agentic-flow 2.0.0-alpha → 2.0.1-alpha

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "agentic-flow",
-  "version": "2.0.0-alpha",
+  "version": "2.0.1-alpha",
   "description": "Production-ready AI agent orchestration platform with 66 specialized agents, 213 MCP tools, ReasoningBank learning memory, quantum-resistant Jujutsu VCS, and autonomous multi-agent swarms. Built by @ruvnet with Claude Agent SDK, neural networks, memory persistence, GitHub integration, and distributed consensus protocols.",
   "type": "module",
   "main": "agentic-flow/dist/index.js",
@@ -14,6 +14,11 @@
   },
   "exports": {
     ".": "./agentic-flow/dist/index.js",
+    "./wrappers": "./agentic-flow/dist/core/index.js",
+    "./wrappers/gnn": "./agentic-flow/dist/core/gnn-wrapper.js",
+    "./wrappers/agentdb-fast": "./agentic-flow/dist/core/agentdb-fast.js",
+    "./wrappers/attention": "./agentic-flow/dist/core/attention-fallbacks.js",
+    "./wrappers/embedding": "./agentic-flow/dist/core/embedding-service.js",
     "./reasoningbank": {
       "node": "./agentic-flow/dist/reasoningbank/index.js",
       "browser": "./agentic-flow/dist/reasoningbank/wasm-adapter.js",
@@ -60,6 +65,9 @@
     "bench:report": "node scripts/generate-benchmark-report.js",
     "bench:parallel": "BENCHMARK_MODE=true ITERATIONS=10 node tests/parallel/benchmark-suite.js",
     "bench:attention": "node benchmarks/attention-gnn-benchmark.js",
+    "bench:sona": "npx tsx tests/sona/sona-performance.bench.ts",
+    "bench:sona:quick": "BENCHMARK_QUICK=1 npx tsx tests/sona/sona-performance.bench.ts",
+    "bench:sona:gc": "node --expose-gc --loader tsx tests/sona/benchmark-runner.ts --gc",
     "test:attention": "jest tests/integration/attention-gnn.test.ts --config=config/jest.config.cjs",
     "docker:test": "cd tests/docker && docker-compose -f docker-compose.parallel.yml up --build",
     "docker:bench": "cd tests/docker && docker-compose -f docker-compose.parallel.yml up --build benchmark",
@@ -74,7 +82,7 @@
     "complexity": "npx complexity-report --format json --output complexity-report.json agentic-flow/src/**/*.ts || echo 'Complexity report generated'",
     "quality:check": "npm run lint && npm run format:check && npm run typecheck:strict && npm run test:coverage",
     "quality:fix": "npm run lint:fix && npm run format",
-    "prepublishOnly-disabled": "npm run quality:check && npm run build"
+    "prepublishOnly": "npm run build || true"
   },
   "keywords": [
     "ai",
@@ -191,6 +199,7 @@
     "@google/genai": "^1.22.0",
     "@ruvector/attention": "^0.1.1",
     "@ruvector/gnn": "^0.1.19",
+    "@ruvector/sona": "^0.1.1",
     "@supabase/supabase-js": "^2.78.0",
     "@types/react": "^19.2.2",
     "@types/react-dom": "^19.2.2",
@@ -222,6 +231,7 @@
   "devDependencies": {
     "@commitlint/cli": "^20.1.0",
     "@commitlint/config-conventional": "^20.0.0",
+    "@e2b/code-interpreter": "^2.3.1",
     "@types/better-sqlite3": "^7.6.13",
     "@types/cors": "^2.8.19",
     "@types/express": "^5.0.3",

package/docs/AGENTIC_JUJUTSU_QUICKSTART.md

@@ -1,491 +0,0 @@
-# 🚀 Agentic-Jujutsu Quick Start Guide
-
-## Quantum-Resistant Version Control for AI Agents
-
-**Version**: v2.3.6 (integrated in Agentic-Flow v2.0.0-alpha)
-**Features**: QuantumDAG consensus, AI agent coordination, AgentDB learning integration
-
----
-
-## What is Agentic-Jujutsu?
-
-Agentic-Jujutsu brings **quantum-resistant version control** to AI agents, enabling multi-agent collaboration on code with automatic conflict resolution and learning capabilities.
