agentic-qe 1.4.0 → 1.4.1

package/CHANGELOG.md

@@ -5,6 +5,63 @@ All notable changes to the Agentic QE project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.4.1] - 2025-10-31
+
+### 🚨 CRITICAL FIX - Emergency Patch Release
+
+This is an emergency patch release to fix a critical bug in v1.4.0 that prevented **all QE agents from spawning**.
+
+### Fixed
+
+- **[CRITICAL]** Fixed duplicate MCP tool names error preventing all QE agents from spawning
+  - **Root Cause**: package.json contained self-dependency `"agentic-qe": "^1.3.3"` causing duplicate tool registration
+  - **Impact**: ALL 18 QE agents failed with `API Error 400: tools: Tool names must be unique`
+  - **Fix 1**: Removed self-dependency from package.json dependencies
+  - **Fix 2**: Updated package.json "files" array to explicitly include only `.claude/agents`, `.claude/skills`, `.claude/commands`
+  - **Fix 3**: Added `.claude/settings*.json` to .npmignore to prevent shipping development configuration
+- Fixed package bundling to exclude development configuration files
+
+### Impact Assessment
+
+- **Affected Users**: All users who installed v1.4.0 from npm
+- **Severity**: CRITICAL - All agent spawning was broken in v1.4.0
+- **Workaround**: Upgrade to v1.4.1 immediately: `npm install agentic-qe@latest`
+
+### Upgrade Instructions
+
+```bash
+# If you installed v1.4.0, upgrade immediately:
+npm install agentic-qe@latest
+
+# Verify the fix:
+aqe --version  # Should show 1.4.1
+
+# Test agent spawning (should now work):
+# In Claude Code: Task("Test", "Generate a simple test", "qe-test-generator")
+```
+
+---
+
+## [1.4.0] - 2025-10-26
+
+### 🎯 Agent Memory & Learning Infrastructure Complete
+
+Phase 2 development complete with agent memory, learning systems, and pattern reuse.
+
+### Added
+
+- **Agent Memory Infrastructure**: AgentDB integration with SwarmMemoryManager
+- **Learning System**: Q-learning with 9 RL algorithms for continuous improvement
+- **Pattern Bank**: Reusable test patterns with vector search
+- **Force Flag**: `aqe init --force` to reinitialize projects
+
+### Known Issues
+
+- **v1.4.0 BROKEN**: All agents fail to spawn due to duplicate MCP tool names
+  - **Fixed in v1.4.1**: Upgrade immediately if you installed v1.4.0
+
+---
+
 ## [1.3.7] - 2025-10-30
 
 ### 📚 Documentation Updates

package/README.md

@@ -7,7 +7,7 @@
 [![TypeScript](https://img.shields.io/badge/TypeScript-5.0+-blue.svg)](https://www.typescriptlang.org/)
 [![Node.js](https://img.shields.io/badge/Node.js-20+-green.svg)](https://nodejs.org/)
 
-**Version 1.4.0** | [Changelog](CHANGELOG.md) | [Issues](https://github.com/proffesor-for-testing/agentic-qe/issues) | [Discussions](https://github.com/proffesor-for-testing/agentic-qe/discussions)
+**Version 1.4.1** | [Changelog](CHANGELOG.md) | [Issues](https://github.com/proffesor-for-testing/agentic-qe/issues) | [Discussions](https://github.com/proffesor-for-testing/agentic-qe/discussions)
 
 > Enterprise-grade test automation with AI learning, comprehensive skills library (34 QE skills), and 85.7% cost savings through intelligent model routing.
 
@@ -506,8 +506,22 @@ Model Usage:
 
 ## 📝 Recent Changes
 
-### v1.4.0 (2025-10-31)
-**Agent Memory & Learning Infrastructure Complete**
+### v1.4.1 (2025-10-31)
+**🚨 CRITICAL FIX - Emergency Patch Release**
+
+- 🔴 **CRITICAL**: Fixed duplicate MCP tool names preventing all QE agents from spawning
+  - Root Cause: package.json self-dependency `"agentic-qe": "^1.3.3"`
+  - Impact: ALL 18 agents failed with API Error 400 in v1.4.0
+  - Fixed: Removed self-dependency, updated package bundling
+- ✅ Agents now spawn correctly via Claude Code Task tool
+- ✅ Package no longer includes development configuration files
+
+**If you installed v1.4.0, upgrade immediately**: `npm install agentic-qe@latest`
+
+---
+
+### v1.4.0 (2025-10-31) ⚠️ BROKEN - DO NOT USE
+**Agent Memory & Learning Infrastructure Complete** (but all agents fail to spawn)
 
 - ✅ **Fixed 11 agents with lifecycle hooks** - Proper memoryStore API usage (retrieve/store signatures)
 - ✅ **Comprehensive learning validation** - All 16 agents inherit BaseAgent learning (89% coverage)

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "agentic-qe",
-  "version": "1.4.0",
+  "version": "1.4.1",
   "description": "Agentic Quality Engineering Fleet System - AI-driven quality management platform with 34 QE skills, learning, pattern reuse, ML-based flaky detection, Multi-Model Router (70-81% cost savings), streaming progress updates, 54 MCP tools, and native TypeScript hooks",
   "main": "dist/cli/index.js",
   "types": "dist/cli/index.d.ts",
@@ -116,7 +116,6 @@
     "@xenova/transformers": "^2.6.0",
     "agentdb": "^1.0.0",
     "agentic-flow": "^1.7.3",
-    "agentic-qe": "^1.3.3",
     "ajv": "^8.17.1",
     "ajv-formats": "^3.0.1",
     "better-sqlite3": "^12.4.1",
@@ -191,7 +190,9 @@
   "files": [
     "dist",
     "bin",
-    ".claude",
+    ".claude/agents",
+    ".claude/skills",
+    ".claude/commands",
     "config",
     "LICENSE",
     "README.md",

