@claude-flow/cli 3.5.43 → 3.5.45

package/README.md

@@ -152,10 +152,10 @@ npx ruflo@latest hooks intelligence --status
 
 ```bash
 # One-line install (recommended)
-curl -fsSL https://cdn.jsdelivr.net/gh/ruvnet/claude-flow@main/scripts/install.sh | bash
+curl -fsSL https://cdn.jsdelivr.net/gh/ruvnet/ruflo@main/scripts/install.sh | bash
 
 # Or full setup with MCP + diagnostics
-curl -fsSL https://cdn.jsdelivr.net/gh/ruvnet/claude-flow@main/scripts/install.sh | bash -s -- --full
+curl -fsSL https://cdn.jsdelivr.net/gh/ruvnet/ruflo@main/scripts/install.sh | bash -s -- --full
 
 # Or via npx
 npx ruflo@latest init --wizard
@@ -438,10 +438,10 @@ claude --dangerously-skip-permissions
 
 ```bash
 # curl-style installer with progress display
-curl -fsSL https://cdn.jsdelivr.net/gh/ruvnet/claude-flow@main/scripts/install.sh | bash
+curl -fsSL https://cdn.jsdelivr.net/gh/ruvnet/ruflo@main/scripts/install.sh | bash
 
 # Full setup (global + MCP + diagnostics)
-curl -fsSL https://cdn.jsdelivr.net/gh/ruvnet/claude-flow@main/scripts/install.sh | bash -s -- --full
+curl -fsSL https://cdn.jsdelivr.net/gh/ruvnet/ruflo@main/scripts/install.sh | bash -s -- --full
 ```
 
 <details>
@@ -668,21 +668,24 @@ npx ruflo@latest init
 # Start MCP server for Claude Code integration
 npx ruflo@latest mcp start
 
-# Run a task with agents
-npx ruflo@latest --agent coder --task "Implement user authentication"
+# Spawn a coding agent
+npx ruflo@latest agent spawn -t coder --name my-coder
 
-# List available agents
-npx ruflo@latest --list
+# Launch a hive-mind swarm with an objective
+npx ruflo@latest hive-mind spawn "Implement user authentication"
+
+# List available agent types
+npx ruflo@latest agent list
 ```
 
 ### Upgrading
 
 ```bash
 # Update helpers and statusline (preserves your data)
-npx ruflo@v3alpha init upgrade
+npx ruflo@latest init upgrade
 
 # Update AND add any missing skills/agents/commands
-npx ruflo@v3alpha init upgrade --add-missing
+npx ruflo@latest init upgrade --add-missing
 ```
 
 The `--add-missing` flag automatically detects and installs new skills, agents, and commands that were added in newer versions, without overwriting your existing customizations.
@@ -838,7 +841,7 @@ Complex projects fail when implementation drifts from the original plan. Ruflo s
 
 | Feature | Description |
 |---------|-------------|
-| **Architecture Decision Records** | 10 ADRs defining system behavior, integration patterns, and security requirements |
+| **Architecture Decision Records** | 70+ ADRs defining system behavior, integration patterns, and security requirements |
 | **Domain-Driven Design** | 5 bounded contexts with clean interfaces preventing cross-domain pollution |
 | **Automated Spec Generation** | Agents create specs from requirements using SPARC methodology |
 | **Drift Detection** | Continuous monitoring flags when code diverges from spec |
@@ -1183,7 +1186,7 @@ Ruflo runs as an MCP (Model Context Protocol) server, allowing you to connect it
 
 ```bash
 # Start Ruflo MCP server in any environment
-npx ruflo@v3alpha mcp start
+npx ruflo@latest mcp start
 ```
 