-
-### Key Features
-
-- 🔒 **Quantum-resistant cryptography** (ML-DSA signatures)
-- 🤖 **AI agent coordination** for version control
-- 🧠 **AgentDB learning integration** (version control teaches agents)
-- ⚡ **Zero dependencies** (embedded Jujutsu binary)
-- 🚀 **Native performance** (NAPI-RS Rust bindings)
-- 🌐 **7 platform support** (Linux, macOS, Windows, etc.)
-
----
-
-## Installation
-
-Agentic-Jujutsu is included with Agentic-Flow v2.0.0-alpha:
-
-```bash
-npm install agentic-flow@alpha
-```
-
-Or install standalone:
-
-```bash
-npm install -g agentic-jujutsu
-```
-
----
-
-## CLI Usage
-
-### Basic Commands
-
-```bash
-# Show repository status
-npx agentic-jujutsu status
-# or
-jj-agent status
-
-# View commit history
-npx agentic-jujutsu log --limit 10
-
-# See changes
-npx agentic-jujutsu diff
-
-# Create new commit
-npx agentic-jujutsu new "Add AI agent feature"
-
-# Update commit description
-npx agentic-jujutsu describe "Better description"
-```
-
-### AI Agent Commands
-
-```bash
-# Analyze repository for AI agents
-npx agentic-jujutsu analyze
-
-# Compare performance with Git
-npx agentic-jujutsu compare-git
-```
-
-### Help & Info
-
-```bash
-# Show help
-npx agentic-jujutsu help
-
-# Show version
-npx agentic-jujutsu version
-
-# Show examples
-npx agentic-jujutsu examples
-```
-
----
-
-## Programmatic API
-
-### Basic Usage
-
-```javascript
-import { JjWrapper } from 'agentic-flow/agentic-jujutsu';
-
-// Initialize wrapper
-const jj = new JjWrapper();
-
-// Get repository status
-const status = await jj.status();
-console.log(status);
-
-// View commit log
-const log = await jj.log({ limit: 10 });
-console.log(log);
-
-// Create commit
-await jj.newCommit("AI agent automated commit");
-
-// Show diff
-const diff = await jj.diff();
-console.log(diff);
-```
-
-### Advanced: Quantum Features
-
-```javascript
-import { QuantumBridge } from 'agentic-flow/agentic-jujutsu/quantum';
-
-// Initialize quantum-resistant signing
-const quantum = new QuantumBridge();
-
-// Sign commit with ML-DSA
-const signature = await quantum.signCommit({
-  message: "Quantum-resistant commit",
-  timestamp: Date.now()
-});
-
-// Verify quantum signature
-const isValid = await quantum.verifySignature(signature);
-```
-
-### Multi-Agent Coordination
-
-```javascript
-import { JjWrapper } from 'agentic-flow/agentic-jujutsu';
-import { AgentDB } from 'agentic-flow/agentdb';
-
-// Setup AgentDB learning
-const db = new AgentDB();
-const jj = new JjWrapper();
-
-// Agent 1: Makes changes
-await jj.newCommit("Agent 1: Add feature X");
-
-// Store learning in AgentDB
-await db.storeEpisode({
-  task: "version-control",
-  action: "commit",
-  reward: 1.0,
-  metadata: { tool: "jujutsu", agent: "agent-1" }
-});
-
-// Agent 2: Builds on Agent 1's work
-const log = await jj.log({ limit: 1 });
-const previousWork = log[0];
-
-// AI agents learn from version control patterns
-const similarCommits = await db.searchSimilar({
-  query: previousWork.description,
-  k: 5
-});
-```
-
----
-
-## Why Jujutsu over Git?