package/.claude/aqe-fleet.json

@@ -1,47 +0,0 @@
-{
-  "fleetId": "aqe-fleet-1759773240987",
-  "version": "2.0.0",
-  "topology": "hierarchical",
-  "maxAgents": 6,
-  "agents": [
-    "qe-test-generator",
-    "qe-test-executor",
-    "qe-coverage-analyzer",
-    "qe-quality-gate",
-    "qe-performance-tester",
-    "qe-security-scanner",
-    "qe-fleet-commander",
-    "qe-chaos-engineer",
-    "qe-visual-tester",
-    "qe-requirements-validator",
-    "qe-deployment-readiness",
-    "qe-production-intelligence",
-    "qe-regression-risk-analyzer",
-    "qe-test-data-architect",
-    "qe-api-contract-validator",
-    "qe-flaky-test-hunter"
-  ],
-  "created": "2025-10-06T17:54:00.987Z",
-  "status": "active",
-  "configuration": {
-    "coordination": {
-      "memoryNamespace": "aqe",
-      "hooksEnabled": true,
-      "neuralLearning": true
-    },
-    "testing": {
-      "defaultFramework": "jest",
-      "coverageThreshold": 95,
-      "parallelWorkers": "auto"
-    },
-    "optimization": {
-      "algorithm": "sublinear",
-      "targetCoveragePerTest": "maximize"
-    }
-  },
-  "metadata": {
-    "packageVersion": "2.0.0",
-    "claudeFlowVersion": "alpha",
-    "initDate": "2025-10-06T17:54:00.987Z"
-  }
-}

package/.claude/helpers/checkpoint-manager.sh

@@ -1,251 +0,0 @@
-#!/bin/bash
-# Claude Checkpoint Manager
-# Provides easy rollback and management of Claude Code checkpoints
-
-set -e
-
-# Colors
-RED='\033[0;31m'
-GREEN='\033[0;32m'
-YELLOW='\033[1;33m'
-BLUE='\033[0;34m'
-NC='\033[0m' # No Color
-
-# Configuration
-CHECKPOINT_DIR=".claude/checkpoints"
-BACKUP_DIR=".claude/backups"
-
-# Help function
-show_help() {
-    cat << EOF
-Claude Checkpoint Manager
-========================
-
-Usage: $0 <command> [options]
-
-Commands:
-  list              List all checkpoints
-  show <id>         Show details of a specific checkpoint
-  rollback <id>     Rollback to a specific checkpoint
-  diff <id>         Show diff since checkpoint
-  clean             Clean old checkpoints (older than 7 days)
-  summary           Show session summary
-  
-Options:
-  --hard            For rollback: use git reset --hard (destructive)
-  --soft            For rollback: use git reset --soft (default)
-  --branch          For rollback: create new branch from checkpoint
-
-Examples:
-  $0 list
-  $0 show checkpoint-20240130-143022
-  $0 rollback checkpoint-20240130-143022 --branch
-  $0 diff session-end-session-20240130-150000
-EOF
-}
-
-# List all checkpoints
-function list_checkpoints() {
-    echo -e "${BLUE}📋 Available Checkpoints:${NC}"
-    echo ""
-    
-    # List checkpoint tags
-    echo -e "${YELLOW}Git Tags:${NC}"
-    local tags=$(git tag -l 'checkpoint-*' -l 'session-end-*' -l 'task-*' --sort=-creatordate | head -20)
-    if [ -n "$tags" ]; then
-        echo "$tags"
-    else
-        echo "No checkpoint tags found"
-    fi
-    
-    echo ""
-    
-    # List checkpoint branches
-    echo -e "${YELLOW}Checkpoint Branches:${NC}"
-    local branches=$(git branch -a | grep "checkpoint/" | sed 's/^[ *]*//')
-    if [ -n "$branches" ]; then
-        echo "$branches"
-    else
-        echo "No checkpoint branches found"
-    fi
-    
-    echo ""
-    
-    # List checkpoint files
-    if [ -d "$CHECKPOINT_DIR" ]; then
-        echo -e "${YELLOW}Recent Checkpoint Files:${NC}"
-        find "$CHECKPOINT_DIR" -name "*.json" -type f -printf "%T@ %p\n" | \
-            sort -rn | head -10 | cut -d' ' -f2- | xargs -I {} basename {}
-    fi
-}
-
-# Show checkpoint details
-function show_checkpoint() {
-    local checkpoint_id="$1"
-    
-    echo -e "${BLUE}📍 Checkpoint Details: $checkpoint_id${NC}"
-    echo ""
-    
-    # Check if it's a tag
-    if git tag -l "$checkpoint_id" | grep -q "$checkpoint_id"; then
-        echo -e "${YELLOW}Type:${NC} Git Tag"
-        echo -e "${YELLOW}Commit:${NC} $(git rev-list -n 1 "$checkpoint_id")"
-        echo -e "${YELLOW}Date:${NC} $(git log -1 --format=%ai "$checkpoint_id")"
-        echo -e "${YELLOW}Message:${NC}"
-        git log -1 --format=%B "$checkpoint_id" | sed 's/^/  /'
-        echo ""
-        echo -e "${YELLOW}Files changed:${NC}"
-        git diff-tree --no-commit-id --name-status -r "$checkpoint_id" | sed 's/^/  /'
-    # Check if it's a branch
-    elif git branch -a | grep -q "$checkpoint_id"; then
-        echo -e "${YELLOW}Type:${NC} Git Branch"
-        echo -e "${YELLOW}Latest commit:${NC}"
-        git log -1 --oneline "$checkpoint_id"
-    else
-        echo -e "${RED}❌ Checkpoint not found: $checkpoint_id${NC}"
-        exit 1
-    fi
-}
-
-# Rollback to checkpoint
-function rollback_checkpoint() {
-    local checkpoint_id="$1"
-    local mode="$2"
-    
-    echo -e "${YELLOW}🔄 Rolling back to checkpoint: $checkpoint_id${NC}"
-    echo ""
-    
-    # Verify checkpoint exists
-    if ! git tag -l "$checkpoint_id" | grep -q "$checkpoint_id" && \
-       ! git branch -a | grep -q "$checkpoint_id"; then
-        echo -e "${RED}❌ Checkpoint not found: $checkpoint_id${NC}"
-        exit 1
-    fi
-    
-    # Create backup before rollback
-    local backup_name="backup-$(date +%Y%m%d-%H%M%S)"
-    echo "Creating backup: $backup_name"
-    git tag "$backup_name" -m "Backup before rollback to $checkpoint_id"
-    
-    case "$mode" in
-        "--hard")
-            echo -e "${RED}⚠️  Performing hard reset (destructive)${NC}"
-            git reset --hard "$checkpoint_id"
-            echo -e "${GREEN}✅ Rolled back to $checkpoint_id (hard reset)${NC}"
-            ;;
-        "--branch")
-            local branch_name="rollback-$checkpoint_id-$(date +%Y%m%d-%H%M%S)"
-            echo "Creating new branch: $branch_name"
-            git checkout -b "$branch_name" "$checkpoint_id"
-            echo -e "${GREEN}✅ Created branch $branch_name from $checkpoint_id${NC}"
-            ;;
-        "--stash"|*)
-            echo "Stashing current changes..."
-            git stash push -m "Stash before rollback to $checkpoint_id"
-            git reset --soft "$checkpoint_id"
-            echo -e "${GREEN}✅ Rolled back to $checkpoint_id (soft reset)${NC}"
-            echo "Your changes are stashed. Use 'git stash pop' to restore them."
-            ;;
-    esac
-}
-
-# Show diff since checkpoint
-function diff_checkpoint() {
-    local checkpoint_id="$1"
-    
-    echo -e "${BLUE}📊 Changes since checkpoint: $checkpoint_id${NC}"
-    echo ""
-    
-    if git tag -l "$checkpoint_id" | grep -q "$checkpoint_id"; then
-        git diff "$checkpoint_id"
-    elif git branch -a | grep -q "$checkpoint_id"; then
-        git diff "$checkpoint_id"
-    else
-        echo -e "${RED}❌ Checkpoint not found: $checkpoint_id${NC}"
-        exit 1
-    fi
-}
-
-# Clean old checkpoints
-function clean_checkpoints() {
-    local days=${1:-7}
-    
-    echo -e "${YELLOW}🧹 Cleaning checkpoints older than $days days...${NC}"
-    echo ""
-    
-    # Clean old checkpoint files
-    if [ -d "$CHECKPOINT_DIR" ]; then
-        find "$CHECKPOINT_DIR" -name "*.json" -type f -mtime +$days -delete
-        echo "✅ Cleaned old checkpoint files"
-    fi
-    
-    # List old tags (but don't delete automatically)
-    echo ""
-    echo "Old checkpoint tags (manual deletion required):"
-    git tag -l 'checkpoint-*' --sort=-creatordate | tail -n +50 || echo "No old tags found"
-}
-
-# Show session summary
-function show_summary() {
-    echo -e "${BLUE}📊 Session Summary${NC}"
-    echo ""
-    
-    # Find most recent session summary
-    if [ -d "$CHECKPOINT_DIR" ]; then
-        local latest_summary=$(find "$CHECKPOINT_DIR" -name "summary-*.md" -type f -printf "%T@ %p\n" | \
-            sort -rn | head -1 | cut -d' ' -f2-)
-        
-        if [ -n "$latest_summary" ]; then
-            echo -e "${YELLOW}Latest session summary:${NC}"
-            cat "$latest_summary"
-        else
-            echo "No session summaries found"
-        fi
-    fi
-}
-
-# Main command handling
-case "$1" in
-    list)
-        list_checkpoints
-        ;;
-    show)
-        if [ -z "$2" ]; then
-            echo -e "${RED}Error: Please specify a checkpoint ID${NC}"
-            show_help
-            exit 1
-        fi
-        show_checkpoint "$2"
-        ;;
-    rollback)
-        if [ -z "$2" ]; then
-            echo -e "${RED}Error: Please specify a checkpoint ID${NC}"
-            show_help
-            exit 1
-        fi
-        rollback_checkpoint "$2" "$3"
-        ;;
-    diff)
-        if [ -z "$2" ]; then
-            echo -e "${RED}Error: Please specify a checkpoint ID${NC}"
-            show_help
-            exit 1
-        fi
-        diff_checkpoint "$2"
-        ;;
-    clean)
-        clean_checkpoints "$2"
-        ;;
-    summary)
-        show_summary
-        ;;
-    help|--help|-h)
-        show_help
-        ;;
-    *)
-        echo -e "${RED}Error: Unknown command: $1${NC}"
-        echo ""
-        show_help
-        exit 1
-        ;;
-esac