 <details open>
@@ -1200,7 +1203,7 @@ npx ruflo@v3alpha mcp start
   "mcpServers": {
     "ruflo": {
       "command": "npx",
-      "args": ["ruflo@v3alpha", "mcp", "start"],
+      "args": ["ruflo@latest", "mcp", "start"],
       "env": {
         "ANTHROPIC_API_KEY": "sk-ant-..."
       }
@@ -1220,12 +1223,12 @@ Restart Claude Desktop after saving. Look for the MCP indicator (hammer icon) in
 
 ```bash
 # Add via CLI (recommended)
-claude mcp add ruflo -- npx ruflo@v3alpha mcp start
+claude mcp add ruflo -- npx ruflo@latest mcp start
 
 # Or add with environment variables
 claude mcp add ruflo \
   --env ANTHROPIC_API_KEY=sk-ant-... \
-  -- npx ruflo@v3alpha mcp start
+  -- npx ruflo@latest mcp start
 
 # Verify installation
 claude mcp list
@@ -1254,7 +1257,7 @@ Create `.vscode/mcp.json` in your project:
   "mcpServers": {
     "ruflo": {
       "command": "npx",
-      "args": ["ruflo@v3alpha", "mcp", "start"],
+      "args": ["ruflo@latest", "mcp", "start"],
       "env": {
         "ANTHROPIC_API_KEY": "sk-ant-..."
       }
@@ -1281,7 +1284,7 @@ Create `.cursor/mcp.json` in your project (or global config):
   "mcpServers": {
     "ruflo": {
       "command": "npx",
-      "args": ["ruflo@v3alpha", "mcp", "start"],
+      "args": ["ruflo@latest", "mcp", "start"],
       "env": {
         "ANTHROPIC_API_KEY": "sk-ant-..."
       }
@@ -1308,7 +1311,7 @@ Create `.cursor/mcp.json` in your project (or global config):
   "mcpServers": {
     "ruflo": {
       "command": "npx",
-      "args": ["ruflo@v3alpha", "mcp", "start"],
+      "args": ["ruflo@latest", "mcp", "start"],
       "env": {
         "ANTHROPIC_API_KEY": "sk-ant-..."
       }
@@ -1339,7 +1342,7 @@ For ChatGPT, you need a remote MCP server (not local stdio). Deploy ruflo to a s
 
 ```bash
 # Start with HTTP transport
-npx ruflo@v3alpha mcp start --transport http --port 3000
+npx ruflo@latest mcp start --transport http --port 3000
 ```
 
 Then add the server URL in ChatGPT Connectors settings.
@@ -1370,7 +1373,7 @@ const mcpConfig = {
   servers: [{
     name: 'ruflo',
     command: 'npx',
-    args: ['ruflo@v3alpha', 'mcp', 'start']
+    args: ['ruflo@latest', 'mcp', 'start']
   }]
 };
 ```
@@ -1393,7 +1396,7 @@ JetBrains AI Assistant supports MCP for IntelliJ IDEA, PyCharm, WebStorm, and ot
 {
   "name": "ruflo",
   "command": "npx",
-  "args": ["ruflo@v3alpha", "mcp", "start"]
+  "args": ["ruflo@latest", "mcp", "start"]
 }
 ```
 
@@ -1707,7 +1710,7 @@ npx ruflo@latest hooks task-completed --task-id <id> --train-patterns
 </details>
 
 <details>
-<summary>🔧 <strong>MCP Tools & Integration</strong> — 31+ tools across 7 categories</summary>
+<summary>🔧 <strong>MCP Tools & Integration</strong> — 259 tools across 7 categories</summary>
 
 Full MCP server with tools for coordination, monitoring, memory, and GitHub integration.
 
@@ -2041,8 +2044,8 @@ Workers run automatically based on context, or dispatch manually via MCP tools.
 | **TestGaps** | `testgaps` | Test coverage analysis | Code changes without tests |
 
 ```bash
-npx ruflo@v3alpha worker dispatch --trigger audit --context "./src"
-npx ruflo@v3alpha worker status
+npx ruflo@latest worker dispatch --trigger audit --context "./src"
+npx ruflo@latest worker status
 ```
 
 </details>
@@ -2580,19 +2583,19 @@ Cross-platform TypeScript-based daemon service with auto-scheduling:
 **Commands:**
 ```bash
 # Start daemon (auto-runs on SessionStart hooks)
-npx ruflo@v3alpha daemon start
+npx ruflo@latest daemon start
 
