claude-flow-guidance-implementation 0.1.0

package/.agents/README.md

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+# .agents Directory
+
+This directory contains agent configuration and skills for OpenAI Codex CLI.
+
+## Structure
+
+```
+.agents/
+  config.toml     # Main configuration file
+  skills/         # Skill definitions
+    skill-name/
+      SKILL.md    # Skill instructions
+      scripts/    # Optional scripts
+      docs/       # Optional documentation
+  README.md       # This file
+```
+
+## Configuration
+
+The `config.toml` file controls:
+- Model selection
+- Approval policies
+- Sandbox modes
+- MCP server connections
+- Skills configuration
+
+## Skills
+
+Skills are invoked using `$skill-name` syntax. Each skill has:
+- YAML frontmatter with metadata
+- Trigger and skip conditions
+- Commands and examples
+
+## Documentation
+
+- Main instructions: `AGENTS.md` (project root)
+- Local overrides: `.codex/AGENTS.override.md` (gitignored)
+- Claude Flow: https://github.com/ruvnet/claude-flow

package/.agents/config.toml

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+# =============================================================================
+# Claude Flow V3 - Codex Configuration
+# =============================================================================
+# Generated by: @claude-flow/codex
+# Documentation: https://github.com/ruvnet/claude-flow
+# 
+# This file configures the Codex CLI for Claude Flow integration.
+# Place in .agents/config.toml (project) or .codex/config.toml (user).
+# =============================================================================
+
+# =============================================================================
+# Core Settings
+# =============================================================================
+
+# Model selection - the AI model to use for code generation
+# Options: gpt-5.3-codex, gpt-4o, claude-sonnet, claude-opus
+model = "gpt-5.3-codex"
+
+# Approval policy determines when human approval is required
+# - untrusted: Always require approval
+# - on-failure: Require approval only after failures
+# - on-request: Require approval for significant changes
+# - never: Auto-approve all actions (use with caution)
+approval_policy = "on-request"
+
+# Sandbox mode controls file system access
+# - read-only: Can only read files, no modifications
+# - workspace-write: Can write within workspace directory
+# - danger-full-access: Full file system access (dangerous)
+sandbox_mode = "workspace-write"
+
+# Web search enables internet access for research
+# - disabled: No web access
+# - cached: Use cached results when available
+# - live: Always fetch fresh results
+web_search = "cached"
+
+# =============================================================================
+# Project Documentation
+# =============================================================================
+
+# Maximum bytes to read from AGENTS.md files
+project_doc_max_bytes = 65536
+
+# Fallback filenames if AGENTS.md not found
+project_doc_fallback_filenames = [
+  "AGENTS.md",
+  "TEAM_GUIDE.md",
+  ".agents.md"
+]
+
+# =============================================================================
+# Features
+# =============================================================================
+
+[features]
+# Enable child AGENTS.md guidance
+child_agents_md = true
+
+# Cache shell environment for faster repeated commands
+shell_snapshot = true
+
+# Smart approvals based on request context
+request_rule = true
+
+# Enable remote compaction for large histories
+remote_compaction = true
+
+# =============================================================================
+# MCP Servers
+# =============================================================================
+
+[mcp_servers.claude-flow]
+command = "npx"
+args = ["-y", "@claude-flow/cli@latest"]
+enabled = true
+tool_timeout_sec = 120
+
+# =============================================================================
+# Skills Configuration
+# =============================================================================
+
+[[skills.config]]
+path = ".agents/skills/swarm-orchestration"
+enabled = true
+
+[[skills.config]]
+path = ".agents/skills/memory-management"
+enabled = true
+
+[[skills.config]]
+path = ".agents/skills/sparc-methodology"
+enabled = true
+
+[[skills.config]]
+path = ".agents/skills/security-audit"
+enabled = true
+
+# =============================================================================
+# Profiles
+# =============================================================================
+
+# Development profile - more permissive for local work
+[profiles.dev]
+approval_policy = "never"
+sandbox_mode = "danger-full-access"
+web_search = "live"
+
+# Safe profile - maximum restrictions
+[profiles.safe]