package/.claude/helpers/github-safe.js

@@ -1,106 +0,0 @@
-#!/usr/bin/env node
-
-/**
- * Safe GitHub CLI Helper
- * Prevents timeout issues when using gh commands with special characters
- * 
- * Usage:
- *   ./github-safe.js issue comment 123 "Message with `backticks`"
- *   ./github-safe.js pr create --title "Title" --body "Complex body"
- */
-
-import { execSync } from 'child_process';
-import { writeFileSync, unlinkSync } from 'fs';
-import { tmpdir } from 'os';
-import { join } from 'path';
-import { randomBytes } from 'crypto';
-
-const args = process.argv.slice(2);
-
-if (args.length < 2) {
-  console.log(`
-Safe GitHub CLI Helper
-
-Usage:
-  ./github-safe.js issue comment <number> <body>
-  ./github-safe.js pr comment <number> <body>
-  ./github-safe.js issue create --title <title> --body <body>
-  ./github-safe.js pr create --title <title> --body <body>
-
-This helper prevents timeout issues with special characters like:
-- Backticks in code examples
-- Command substitution \$(...)
-- Directory paths
-- Special shell characters
-`);
-  process.exit(1);
-}
-
-const [command, subcommand, ...restArgs] = args;
-
-// Handle commands that need body content
-if ((command === 'issue' || command === 'pr') && 
-    (subcommand === 'comment' || subcommand === 'create')) {
-  
-  let bodyIndex = -1;
-  let body = '';
-  
-  if (subcommand === 'comment' && restArgs.length >= 2) {
-    // Simple format: github-safe.js issue comment 123 "body"
-    body = restArgs[1];
-    bodyIndex = 1;
-  } else {
-    // Flag format: --body "content" 
-    bodyIndex = restArgs.indexOf('--body');
-    if (bodyIndex !== -1 && bodyIndex < restArgs.length - 1) {
-      body = restArgs[bodyIndex + 1];
-    }
-  }
-  
-  if (body) {
-    // Use temporary file for body content
-    const tmpFile = join(tmpdir(), `gh-body-${randomBytes(8).toString('hex')}.tmp`);
-    
-    try {
-      writeFileSync(tmpFile, body, 'utf8');
-      
-      // Build new command with --body-file
-      const newArgs = [...restArgs];
-      if (subcommand === 'comment' && bodyIndex === 1) {
-        // Replace body with --body-file
-        newArgs[1] = '--body-file';
-        newArgs.push(tmpFile);
-      } else if (bodyIndex !== -1) {
-        // Replace --body with --body-file
-        newArgs[bodyIndex] = '--body-file';
-        newArgs[bodyIndex + 1] = tmpFile;
-      }
-      
-      // Execute safely
-      const ghCommand = `gh ${command} ${subcommand} ${newArgs.join(' ')}`;
-      console.log(`Executing: ${ghCommand}`);
-      
-      const result = execSync(ghCommand, { 
-        stdio: 'inherit',
-        timeout: 30000 // 30 second timeout
-      });
-      
-    } catch (error) {
-      console.error('Error:', error.message);
-      process.exit(1);
-    } finally {
-      // Clean up
-      try {
-        unlinkSync(tmpFile);
-      } catch (e) {
-        // Ignore cleanup errors
-      }
-    }
-  } else {
-    // No body content, execute normally
-    execSync(`gh ${args.join(' ')}`, { stdio: 'inherit' });
-  }
-} else {
-  // Other commands, execute normally
-  execSync(`gh ${args.join(' ')}`, { stdio: 'inherit' });
-}

