NOT EXISTS for idempotency
  • ✅ Proper indexes on foreign keys
  • ✅ FTS5 with Porter stemming for better search
  • ✅ Triggers keep FTS5 in sync automatically

Missing Optimizations:

  • ⚠️ Multiple db.exec() calls instead of single transaction
  • ⚠️ No PRAGMA journal_mode = WAL for better concurrency
  • ⚠️ No PRAGMA synchronous = NORMAL for speed/safety balance

Potential Issues:

  db.exec(`
    CREATE INDEX IF NOT EXISTS idx_documents_type ON documents(type);
    CREATE INDEX IF NOT EXISTS idx_documents_indexed_at ON documents(indexed_at);
    CREATE INDEX IF NOT EXISTS idx_documents_modified_at ON documents(modified_at);

Multiple indexes created separately. Could use single exec with multiple statements for better performance.

🪞 Critical Reflection

Schema is well-designed for performance, but implementation doesn't wrap everything in a transaction. For 100+ tables/indexes, this could be noticeable.

⚖️ Score: 7/10

Good design, missing production-grade optimizations.


5. Security Scan

🎯 Checking OWASP Top 10 + Project Security Rules

OWASP Top 10 (2021) Analysis:

  1. A01: Broken Access Control - N/A (no auth layer yet)
  2. A02: Cryptographic Failures - ⚠️ See below
  3. A03: Injection - ✅ Safe (uses prepared statements in tests)
  4. A04: Insecure Design - ✅ Good (structured schema, constraints)
  5. A05: Security Misconfiguration - ⚠️ See below
  6. A06: Vulnerable Components - ✅ Good (better-sqlite3 is well-maintained)
  7. A07: Identification/Authentication - N/A
  8. A08: Software/Data Integrity - ⚠️ See below
  9. A09: Security Logging - N/A (no auth to log yet)
  10. A10: SSRF - N/A

💡 Security Issues Found

A02: Cryptographic Failures ⚠️

      hash TEXT NOT NULL,

Design doc mentions SHA256 for change detection, but no validation that hashes use cryptographic functions. Should enforce in schema or docs.

A05: Security Misconfiguration ⚠️

  // Enable foreign keys
  db.exec("PRAGMA foreign_keys = ON");

Missing security-relevant PRAGMAs:

  • PRAGMA trusted_schema = OFF - Prevents malicious views/triggers
  • PRAGMA cell_size_check = ON - Detects corruption

A08: Software/Data Integrity ⚠️

  // Record schema version
  const version = 1;
  const now = Date.now();

  const existing = db
    .prepare("SELECT version FROM schema_version WHERE version = ?")
    .get(version);
  if (!existing) {
    db.prepare(
      "INSERT INTO schema_version (version, applied_at) VALUES (?, ?)",

No integrity checks. If database is tampered with, no detection mechanism. Consider adding:

  • Schema checksums
  • Version signature verification
  • Corruption detection on load

Input Validation: ✅ Good

Tests show proper use of prepared statements, avoiding SQL injection.

🔭 Broader Context

This is infrastructure code, so security is primarily about data integrity and safe defaults. No immediate vulnerabilities, but missing defense-in-depth layers.

⚖️ Score: 7.5/10

No critical vulnerabilities, but missing security hardening.


6. Architectural Patterns & Design Decisions

🎯 Evaluating

Design decisions against project goals and best practices.

💡 Analysis

Decision 1: Bun-Specific Implementation

import { Database } from "bun:sqlite";

Reasoning (from design doc):

"Bun-native - better-sqlite3 synchronous API"

Critical Reflection: ❌

  • better-sqlite3 is already a dependency
  • Bun isn't mentioned in package.json engines
  • Breaking CI is a red flag
  • Design doc says "better-sqlite3" but code uses "bun:sqlite"

Verdict: Architectural mismatch. Should use better-sqlite3 for cross-runtime compatibility.

Decision 2: SQLite Over Alternatives

Rationale (from design doc):

  • Zero infrastructure ✅
  • TDD-friendly ✅
  • Portable ✅
  • Fast ✅

Verdict: ✅ Excellent choice for use case.

Decision 3: Hybrid Document + Structured Storage

  // Documents table - main frontmatter index
  db.exec(`
    CREATE TABLE IF NOT EXISTS documents (
      path TEXT PRIMARY KEY,
      type TEXT NOT NULL,
      frontmatter JSON,
      content TEXT,
      hash TEXT NOT NULL,
      indexed_at INTEGER NOT NULL,
      file_size INTEGER,
      modified_at INTEGER
    )
  `);

Verdict: ✅ Smart. Flexible JSON for varying schemas, structured tables for complex queries.

Decision 4: FTS5 with Triggers

  // Triggers to keep FTS5 in sync with documents table
  db.exec(`
    DROP TRIGGER IF EXISTS documents_fts_insert;
    CREATE TRIGGER documents_fts_insert AFTER INSERT ON documents BEGIN

Verdict: ✅ Excellent. Automatic sync prevents stale search results.

🪞 Critical Reflection

Strong architectural decisions overall, but critical error: Implementation uses bun:sqlite when design doc specifies better-sqlite3. This breaks cross-runtime compatibility and CI.

⚖️ Score: 6/10

Great design marred by implementation that contradicts design doc.


7. Documentation & Commit Quality

🎯 Checking

Documentation completeness, commit messages, inline comments.