 # Check status with worker history
-npx ruflo@v3alpha daemon status
+npx ruflo@latest daemon status
 
 # Manually trigger a worker
-npx ruflo@v3alpha daemon trigger map
+npx ruflo@latest daemon trigger map
 
 # Enable/disable workers
-npx ruflo@v3alpha daemon enable map audit optimize
+npx ruflo@latest daemon enable map audit optimize
 
 # Stop daemon
-npx ruflo@v3alpha daemon stop
+npx ruflo@latest daemon stop
 ```
 
 **Daemon Status Output:**
@@ -2708,25 +2711,25 @@ Complete command-line interface for all Ruflo operations.
 
 ```bash
 # Initialize project with wizard
-npx ruflo@v3alpha init --wizard
+npx ruflo@latest init --wizard
 
 # Start daemon with background workers
-npx ruflo@v3alpha daemon start
+npx ruflo@latest daemon start
 
 # Spawn an agent with specific type
-npx ruflo@v3alpha agent spawn -t coder --name my-coder
+npx ruflo@latest agent spawn -t coder --name my-coder
 
 # Initialize swarm with V3 mode
-npx ruflo@v3alpha swarm init --v3-mode
+npx ruflo@latest swarm init --v3-mode
 
 # Search memory (HNSW-indexed, 150x faster)
-npx ruflo@v3alpha memory search -q "authentication patterns"
+npx ruflo@latest memory search -q "authentication patterns"
 
 # Run security scan
-npx ruflo@v3alpha security scan --depth full
+npx ruflo@latest security scan --depth full
 
 # Performance benchmark
-npx ruflo@v3alpha performance benchmark --suite all
+npx ruflo@latest performance benchmark --suite all
 ```
 
 </details>
@@ -2734,7 +2737,7 @@ npx ruflo@v3alpha performance benchmark --suite all
 <details>
 <summary>🩺 <strong>Doctor Health Checks</strong> — System diagnostics with auto-fix</summary>
 
-Run `npx ruflo@v3alpha doctor` to diagnose and fix common issues.
+Run `npx ruflo@latest doctor` to diagnose and fix common issues.
 
 **Health Checks Performed:**
 
@@ -2755,22 +2758,22 @@ Run `npx ruflo@v3alpha doctor` to diagnose and fix common issues.
 
 ```bash
 # Run full diagnostics
-npx ruflo@v3alpha doctor
+npx ruflo@latest doctor
 
 # Run diagnostics with auto-fix
-npx ruflo@v3alpha doctor --fix
+npx ruflo@latest doctor --fix
 
 # Check specific component
-npx ruflo@v3alpha doctor --component memory
+npx ruflo@latest doctor --component memory
 
 # Verbose output
-npx ruflo@v3alpha doctor --verbose
+npx ruflo@latest doctor --verbose
 ```
 
 **Output Example:**
 
 ```
-🩺 Ruflo Doctor v3.0.0-alpha
+🩺 Ruflo Doctor v3.5
 
 ✅ Node.js      20.11.0 (required: 20+)
 ✅ npm          10.2.4 (required: 9+)
@@ -2814,16 +2817,16 @@ The embeddings package (v3.0.0-alpha.12) provides high-performance vector embedd
 
 ```bash
 # Initialize embeddings system
-npx ruflo@v3alpha embeddings init
+npx ruflo@latest embeddings init
 
 # Generate embedding for text
-npx ruflo@v3alpha embeddings embed "authentication patterns"
+npx ruflo@latest embeddings embed "authentication patterns"
 
 # Batch embed multiple texts
-npx ruflo@v3alpha embeddings batch --file texts.txt
+npx ruflo@latest embeddings batch --file texts.txt
 
 # Search with semantic similarity
-npx ruflo@v3alpha embeddings search "login flow" --top-k 5
+npx ruflo@latest embeddings search "login flow" --top-k 5
 ```
 