package/.claude/helpers/github-setup.sh

@@ -1,28 +0,0 @@
-#!/bin/bash
-# Setup GitHub integration for Claude Flow
-
-echo "🔗 Setting up GitHub integration..."
-
-# Check for gh CLI
-if ! command -v gh &> /dev/null; then
-    echo "⚠️  GitHub CLI (gh) not found"
-    echo "Install from: https://cli.github.com/"
-    echo "Continuing without GitHub features..."
-else
-    echo "✅ GitHub CLI found"
-    
-    # Check auth status
-    if gh auth status &> /dev/null; then
-        echo "✅ GitHub authentication active"
-    else
-        echo "⚠️  Not authenticated with GitHub"
-        echo "Run: gh auth login"
-    fi
-fi
-
-echo ""
-echo "📦 GitHub swarm commands available:"
-echo "  - npx claude-flow github swarm"
-echo "  - npx claude-flow repo analyze"
-echo "  - npx claude-flow pr enhance"
-echo "  - npx claude-flow issue triage"

package/.claude/helpers/quick-start.sh

@@ -1,19 +0,0 @@
-#!/bin/bash
-# Quick start guide for Claude Flow
-
-echo "🚀 Claude Flow Quick Start"
-echo "=========================="
-echo ""
-echo "1. Initialize a swarm:"
-echo "   npx claude-flow swarm init --topology hierarchical"
-echo ""
-echo "2. Spawn agents:"
-echo "   npx claude-flow agent spawn --type coder --name "API Developer""
-echo ""
-echo "3. Orchestrate tasks:"
-echo "   npx claude-flow task orchestrate --task "Build REST API""
-echo ""
-echo "4. Monitor progress:"
-echo "   npx claude-flow swarm monitor"
-echo ""
-echo "📚 For more examples, see .claude/commands/"

package/.claude/helpers/setup-mcp.sh

@@ -1,18 +0,0 @@
-#!/bin/bash
-# Setup MCP server for Claude Flow
-
-echo "🚀 Setting up Claude Flow MCP server..."
-
-# Check if claude command exists
-if ! command -v claude &> /dev/null; then
-    echo "❌ Error: Claude Code CLI not found"
-    echo "Please install Claude Code first"
-    exit 1
-fi
-
-# Add MCP server
-echo "📦 Adding Claude Flow MCP server..."
-claude mcp add claude-flow npx claude-flow mcp start
-
-echo "✅ MCP server setup complete!"
-echo "🎯 You can now use mcp__claude-flow__ tools in Claude Code"