+approval_policy = "untrusted"
+sandbox_mode = "read-only"
+web_search = "disabled"
+
+# CI profile - for automated pipelines
+[profiles.ci]
+approval_policy = "never"
+sandbox_mode = "workspace-write"
+web_search = "cached"
+
+# =============================================================================
+# History
+# =============================================================================
+
+[history]
+# Save all session transcripts
+persistence = "save-all"
+
+# =============================================================================
+# Shell Environment
+# =============================================================================
+
+[shell_environment_policy]
+# Inherit environment variables
+inherit = "core"
+
+# Exclude sensitive variables
+exclude = ["*_KEY", "*_SECRET", "*_TOKEN", "*_PASSWORD"]
+
+# =============================================================================
+# Sandbox Workspace Write Settings
+# =============================================================================
+
+[sandbox_workspace_write]
+# Additional writable paths beyond workspace
+writable_roots = []
+
+# Allow network access
+network_access = true
+
+# Exclude temp directories
+exclude_slash_tmp = false
+
+# =============================================================================
+# Security Settings
+# =============================================================================
+
+[security]
+# Enable input validation for all user inputs
+input_validation = true
+
+# Prevent directory traversal attacks
+path_traversal_prevention = true
+
+# Scan for hardcoded secrets
+secret_scanning = true
+
+# Scan dependencies for known CVEs
+cve_scanning = true
+
+# Maximum file size for operations (bytes)
+max_file_size = 10485760
+
+# Allowed file extensions (empty = allow all)
+allowed_extensions = []
+
+# Blocked file patterns (regex)
+blocked_patterns = ["\\.env$", "credentials\\.json$", "\\.pem$", "\\.key$"]
+
+# =============================================================================
+# Performance Settings
+# =============================================================================
+
+[performance]
+# Maximum concurrent agents
+max_agents = 8
+
+# Task timeout in seconds
+task_timeout = 300
+
+# Memory limit per agent
+memory_limit = "512MB"
+
+# Enable response caching
+cache_enabled = true
+
+# Cache TTL in seconds
+cache_ttl = 3600
+
+# Enable parallel task execution
+parallel_execution = true
+
+# =============================================================================
+# Logging Settings
+# =============================================================================
+
+[logging]
+# Log level: debug, info, warn, error
+level = "info"
+
+# Log format: json, text, pretty
+format = "pretty"
+
+# Log destination: stdout, file, both
+destination = "stdout"
+
+# =============================================================================
+# Neural Intelligence Settings
+# =============================================================================
+
+[neural]
+# Enable SONA (Self-Optimizing Neural Architecture)
+sona_enabled = true
+
+# Enable HNSW vector search
+hnsw_enabled = true
+
+# HNSW index parameters
+hnsw_m = 16
+hnsw_ef_construction = 200
+hnsw_ef_search = 100
+
+# Enable pattern learning
+pattern_learning = true
+
+# Learning rate for neural adaptation
+learning_rate = 0.01
+
+# =============================================================================
+# Swarm Orchestration Settings
+# =============================================================================
+
+[swarm]
+# Default topology: hierarchical, mesh, ring, star
+default_topology = "hierarchical"
+
+# Default strategy: balanced, specialized, adaptive
+default_strategy = "specialized"
+
+# Consensus algorithm: raft, byzantine, gossip
+consensus = "raft"
+
+# Enable anti-drift measures
+anti_drift = true
+
+# Checkpoint interval (tasks)
+checkpoint_interval = 10
+
+# =============================================================================
+# Hooks Configuration
+# =============================================================================
+
+[hooks]
+# Enable lifecycle hooks
+enabled = true
+
+# Pre-task hook
+pre_task = true
+
+# Post-task hook (for learning)
+post_task = true
+
+# Enable neural training on post-edit
+train_on_edit = true
+
+# =============================================================================
+# Background Workers
+# =============================================================================
+
+[workers]
+# Enable background workers
+enabled = true
+
+# Worker configuration
+[workers.audit]
+enabled = true
+priority = "critical"
+interval = 300
+
+[workers.optimize]
+enabled = true
+priority = "high"
+interval = 600
+
+[workers.consolidate]
+enabled = true
+priority = "low"
+interval = 1800