-
-### Traditional Git vs. Agentic-Jujutsu
-
-| Feature | Git | Agentic-Jujutsu |
-|---------|-----|-----------------|
-| **Architecture** | Commit-based | Change-based |
-| **Conflicts** | Manual resolution | AI-assisted |
-| **Performance** | O(n) operations | O(log n) with QuantumDAG |
-| **Agent Learning** | ❌ None | ✅ AgentDB integration |
-| **Quantum-Ready** | ❌ No | ✅ ML-DSA signatures |
-| **Dependencies** | System binary | ✅ Zero (embedded) |
-| **Multi-Agent** | ❌ Limited | ✅ Native support |
-
-### QuantumDAG Consensus
-
-Agentic-Jujutsu uses **QuantumDAG** (Quantum Directed Acyclic Graph) for:
-- Post-quantum cryptographic signatures
-- Distributed consensus without central authority
-- Lock-free concurrent operations
-- Automatic conflict resolution
-
----
-
-## Use Cases
-
-### 1. Multi-Agent Development
-
-```javascript
-// Agent swarm collaborating on code
-import { AgentCoordinator } from 'agentic-flow';
-import { JjWrapper } from 'agentic-flow/agentic-jujutsu';
-
-const coordinator = new AgentCoordinator({
-  agents: ['coder', 'reviewer', 'tester'],
-  vcs: new JjWrapper()
-});
-
-// Agents work concurrently on different branches
-await coordinator.parallelDevelopment({
-  task: "Implement new API endpoint",
-  autoMerge: true,  // AI-assisted conflict resolution
-  learnFromHistory: true  // AgentDB learning
-});
-```
-
-### 2. Automated Code Reviews
-
-```javascript
-// AI agent reviews code changes
-const jj = new JjWrapper();
-const diff = await jj.diff();
-
-// Send to code review agent
-const review = await reviewAgent.analyze(diff);
-
-if (review.approved) {
-  await jj.newCommit(`Automated review: ${review.summary}`);
-}
-```
-
-### 3. Version Control Learning
-
-```javascript
-// Agents learn from version control patterns
-import { AgentDB } from 'agentic-flow/agentdb';
-import { JjWrapper } from 'agentic-flow/agentic-jujutsu';
-
-const db = new AgentDB();
-const jj = new JjWrapper();
-
-// Store successful commit patterns
-const log = await jj.log({ limit: 100 });
-for (const commit of log) {
-  await db.storePattern({
-    task: "commit",
-    input: commit.description,
-    output: commit.changes,
-    reward: commit.successMetrics.score
-  });
-}
-
-// Future agents learn from past commits
-const bestPractices = await db.searchPatterns({
-  task: "commit",
-  k: 10,
-  minReward: 0.8
-});
-```
-
----
-
-## Configuration
-
-### Environment Variables
-
-```bash
-# Set Jujutsu working directory
-export JJ_WORKING_DIR=/path/to/repo
-
-# Enable quantum features
-export JJ_QUANTUM_ENABLED=true
-
-# AgentDB integration
-export JJ_AGENTDB_PATH=/path/to/agentdb
-
-# Debug mode
-export JJ_DEBUG=true
-```
-
-### Config File (`.jjconfig`)
-
-```json
-{
-  "quantum": {
-    "enabled": true,
-    "algorithm": "ML-DSA"
-  },
-  "agentdb": {
-    "enabled": true,
-    "learnFromCommits": true
-  },
-  "multiAgent": {
-    "conflictResolution": "ai-assisted",
-    "parallelBranches": true
-  }
-}
-```
-
----
-
-## MCP Tools Integration
-
-Agentic-Jujutsu is exposed via MCP (Model Context Protocol) tools:
-
-```javascript
-// Available MCP tools:
-- mcp__agentic-jujutsu__status
-- mcp__agentic-jujutsu__log
-- mcp__agentic-jujutsu__diff
-- mcp__agentic-jujutsu__new_commit
-- mcp__agentic-jujutsu__describe
-- mcp__agentic-jujutsu__analyze
-```
-
-### Using with Claude Code
-
-```javascript
-// Claude Code can use Jujutsu via MCP
-await claude.useTool('mcp__agentic-jujutsu__status');
-await claude.useTool('mcp__agentic-jujutsu__new_commit', {
-  message: "AI-generated commit"
-});
-```
-
----
-
-## Performance Benchmarks
-
-### vs. Git
-
-| Operation | Git | Jujutsu | Improvement |
-|-----------|-----|---------|-------------|
-| Status check | 45ms | 12ms | **3.7x faster** |
-| Log (100 commits) | 230ms | 35ms | **6.6x faster** |
-| Diff | 85ms | 18ms | **4.7x faster** |
-| Commit | 120ms | 22ms | **5.5x faster** |
-
-### With AgentDB Learning
-
-| Feature | Without | With AgentDB | Benefit |
-|---------|---------|--------------|---------|
-| Conflict resolution | Manual | Auto (95%) | **20x faster** |
-| Commit message quality | Variable | Learned | **Consistent** |
-| Agent coordination | Manual | Automatic | **Zero overhead** |
-
----
-
-## Examples
-
-### Example 1: Automated Workflow
-
-```javascript
-import { JjWrapper } from 'agentic-flow/agentic-jujutsu';
-
-async function automatedWorkflow() {
-  const jj = new JjWrapper();
-
-  // 1. Check status
-  const status = await jj.status();
-  console.log('Status:', status);
-
-  // 2. Make changes (simulated)
-  // ... your code changes ...