package/.claude/helpers/standard-checkpoint-hooks.sh

@@ -1,179 +0,0 @@
-#!/bin/bash
-# Standard checkpoint hook functions for Claude settings.json (without GitHub features)
-
-# Function to handle pre-edit checkpoints
-pre_edit_checkpoint() {
-    local tool_input="$1"
-    local file=$(echo "$tool_input" | jq -r '.file_path // empty')
-    
-    if [ -n "$file" ]; then
-        local checkpoint_branch="checkpoint/pre-edit-$(date +%Y%m%d-%H%M%S)"
-        local current_branch=$(git branch --show-current)
-        
-        # Create checkpoint
-        git add -A
-        git stash push -m "Pre-edit checkpoint for $file" >/dev/null 2>&1
-        git branch "$checkpoint_branch"
-        
-        # Store metadata
-        mkdir -p .claude/checkpoints
-        cat > ".claude/checkpoints/$(date +%s).json" <<EOF
-{
-  "branch": "$checkpoint_branch",
-  "file": "$file",
-  "timestamp": "$(date -u +%Y-%m-%dT%H:%M:%SZ)",
-  "type": "pre-edit",
-  "original_branch": "$current_branch"
-}
-EOF
-        
-        # Restore working directory
-        git stash pop --quiet >/dev/null 2>&1 || true
-        
-        echo "✅ Created checkpoint: $checkpoint_branch for $file"
-    fi
-}
-
-# Function to handle post-edit checkpoints
-post_edit_checkpoint() {
-    local tool_input="$1"
-    local file=$(echo "$tool_input" | jq -r '.file_path // empty')
-    
-    if [ -n "$file" ] && [ -f "$file" ]; then
-        # Check if file was modified - first check if file is tracked
-        if ! git ls-files --error-unmatch "$file" >/dev/null 2>&1; then
-            # File is not tracked, add it first
-            git add "$file"
-        fi
-        
-        # Now check if there are changes
-        if git diff --cached --quiet "$file" 2>/dev/null && git diff --quiet "$file" 2>/dev/null; then
-            echo "ℹ️  No changes to checkpoint for $file"
-        else
-            local tag_name="checkpoint-$(date +%Y%m%d-%H%M%S)"
-            local current_branch=$(git branch --show-current)
-            
-            # Create commit
-            git add "$file"
-            if git commit -m "🔖 Checkpoint: Edit $file
-
-Automatic checkpoint created by Claude
-- File: $file
-- Branch: $current_branch
-- Timestamp: $(date -u +%Y-%m-%dT%H:%M:%SZ)
-
-[Auto-checkpoint]" --quiet; then
-                # Create tag only if commit succeeded
-                git tag -a "$tag_name" -m "Checkpoint after editing $file"
-                
-                # Store metadata
-                mkdir -p .claude/checkpoints
-                local diff_stats=$(git diff HEAD~1 --stat | tr '\n' ' ' | sed 's/"/\"/g')
-                cat > ".claude/checkpoints/$(date +%s).json" <<EOF
-{
-  "tag": "$tag_name",
-  "file": "$file",
-  "timestamp": "$(date -u +%Y-%m-%dT%H:%M:%SZ)",
-  "type": "post-edit",
-  "branch": "$current_branch",
-  "diff_summary": "$diff_stats"
-}
-EOF
-                
-                echo "✅ Created checkpoint: $tag_name for $file"
-            else
-                echo "ℹ️  No commit created (no changes or commit failed)"
-            fi
-        fi
-    fi
-}
-
-# Function to handle task checkpoints
-task_checkpoint() {
-    local user_prompt="$1"
-    local task=$(echo "$user_prompt" | head -c 100 | tr '\n' ' ')
-    
-    if [ -n "$task" ]; then
-        local checkpoint_name="task-$(date +%Y%m%d-%H%M%S)"
-        
-        # Commit current state
-        git add -A
-        git commit -m "🔖 Task checkpoint: $task..." --quiet || true
-        
-        # Store metadata
-        mkdir -p .claude/checkpoints
-        cat > ".claude/checkpoints/task-$(date +%s).json" <<EOF
-{
-  "checkpoint": "$checkpoint_name",
-  "task": "$task",
-  "timestamp": "$(date -u +%Y-%m-%dT%H:%M:%SZ)",
-  "commit": "$(git rev-parse HEAD)"
-}
-EOF
-        
-        echo "✅ Created task checkpoint: $checkpoint_name"
-    fi
-}
-
-# Function to handle session end
-session_end_checkpoint() {
-    local session_id="session-$(date +%Y%m%d-%H%M%S)"
-    local summary_file=".claude/checkpoints/summary-$session_id.md"
-    
-    mkdir -p .claude/checkpoints
-    
-    # Create summary
-    cat > "$summary_file" <<EOF
-# Session Summary - $(date +'%Y-%m-%d %H:%M:%S')
-
-## Checkpoints Created
-$(find .claude/checkpoints -name '*.json' -mtime -1 -exec basename {} \; | sort)
-
-## Files Modified
-$(git diff --name-only $(git log --format=%H -n 1 --before="1 hour ago" 2>/dev/null) 2>/dev/null || echo "No files tracked")
-
-## Recent Commits
-$(git log --oneline -10 --grep="Checkpoint" || echo "No checkpoint commits")
-
-## Rollback Instructions
-To rollback to a specific checkpoint:
-\`\`\`bash
-# List all checkpoints
-git tag -l 'checkpoint-*' | sort -r
-
-# Rollback to a checkpoint
-git checkout checkpoint-YYYYMMDD-HHMMSS
-
-# Or reset to a checkpoint (destructive)
-git reset --hard checkpoint-YYYYMMDD-HHMMSS
-\`\`\`
-EOF
-    
-    # Create final checkpoint
-    git add -A
-    git commit -m "🏁 Session end checkpoint: $session_id" --quiet || true
-    git tag -a "session-end-$session_id" -m "End of Claude session"
-    
-    echo "✅ Session summary saved to: $summary_file"
-    echo "📌 Final checkpoint: session-end-$session_id"
-}
-
-# Main entry point
-case "$1" in
-    pre-edit)
-        pre_edit_checkpoint "$2"
-        ;;
-    post-edit)
-        post_edit_checkpoint "$2"
-        ;;
-    task)
-        task_checkpoint "$2"
-        ;;
-    session-end)
-        session_end_checkpoint
-        ;;
-    *)
-        echo "Usage: $0 {pre-edit|post-edit|task|session-end} [input]"
-        exit 1
-        ;;
-esac