package/.agents/skills/memory-management/SKILL.md

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+---
+name: memory-management
+description: >
+  AgentDB memory system with HNSW vector search. Provides 150x-12,500x faster pattern retrieval, persistent storage, and semantic search capabilities for learning and knowledge management.
+  Use when: need to store successful patterns, searching for similar solutions, semantic lookup of past work, learning from previous tasks, sharing knowledge between agents, building knowledge base.
+  Skip when: no learning needed, ephemeral one-off tasks, external data sources available, read-only exploration.
+---
+
+# Memory Management Skill
+
+## Purpose
+AgentDB memory system with HNSW vector search. Provides 150x-12,500x faster pattern retrieval, persistent storage, and semantic search capabilities for learning and knowledge management.
+
+## When to Trigger
+- need to store successful patterns
+- searching for similar solutions
+- semantic lookup of past work
+- learning from previous tasks
+- sharing knowledge between agents
+- building knowledge base
+
+## When to Skip
+- no learning needed
+- ephemeral one-off tasks
+- external data sources available
+- read-only exploration
+
+## Commands
+
+### Store Pattern
+Store a pattern or knowledge item in memory
+
+```bash
+npx @claude-flow/cli memory store --key "[key]" --value "[value]" --namespace patterns
+```
+
+**Example:**
+```bash
+npx @claude-flow/cli memory store --key "auth-jwt-pattern" --value "JWT validation with refresh tokens" --namespace patterns
+```
+
+### Semantic Search
+Search memory using semantic similarity
+
+```bash
+npx @claude-flow/cli memory search --query "[search terms]" --limit 10
+```
+
+**Example:**
+```bash
+npx @claude-flow/cli memory search --query "authentication best practices" --limit 5
+```
+
+### Retrieve Entry
+Retrieve a specific memory entry by key
+
+```bash
+npx @claude-flow/cli memory get --key "[key]" --namespace [namespace]
+```
+
+**Example:**
+```bash
+npx @claude-flow/cli memory get --key "auth-jwt-pattern" --namespace patterns
+```
+
+### List Entries
+List all entries in a namespace
+
+```bash
+npx @claude-flow/cli memory list --namespace [namespace]
+```
+
+**Example:**
+```bash
+npx @claude-flow/cli memory list --namespace patterns --limit 20
+```
+
+### Delete Entry
+Delete a memory entry
+
+```bash
+npx @claude-flow/cli memory delete --key "[key]" --namespace [namespace]
+```
+
+### Initialize HNSW Index
+Initialize HNSW vector search index
+
+```bash
+npx @claude-flow/cli memory init --enable-hnsw
+```
+
+### Memory Stats
+Show memory usage statistics
+
+```bash
+npx @claude-flow/cli memory stats
+```
+
+### Export Memory
+Export memory to JSON
+
+```bash
+npx @claude-flow/cli memory export --output memory-backup.json
+```
+
+
+## Scripts
+
+| Script | Path | Description |
+|--------|------|-------------|
+| `memory-backup` | `.agents/scripts/memory-backup.sh` | Backup memory to external storage |
+| `memory-consolidate` | `.agents/scripts/memory-consolidate.sh` | Consolidate and optimize memory |
+
+
+## References
+
+| Document | Path | Description |
+|----------|------|-------------|
+| `HNSW Guide` | `docs/hnsw.md` | HNSW vector search configuration |
+| `Memory Schema` | `docs/memory-schema.md` | Memory namespace and schema reference |
+
+## Best Practices
+1. Check memory for existing patterns before starting
+2. Use hierarchical topology for coordination
+3. Store successful patterns after completion
+4. Document any new learnings

package/.agents/skills/memory-management/scripts/memory-backup.sh

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+#!/bin/bash
+# Memory Management - Backup Script
+# Export memory to backup file
+
+set -e
+
+BACKUP_DIR="${BACKUP_DIR:-./.backups}"
+TIMESTAMP=$(date +%Y%m%d_%H%M%S)
+BACKUP_FILE="${BACKUP_DIR}/memory_${TIMESTAMP}.json"
+
+mkdir -p "$BACKUP_DIR"
+
+echo "Backing up memory to $BACKUP_FILE..."
+npx @claude-flow/cli memory export --output "$BACKUP_FILE"
+
+echo "Backup complete: $BACKUP_FILE"

package/.agents/skills/memory-management/scripts/memory-consolidate.sh

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+#!/bin/bash
+# Memory Management - Consolidate Script
+# Optimize and consolidate memory
+
+set -e
+
+echo "Running memory consolidation..."
+npx @claude-flow/cli hooks worker dispatch --trigger consolidate
+
+echo "Memory consolidation complete"
+npx @claude-flow/cli memory stats