-
-  // 3. Create commit
-  await jj.newCommit('Automated: Add new feature');
-
-  // 4. Verify
-  const log = await jj.log({ limit: 1 });
-  console.log('Latest commit:', log[0]);
-}
-
-automatedWorkflow();
-```
-
-### Example 2: Multi-Agent Collaboration
-
-```javascript
-import { AgentFlow } from 'agentic-flow';
-import { JjWrapper } from 'agentic-flow/agentic-jujutsu';
-
-async function multiAgentDevelopment() {
-  const flow = new AgentFlow();
-  const jj = new JjWrapper();
-
-  // Spawn agent swarm
-  const agents = await flow.spawnSwarm({
-    agents: [
-      { type: 'coder', name: 'agent-1' },
-      { type: 'reviewer', name: 'agent-2' },
-      { type: 'tester', name: 'agent-3' }
-    ],
-    coordination: 'jujutsu'
-  });
-
-  // Parallel development
-  await Promise.all(agents.map(async (agent) => {
-    // Each agent works independently
-    await agent.work();
-
-    // Automatic commit via Jujutsu
-    await jj.newCommit(`${agent.name}: ${agent.workSummary}`);
-  }));
-
-  // AI-assisted merge
-  const log = await jj.log({ limit: 3 });
-  console.log('All agents completed:', log);
-}
-
-multiAgentDevelopment();
-```
-
----
-
-## Troubleshooting
-
-### Common Issues
-
-**Issue**: `jj-agent: command not found`
-**Solution**: Run `npm install -g agentic-flow@alpha` to install globally
-
-**Issue**: `Native binding not found`
-**Solution**: Check your platform is supported. Run `npx agentic-jujutsu info`
-
-**Issue**: `Quantum features not available`
-**Solution**: Set `JJ_QUANTUM_ENABLED=true` environment variable
-
-### Debug Mode
-
-```bash
-# Enable debug logging
-JJ_DEBUG=true npx agentic-jujutsu status
-
-# Or programmatically
-const jj = new JjWrapper({ debug: true });
-```
-
----
-
-## Platform Support
-
-Agentic-Jujutsu supports **7 platforms** via pre-built binaries:
-
-- ✅ Linux x64 (glibc)
-- ✅ Linux x64 (musl/Alpine)
-- ✅ Linux ARM64
-- ✅ macOS x64 (Intel)
-- ✅ macOS ARM64 (M1/M2/M3)
-- ✅ Windows x64
-- ✅ Android ARM64
-
----
-
-## Resources
-
-- **Package**: `packages/agentic-jujutsu/`
-- **Documentation**: `packages/agentic-jujutsu/docs/`
-- **Examples**: `examples/jujutsu-workflows/`
-- **Jujutsu VCS**: https://github.com/martinvonz/jj
-
----
-
-## Next Steps
-
-1. **Try the CLI**: Run `npx agentic-jujutsu status`
-2. **Explore API**: Import and use `JjWrapper`
-3. **Multi-Agent**: Integrate with AgentDB learning
-4. **Quantum Features**: Enable ML-DSA signatures
-
----
-
-## FAQ
-
-**Q: Do I need Jujutsu installed separately?**
-A: No! Agentic-Jujutsu includes an embedded binary (zero dependencies).
-
-**Q: Can I use this with existing Git repos?**
-A: Yes! Jujutsu can coexist with Git and convert repositories.
-
-**Q: Is this production-ready?**
-A: Yes! Jujutsu v2.3.6 is stable. Quantum features are experimental.
-
-**Q: How does AgentDB learning work?**
-A: Jujutsu operations are stored as episodes in AgentDB, enabling agents to learn from version control patterns.
-
----
-
-**Integrated in**: Agentic-Flow v2.0.0-alpha
-**License**: MIT
-**Author**: @ruvnet
-
-🤖 Generated with [Claude Code](https://claude.com/claude-code)
-
-Co-Authored-By: Claude <noreply@anthropic.com>