package/.claude/settings.json

@@ -1,153 +0,0 @@
-
-{
-  "env": {
-    "CLAUDE_FLOW_AUTO_COMMIT": "false",
-    "CLAUDE_FLOW_AUTO_PUSH": "false",
-    "CLAUDE_FLOW_HOOKS_ENABLED": "true",
-    "CLAUDE_FLOW_TELEMETRY_ENABLED": "true",
-    "CLAUDE_FLOW_REMOTE_EXECUTION": "true",
-    "CLAUDE_FLOW_CHECKPOINTS_ENABLED": "true",
-    "AGENTDB_LEARNING_ENABLED": "true",
-    "AGENTDB_REASONING_ENABLED": "true",
-    "AGENTDB_AUTO_TRAIN": "true"
-  },
-  "permissions": {
-    "allow": [
-      "Bash(npx claude-flow:*)",
-      "Bash(npx agentdb:*)",
-      "Bash(npm run lint)",
-      "Bash(npm run test:*)",
-      "Bash(npm test:*)",
-      "Bash(git status)",
-      "Bash(git diff:*)",
-      "Bash(git log:*)",
-      "Bash(git add:*)",
-      "Bash(git commit:*)",
-      "Bash(git push)",
-      "Bash(git config:*)",
-      "Bash(git tag:*)",
-      "Bash(git branch:*)",
-      "Bash(git checkout:*)",
-      "Bash(git stash:*)",
-      "Bash(jq:*)",
-      "Bash(node:*)",
-      "Bash(which:*)",
-      "Bash(pwd)",
-      "Bash(ls:*)"
-    ],
-    "deny": [
-      "Bash(rm -rf /)"
-    ]
-  },
-  "hooks": {
-    "PreToolUse": [
-      {
-        "matcher": "Bash",
-        "hooks": [
-          {
-            "type": "command",
-            "command": "cat | jq -r '.tool_input.command // empty' | tr '\\n' '\\0' | xargs -0 -I {} npx claude-flow@alpha hooks pre-command --command '{}' --validate-safety true --prepare-resources true"
-          }
-        ]
-      },
-      {
-        "matcher": "Write|Edit|MultiEdit",
-        "hooks": [
-          {
-            "type": "command",
-            "description": "3. Semantic Search Memory - Query similar successful past edits",
-            "command": "cat | jq -r '.tool_input.file_path // .tool_input.path // empty' | tr '\\n' '\\0' | xargs -0 -I {} bash -c 'FILE=\"{}\"; echo \"🔍 Semantic Search: Querying similar successful edits for $FILE...\"; npx agentdb@latest query --domain \"successful-edits\" --query \"file:$FILE\" --k 5 --min-confidence 0.8 --format json 2>/dev/null || echo \"{}\" | jq -r \".memories[]? | \\\"💡 Past Success: \\(.pattern.summary // \\\"No similar patterns found\\\")\\\" \" 2>/dev/null; npx claude-flow@alpha hooks pre-edit --file \"$FILE\" --auto-assign-agents true --load-context true'"
-          },
-          {
-            "type": "command",
-            "description": "5. Failure Pattern Recognition - Warn about known failure patterns",
-            "command": "cat | jq -r '.tool_input.file_path // .tool_input.path // empty' | tr '\\n' '\\0' | xargs -0 -I {} bash -c 'FILE=\"{}\"; echo \"⚠️ Failure Detection: Checking for known failure patterns...\"; npx agentdb@latest query --domain \"failed-edits\" --query \"file:$FILE\" --k 3 --min-confidence 0.7 --format json 2>/dev/null | jq -r \".memories[]? | \\\"🚨 Warning: Similar edit failed - \\(.pattern.reason // \\\"unknown\\\")\\\" \" 2>/dev/null || true'"
-          }
-        ]
-      },
-      {
-        "matcher": "Task",
-        "hooks": [
-          {
-            "type": "command",
-            "description": "4. Trajectory Prediction - Predict optimal task sequence",
-            "command": "cat | jq -r '.tool_input.prompt // .tool_input.task // empty' | tr '\\n' '\\0' | xargs -0 -I {} bash -c 'TASK=\"{}\"; echo \"🎯 Trajectory Prediction: Analyzing optimal workflow for task...\"; npx agentdb@latest query --domain \"task-trajectories\" --query \"task:$TASK\" --k 3 --min-confidence 0.75 --format json 2>/dev/null | jq -r \".memories[]? | \\\"📋 Predicted Steps: \\(.pattern.trajectory // \\\"No trajectory data\\\") (Success Rate: \\(.confidence // 0))\\\" \" 2>/dev/null || echo \"📋 No historical trajectory data - learning from this task...\"; npx claude-flow@alpha hooks pre-task --description \"$TASK\" --auto-spawn-agents true --load-memory true'"
-          }
-        ]
-      }
-    ],
-    "PostToolUse": [
-      {
-        "matcher": "Bash",
-        "hooks": [
-          {
-            "type": "command",
-            "command": "cat | jq -r '.tool_input.command // empty' | tr '\\n' '\\0' | xargs -0 -I {} npx claude-flow@alpha hooks post-command --command '{}' --track-metrics true --store-results true"
-          }
-        ]
-      },
-      {
-        "matcher": "Write|Edit|MultiEdit",
-        "hooks": [
-          {
-            "type": "command",
-            "description": "1. Experience Replay Developer - Capture edit as RL experience",
-            "command": "cat | jq -r '.tool_input.file_path // .tool_input.path // empty' | tr '\\n' '\\0' | xargs -0 -I {} bash -c 'FILE=\"{}\"; echo \"💾 Experience Replay: Storing edit experience for $FILE...\"; TIMESTAMP=$(date +%s); npx agentdb@latest store-pattern --type \"experience\" --domain \"code-edits\" --pattern \"{\\\"file\\\":\\\"$FILE\\\",\\\"timestamp\\\":$TIMESTAMP,\\\"action\\\":\\\"edit\\\",\\\"state\\\":\\\"pre-test\\\"}\" --confidence 0.5 2>/dev/null || true; npx claude-flow@alpha hooks post-edit --file \"$FILE\" --format true --update-memory true --train-patterns true'"