💡 Analysis

Planning Documentation: Excellent ✅

  • Comprehensive research summaries
  • Clear phase breakdown
  • Detailed database design
  • Rationale for all decisions

Code Documentation: Weak ❌

#!/usr/bin/env bun
/**
 * SQLite Schema Creation
 * Creates the complete database schema for aidd indexing system
 */

import { Database } from "bun:sqlite";

/**
 * Creates the complete database schema
 * @param {Database} db - SQLite database instance
 */

Missing:

  • Return type documentation
  • Error conditions
  • Usage examples
  • Link to design doc

Commit Messages: Good ✅

82be9da Add SQLite schema foundation for document indexing
5bb8333 Apply prettier formatting to schema files

Follows conventional commits, clear descriptions.

Index Files: Broken ❌

# tools

This index provides an overview of the contents in this directory.

*This directory is empty.*

Says "empty" but contains 2 files. Pre-commit hook should have caught this.

🔭 Expansion

Per AGENTS.md:

The ai/**/index.md files are auto-generated from frontmatter. Do not create or edit these files manually—they will be overwritten by the pre-commit hook.

Issue: Pre-commit hook didn't update index, OR files are missing frontmatter.

Let me check:

#!/usr/bin/env bun
/**
 * SQLite Schema Creation
 * Creates the complete database schema for aidd indexing system
 */

❌ No frontmatter. Should have:

---
description: Creates complete SQLite schema for aidd indexing
---

⚖️ Score: 6/10

Excellent planning docs, weak code docs, broken index generation.


8. Missing TypeScript Definitions

🎯 Checking

Type safety and developer experience.

💡 Issue

Project has .d.ts files for other modules:

  • utils/index.d.ts
  • src/server/index.d.ts
  • lib/index-generator.d.ts

But missing:

  • ai/tools/create-schema.d.ts

Should export:

import type { Database } from 'better-sqlite3';

export interface SchemaResult {
  version: number;
  tablesCreated: boolean;
}

export function createSchema(db: Database): SchemaResult;

⚖️ Score: 5/10

Inconsistent with project patterns.


9. Comparison to Requirements

🎯 Checking

Implementation against Phase 1 success criteria.

From Epic (EPIC-rlm-database-jiron-skills.md):

Success Criteria:

  • Schema creates all tables with indexes ✅ (implemented)
  • Indexers handle 100+ files in <1 second ⚠️ (no indexer yet, just schema)
  • FTS5 search finds relevant content ⚠️ (schema ready, no query tools)
  • Fan-out search aggregates multiple strategies ❌ (not in this PR)
  • All unit tests pass (>90% coverage) ❌ (tests fail in CI)

Verdict: Partial implementation. Schema foundation is solid, but missing query tools and failing CI.


📋 Summary & Actionable Recommendations

Critical Issues (Must Fix)

  1. CI Failure - Bun/Node Compatibility 🚨

    • Problem: Uses bun:sqlite but CI runs Node.js
    • Fix: Use better-sqlite3 or add runtime detection
    • Priority: P0 - Blocks merge
  2. Outdated Index Files 🚨

    • Problem: ai/tools/index.md says "empty" but contains files
    • Fix: Add frontmatter to .js files, run pre-commit hook
    • Priority: P0 - Breaks discoverability

High Priority (Should Fix)

  1. Missing TypeScript Definitions

    • Problem: No .d.ts file for public API
    • Fix: Create create-schema.d.ts with proper types
    • Priority: P1 - Developer experience
  2. Missing JSDoc

    • Problem: Public API lacks comprehensive documentation
    • Fix: Add complete JSDoc with examples
    • Priority: P1 - Code clarity
  3. No Integration Tests

    • Problem: CLI path untested, no performance validation
    • Fix: Add integration tests, benchmark against goals
    • Priority: P1 - Quality assurance

Medium Priority (Good to Have)

  1. Performance Optimizations

    • Wrap schema creation in transaction
    • Add PRAGMA journal_mode = WAL
    • Add PRAGMA synchronous = NORMAL
  2. Security Hardening

    • Add PRAGMA trusted_schema = OFF
    • Add schema integrity checks
    • Document hash requirements
  3. Code Quality

    • Remove unnecessary async in tests
    • Mock Date.now() for deterministic tests
    • Simplify file naming (schema.js vs create-schema.js)

⚖️ Overall Scores

Category Score Weight Weighted
Structure 7/10 10% 0.7
Standards 8/10 15% 1.2
Tests 8.5/10 20% 1.7
Performance 7/10 10% 0.7
Security 7.5/10 15% 1.125
Architecture 6/10 20% 1.2
Documentation 6/10 10% 0.6

Overall: 7.2/10 - Good foundation with critical CI issue


🎯 Recommendation

DO NOT MERGE until CI passes. Fix the Bun/Node compatibility issue and update index files. The architectural foundation is solid, but implementation contradicts design doc and breaks CI.

Once CI is green, this is a strong foundation for Phase 1. The planning documentation is excellent and shows thoughtful design.


💬 Specific Code Changes Needed

Fix 1: Runtime Compatibility

// ai/tools/create-schema.js
let Database;
if (globalThis.Bun) {
  Database = (await import('bun:sqlite')).Database;
} else {
  Database = (await import('better-sqlite3')).default;
}

export function createSchema(db) {
  // ... rest of implementation
}

Fix 2: Add Frontmatter

---
description: Creates complete SQLite schema for aidd indexing system with FTS5, ProductManager tables, and dependency tracking
---
#!/usr/bin/env bun
/**
 * SQLite Schema Creation

Fix 3: Update Index (will auto-generate after adding frontmatter)

Run: npm run prepare (triggers pre-commit hook)

Fix 4: Add TypeScript Definitions

Create ai/tools/create-schema.d.ts:

import type { Database } from 'better-sqlite3';

export interface SchemaResult {
  version: number;
  tablesCreated: boolean;
}

export function createSchema(db: Database): SchemaResult;

This review follows the systematic process from review.mdc and identifies both the immediate CI blocker and the broader quality improvements needed for production readiness.

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3 participants