package/.agents/skills/security-audit/SKILL.md

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+---
+name: security-audit
+description: >
+  Comprehensive security scanning and vulnerability detection. Includes input validation, path traversal prevention, CVE detection, and secure coding pattern enforcement.
+  Use when: authentication implementation, authorization logic, payment processing, user data handling, API endpoint creation, file upload handling, database queries, external API integration.
+  Skip when: read-only operations on public data, internal development tooling, static documentation, styling changes.
+---
+
+# Security Audit Skill
+
+## Purpose
+Comprehensive security scanning and vulnerability detection. Includes input validation, path traversal prevention, CVE detection, and secure coding pattern enforcement.
+
+## When to Trigger
+- authentication implementation
+- authorization logic
+- payment processing
+- user data handling
+- API endpoint creation
+- file upload handling
+- database queries
+- external API integration
+
+## When to Skip
+- read-only operations on public data
+- internal development tooling
+- static documentation
+- styling changes
+
+## Commands
+
+### Full Security Scan
+Run comprehensive security analysis on the codebase
+
+```bash
+npx @claude-flow/cli security scan --depth full
+```
+
+**Example:**
+```bash
+npx @claude-flow/cli security scan --depth full --output security-report.json
+```
+
+### Input Validation Check
+Check for input validation issues
+
+```bash
+npx @claude-flow/cli security scan --check input-validation
+```
+
+**Example:**
+```bash
+npx @claude-flow/cli security scan --check input-validation --path ./src/api
+```
+
+### Path Traversal Check
+Check for path traversal vulnerabilities
+
+```bash
+npx @claude-flow/cli security scan --check path-traversal
+```
+
+### SQL Injection Check
+Check for SQL injection vulnerabilities
+
+```bash
+npx @claude-flow/cli security scan --check sql-injection
+```
+
+### XSS Check
+Check for cross-site scripting vulnerabilities
+
+```bash
+npx @claude-flow/cli security scan --check xss
+```
+
+### CVE Scan
+Scan dependencies for known CVEs
+
+```bash
+npx @claude-flow/cli security cve --scan
+```
+
+**Example:**
+```bash
+npx @claude-flow/cli security cve --scan --severity high
+```
+
+### Security Audit Report
+Generate full security audit report
+
+```bash
+npx @claude-flow/cli security audit --report
+```
+
+**Example:**
+```bash
+npx @claude-flow/cli security audit --report --format markdown --output SECURITY.md
+```
+
+### Threat Modeling
+Run threat modeling analysis
+
+```bash
+npx @claude-flow/cli security threats --analyze
+```
+
+### Validate Secrets
+Check for hardcoded secrets
+
+```bash
+npx @claude-flow/cli security validate --check secrets
+```
+
+
+## Scripts
+
+| Script | Path | Description |
+|--------|------|-------------|
+| `security-scan` | `.agents/scripts/security-scan.sh` | Run full security scan pipeline |
+| `cve-remediate` | `.agents/scripts/cve-remediate.sh` | Auto-remediate known CVEs |
+
+
+## References
+
+| Document | Path | Description |
+|----------|------|-------------|
+| `Security Checklist` | `docs/security-checklist.md` | Security review checklist |
+| `OWASP Guide` | `docs/owasp-top10.md` | OWASP Top 10 mitigation guide |
+
+## Best Practices
+1. Check memory for existing patterns before starting
+2. Use hierarchical topology for coordination
+3. Store successful patterns after completion
+4. Document any new learnings

package/.agents/skills/security-audit/scripts/cve-remediate.sh

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+#!/bin/bash
+# Security Audit - CVE Remediation Script
+# Auto-remediate known CVEs
+
+set -e
+
+echo "Scanning for CVEs..."
+npx @claude-flow/cli security cve --scan --severity high
+
+echo "Attempting auto-remediation..."
+npm audit fix
+
+echo "Re-scanning after remediation..."
+npx @claude-flow/cli security cve --scan
+
+echo "CVE remediation complete"

package/.agents/skills/security-audit/scripts/security-scan.sh

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+#!/bin/bash
+# Security Audit - Full Scan Script
+# Run comprehensive security scan pipeline
+
+set -e
+
+echo "Running full security scan..."
+
+# Input validation
+echo "Checking input validation..."
+npx @claude-flow/cli security scan --check input-validation
+
+# Path traversal
+echo "Checking path traversal..."
+npx @claude-flow/cli security scan --check path-traversal
+
+# SQL injection
+echo "Checking SQL injection..."
+npx @claude-flow/cli security scan --check sql-injection
+
+# XSS
+echo "Checking XSS..."
+npx @claude-flow/cli security scan --check xss
+
+# Secrets
+echo "Checking for hardcoded secrets..."
+npx @claude-flow/cli security validate --check secrets
+
+# CVE scan
+echo "Scanning dependencies for CVEs..."
+npx @claude-flow/cli security cve --scan
+
+echo "Security scan complete"