-          },
-          {
-            "type": "command",
-            "description": "2. Verdict-Based Quality - Async verdict assignment after tests",
-            "command": "cat | jq -r '.tool_input.file_path // .tool_input.path // empty' | tr '\\n' '\\0' | xargs -0 -I {} bash -c 'FILE=\"{}\"; (sleep 2; TEST_RESULT=$(npm test --silent 2>&1 | grep -q \"pass\" && echo \"ACCEPT\" || echo \"REJECT\"); REWARD=$([ \"$TEST_RESULT\" = \"ACCEPT\" ] && echo \"1.0\" || echo \"-1.0\"); echo \"⚖️ Verdict: $TEST_RESULT (reward: $REWARD) for $FILE\"; npx agentdb@latest store-pattern --type \"verdict\" --domain \"code-quality\" --pattern \"{\\\"file\\\":\\\"$FILE\\\",\\\"verdict\\\":\\\"$TEST_RESULT\\\",\\\"reward\\\":$REWARD}\" --confidence $([ \"$TEST_RESULT\" = \"ACCEPT\" ] && echo \"0.95\" || echo \"0.3\") 2>/dev/null; if [ \"$TEST_RESULT\" = \"ACCEPT\" ]; then npx agentdb@latest store-pattern --type \"success\" --domain \"successful-edits\" --pattern \"{\\\"file\\\":\\\"$FILE\\\",\\\"summary\\\":\\\"Edit passed tests\\\"}\" --confidence 0.9 2>/dev/null; else npx agentdb@latest store-pattern --type \"failure\" --domain \"failed-edits\" --pattern \"{\\\"file\\\":\\\"$FILE\\\",\\\"reason\\\":\\\"Tests failed\\\"}\" --confidence 0.8 2>/dev/null; fi) &'"
-          }
-        ]
-      },
-      {
-        "matcher": "Task",
-        "hooks": [
-          {
-            "type": "command",
-            "description": "4. Trajectory Storage - Record task trajectory for learning",
-            "command": "cat | jq -r '.tool_input.prompt // .tool_input.task // empty, .result.success // \"unknown\"' | tr '\\n' '\\0' | xargs -0 bash -c 'TASK=\"$1\"; SUCCESS=\"$2\"; echo \"📊 Trajectory Storage: Recording task workflow...\"; CONFIDENCE=$([ \"$SUCCESS\" = \"true\" ] && echo \"0.95\" || echo \"0.5\"); npx agentdb@latest store-pattern --type \"trajectory\" --domain \"task-trajectories\" --pattern \"{\\\"task\\\":\\\"$TASK\\\",\\\"success\\\":$SUCCESS,\\\"trajectory\\\":\\\"search→scaffold→test→refine\\\"}\" --confidence \"$CONFIDENCE\" 2>/dev/null || true; npx claude-flow@alpha hooks post-task --analyze-performance true --store-decisions true --export-learnings true' _"
-          }
-        ]
-      }
-    ],
-    "PreCompact": [
-      {
-        "matcher": "manual",
-        "hooks": [
-          {
-            "type": "command",
-            "command": "/bin/bash -c 'INPUT=$(cat); CUSTOM=$(echo \"$INPUT\" | jq -r \".custom_instructions // \\\"\\\"\"); echo \"🔄 PreCompact Guidance:\"; echo \"📋 IMPORTANT: Review CLAUDE.md in project root for:\"; echo \"   • 54 available agents and concurrent usage patterns\"; echo \"   • Swarm coordination strategies (hierarchical, mesh, adaptive)\"; echo \"   • SPARC methodology workflows with batchtools optimization\"; echo \"   • Critical concurrent execution rules (GOLDEN RULE: 1 MESSAGE = ALL OPERATIONS)\"; if [ -n \"$CUSTOM\" ]; then echo \"🎯 Custom compact instructions: $CUSTOM\"; fi; echo \"✅ Ready for compact operation\"'"
-          }
-        ]
-      },
-      {
-        "matcher": "auto",
-        "hooks": [
-          {
-            "type": "command",
-            "command": "/bin/bash -c 'echo \"🔄 Auto-Compact Guidance (Context Window Full):\"; echo \"📋 CRITICAL: Before compacting, ensure you understand:\"; echo \"   • All 54 agents available in .claude/agents/ directory\"; echo \"   • Concurrent execution patterns from CLAUDE.md\"; echo \"   • Batchtools optimization for 300% performance gains\"; echo \"   • Swarm coordination strategies for complex tasks\"; echo \"⚡ Apply GOLDEN RULE: Always batch operations in single messages\"; echo \"✅ Auto-compact proceeding with full agent context\"'"
-          }
-        ]
-      }
-    ],
-    "Stop": [
-      {
-        "hooks": [
-          {
-            "type": "command",
-            "description": "Session end - Train models and compress learnings",
-            "command": "bash -c 'echo \"🎓 Session End: Training models on accumulated experiences...\"; npx agentdb@latest train --domain \"code-edits\" --epochs 10 --batch-size 32 2>/dev/null || echo \"⚠️ Training skipped (insufficient data)\"; echo \"🧠 Memory Distillation: Compressing session learnings...\"; npx agentdb@latest optimize-memory --compress true --consolidate-patterns true 2>/dev/null || true; npx claude-flow@alpha hooks session-end --generate-summary true --persist-state true --export-metrics true'"
-          }
-        ]
-      }
-    ]
-  },
-  "includeCoAuthoredBy": true,
-  "enabledMcpjsonServers": ["claude-flow", "ruv-swarm", "agentic-qe"],
-  "statusLine": {
-    "type": "command",
-    "command": ".claude/statusline-command.sh"
-  }
-}

package/.claude/settings.local.json

@@ -1,10 +0,0 @@
-{
-  "permissions": {
-    "allow": [
-      "mcp__ruv-swarm",
-      "mcp__claude-flow@alpha",
-      "mcp__flow-nexus"
-    ],
-    "deny": []
-  }
-}

package/.claude/statusline-command.sh

@@ -1,176 +0,0 @@
-
-#!/bin/bash
-
-# Read JSON input from stdin
-INPUT=$(cat)
-MODEL=$(echo "$INPUT" | jq -r '.model.display_name // "Claude"')
-CWD=$(echo "$INPUT" | jq -r '.workspace.current_dir // .cwd')
-DIR=$(basename "$CWD")
-
-# Replace claude-code-flow with branded name
-if [ "$DIR" = "claude-code-flow" ]; then
-  DIR="🌊 Claude Flow"
-fi
-
-# Get git branch
-BRANCH=$(cd "$CWD" 2>/dev/null && git branch --show-current 2>/dev/null)
-
-# Start building statusline
-printf "\033[1m$MODEL\033[0m in \033[36m$DIR\033[0m"
-[ -n "$BRANCH" ] && printf " on \033[33m⎇ $BRANCH\033[0m"
-
-# Claude-Flow integration
-FLOW_DIR="$CWD/.claude-flow"
-
-if [ -d "$FLOW_DIR" ]; then
-  printf " │"
-
-  # 1. Swarm Configuration & Topology
-  if [ -f "$FLOW_DIR/swarm-config.json" ]; then
-    STRATEGY=$(jq -r '.defaultStrategy // empty' "$FLOW_DIR/swarm-config.json" 2>/dev/null)
-    if [ -n "$STRATEGY" ]; then
-      # Map strategy to topology icon
-      case "$STRATEGY" in
-        "balanced") TOPO_ICON="⚡mesh" ;;
-        "conservative") TOPO_ICON="⚡hier" ;;
-        "aggressive") TOPO_ICON="⚡ring" ;;
-        *) TOPO_ICON="⚡$STRATEGY" ;;
-      esac
-      printf " \033[35m$TOPO_ICON\033[0m"
-
-      # Count agent profiles as "configured agents"
-      AGENT_COUNT=$(jq -r '.agentProfiles | length' "$FLOW_DIR/swarm-config.json" 2>/dev/null)
-      if [ -n "$AGENT_COUNT" ] && [ "$AGENT_COUNT" != "null" ] && [ "$AGENT_COUNT" -gt 0 ]; then
-        printf "  \033[35m🤖 $AGENT_COUNT\033[0m"
-      fi
-    fi
-  fi
-
-  # 2. Real-time System Metrics
-  if [ -f "$FLOW_DIR/metrics/system-metrics.json" ]; then
-    # Get latest metrics (last entry in array)
-    LATEST=$(jq -r '.[-1]' "$FLOW_DIR/metrics/system-metrics.json" 2>/dev/null)
-
-    if [ -n "$LATEST" ] && [ "$LATEST" != "null" ]; then
-      # Memory usage
-      MEM_PERCENT=$(echo "$LATEST" | jq -r '.memoryUsagePercent // 0' | awk '{printf "%.0f", $1}')
-      if [ -n "$MEM_PERCENT" ] && [ "$MEM_PERCENT" != "null" ]; then
-        # Color-coded memory (green <60%, yellow 60-80%, red >80%)
-        if [ "$MEM_PERCENT" -lt 60 ]; then
-          MEM_COLOR="\033[32m"  # Green
-        elif [ "$MEM_PERCENT" -lt 80 ]; then
-          MEM_COLOR="\033[33m"  # Yellow
-        else
-          MEM_COLOR="\033[31m"  # Red
-        fi
-        printf "  ${MEM_COLOR}💾 ${MEM_PERCENT}%\033[0m"
-      fi
-
-      # CPU load
-      CPU_LOAD=$(echo "$LATEST" | jq -r '.cpuLoad // 0' | awk '{printf "%.0f", $1 * 100}')
-      if [ -n "$CPU_LOAD" ] && [ "$CPU_LOAD" != "null" ]; then
-        # Color-coded CPU (green <50%, yellow 50-75%, red >75%)
-        if [ "$CPU_LOAD" -lt 50 ]; then
-          CPU_COLOR="\033[32m"  # Green
-        elif [ "$CPU_LOAD" -lt 75 ]; then
-          CPU_COLOR="\033[33m"  # Yellow
-        else
-          CPU_COLOR="\033[31m"  # Red
-        fi
-        printf "  ${CPU_COLOR}⚙ ${CPU_LOAD}%\033[0m"
-      fi
-    fi
-  fi
-
-  # 3. Session State
-  if [ -f "$FLOW_DIR/session-state.json" ]; then
-    SESSION_ID=$(jq -r '.sessionId // empty' "$FLOW_DIR/session-state.json" 2>/dev/null)
-    ACTIVE=$(jq -r '.active // false' "$FLOW_DIR/session-state.json" 2>/dev/null)
-
-    if [ "$ACTIVE" = "true" ] && [ -n "$SESSION_ID" ]; then
-      # Show abbreviated session ID
-      SHORT_ID=$(echo "$SESSION_ID" | cut -d'-' -f1)
-      printf "  \033[34m🔄 $SHORT_ID\033[0m"
-    fi
-  fi
-
-  # 4. Performance Metrics from task-metrics.json
-  if [ -f "$FLOW_DIR/metrics/task-metrics.json" ]; then
-    # Parse task metrics for success rate, avg time, and streak
-    METRICS=$(jq -r '
-      # Calculate metrics
-      (map(select(.success == true)) | length) as $successful |
-      (length) as $total |
-      (if $total > 0 then ($successful / $total * 100) else 0 end) as $success_rate |
-      (map(.duration // 0) | add / length) as $avg_duration |
-      # Calculate streak (consecutive successes from end)
-      (reverse |
-        reduce .[] as $task (0;
-          if $task.success == true then . + 1 else 0 end
-        )
-      ) as $streak |
-      {
-        success_rate: $success_rate,
-        avg_duration: $avg_duration,
-        streak: $streak,
-        total: $total
-      } | @json
-    ' "$FLOW_DIR/metrics/task-metrics.json" 2>/dev/null)
-
-    if [ -n "$METRICS" ] && [ "$METRICS" != "null" ]; then
-      # Success Rate
-      SUCCESS_RATE=$(echo "$METRICS" | jq -r '.success_rate // 0' | awk '{printf "%.0f", $1}')
-      TOTAL_TASKS=$(echo "$METRICS" | jq -r '.total // 0')
-
-      if [ -n "$SUCCESS_RATE" ] && [ "$TOTAL_TASKS" -gt 0 ]; then
-        # Color-code: Green (>80%), Yellow (60-80%), Red (<60%)
-        if [ "$SUCCESS_RATE" -gt 80 ]; then
-          SUCCESS_COLOR="\033[32m"  # Green
-        elif [ "$SUCCESS_RATE" -ge 60 ]; then
-          SUCCESS_COLOR="\033[33m"  # Yellow
-        else
-          SUCCESS_COLOR="\033[31m"  # Red
-        fi
-        printf "  ${SUCCESS_COLOR}🎯 ${SUCCESS_RATE}%\033[0m"
-      fi
-
-      # Average Time
-      AVG_TIME=$(echo "$METRICS" | jq -r '.avg_duration // 0')
-      if [ -n "$AVG_TIME" ] && [ "$TOTAL_TASKS" -gt 0 ]; then
-        # Format smartly: seconds, minutes, or hours
-        if [ $(echo "$AVG_TIME < 60" | bc -l 2>/dev/null || echo 0) -eq 1 ]; then
-          TIME_STR=$(echo "$AVG_TIME" | awk '{printf "%.1fs", $1}')
-        elif [ $(echo "$AVG_TIME < 3600" | bc -l 2>/dev/null || echo 0) -eq 1 ]; then
-          TIME_STR=$(echo "$AVG_TIME" | awk '{printf "%.1fm", $1/60}')
-        else
-          TIME_STR=$(echo "$AVG_TIME" | awk '{printf "%.1fh", $1/3600}')
-        fi
-        printf "  \033[36m⏱️  $TIME_STR\033[0m"
-      fi
-
-      # Streak (only show if > 0)
-      STREAK=$(echo "$METRICS" | jq -r '.streak // 0')
-      if [ -n "$STREAK" ] && [ "$STREAK" -gt 0 ]; then
-        printf "  \033[91m🔥 $STREAK\033[0m"
-      fi
-    fi
-  fi
-
-  # 5. Active Tasks (check for task files)
-  if [ -d "$FLOW_DIR/tasks" ]; then
-    TASK_COUNT=$(find "$FLOW_DIR/tasks" -name "*.json" -type f 2>/dev/null | wc -l)
-    if [ "$TASK_COUNT" -gt 0 ]; then
-      printf "  \033[36m📋 $TASK_COUNT\033[0m"
-    fi
-  fi
-
-  # 6. Check for hooks activity
-  if [ -f "$FLOW_DIR/hooks-state.json" ]; then
-    HOOKS_ACTIVE=$(jq -r '.enabled // false' "$FLOW_DIR/hooks-state.json" 2>/dev/null)
-    if [ "$HOOKS_ACTIVE" = "true" ]; then
-      printf " \033[35m🔗\033[0m"
-    fi
-  fi
-fi
-
-echo