 **Programmatic:**
@@ -2860,59 +2863,59 @@ Real-world scenarios and pre-built workflows for common tasks.
 
 | Scenario | What It Solves | How To Do It |
 |----------|----------------|--------------|
-| **Code Review** | Get thorough reviews with security, performance, and style checks | `npx ruflo@v3alpha --agent reviewer --task "Review PR #123"` |
-| **Test Generation** | Auto-generate unit, integration, and e2e tests for existing code | `npx ruflo@v3alpha --agent tester --task "Write tests for auth module"` |
-| **Refactoring** | Safely restructure code while maintaining behavior | `npx ruflo@v3alpha --agent coder --task "Refactor user service to use repository pattern"` |
-| **Bug Fixing** | Diagnose and fix bugs with full context analysis | `npx ruflo@v3alpha --agent coder --task "Fix race condition in checkout flow"` |
+| **Code Review** | Get thorough reviews with security, performance, and style checks | `npx ruflo@latest agent spawn -t reviewer --name pr-review` |
+| **Test Generation** | Auto-generate unit, integration, and e2e tests for existing code | `npx ruflo@latest agent spawn -t tester --name test-gen` |
+| **Refactoring** | Safely restructure code while maintaining behavior | `npx ruflo@latest hive-mind spawn "Refactor user service to repository pattern"` |
+| **Bug Fixing** | Diagnose and fix bugs with full context analysis | `npx ruflo@latest hive-mind spawn "Fix race condition in checkout flow"` |
 
 ### 🔒 Security & Compliance
 
 | Scenario | What It Solves | How To Do It |
 |----------|----------------|--------------|
-| **Security Audit** | Find vulnerabilities before attackers do | `npx ruflo@v3alpha --agent security-architect --task "Audit for OWASP Top 10"` |
-| **Dependency Scan** | Identify vulnerable packages and suggest upgrades | `npx ruflo@v3alpha security scan --depth full` |
-| **Compliance Check** | Ensure code meets security standards | `npx ruflo@v3alpha --agent security-architect --task "Check PCI-DSS compliance"` |
+| **Security Audit** | Find vulnerabilities before attackers do | `npx ruflo@latest security scan --depth full` |
+| **Dependency Scan** | Identify vulnerable packages and suggest upgrades | `npx ruflo@latest security cve --check` |
+| **Compliance Check** | Ensure code meets security standards | `npx ruflo@latest security audit` |
 
 ### 🐝 Multi-Agent Swarms
 
 | Scenario | What It Solves | How To Do It |
 |----------|----------------|--------------|
-| **Feature Development** | Coordinate multiple agents on complex features | `npx ruflo@v3alpha swarm init --topology hierarchical && npx ruflo@v3alpha task orchestrate "Build user dashboard"` |
-| **Large Refactors** | Parallel refactoring across many files without conflicts | `npx ruflo@v3alpha swarm init --topology mesh --max-agents 8` |
-| **Codebase Migration** | Migrate frameworks, languages, or patterns systematically | `npx ruflo@v3alpha task orchestrate "Migrate from Express to Fastify" --strategy adaptive` |
+| **Feature Development** | Coordinate multiple agents on complex features | `npx ruflo@latest swarm init --topology hierarchical && npx ruflo@latest task orchestrate "Build user dashboard"` |
+| **Large Refactors** | Parallel refactoring across many files without conflicts | `npx ruflo@latest swarm init --topology mesh --max-agents 8` |
+| **Codebase Migration** | Migrate frameworks, languages, or patterns systematically | `npx ruflo@latest task orchestrate "Migrate from Express to Fastify" --strategy adaptive` |
 
 ### 📊 Performance & Optimization
 
 | Scenario | What It Solves | How To Do It |
 |----------|----------------|--------------|
-| **Performance Profiling** | Find and fix bottlenecks in your application | `npx ruflo@v3alpha --agent perf-analyzer --task "Profile API endpoints"` |
-| **Query Optimization** | Speed up slow database queries | `npx ruflo@v3alpha hooks route "Optimize database queries"` |
-| **Memory Analysis** | Reduce memory usage and fix leaks | `npx ruflo@v3alpha --agent perf-analyzer --task "Analyze memory usage patterns"` |
+| **Performance Profiling** | Find and fix bottlenecks in your application | `npx ruflo@latest performance profile --target src/` |
+| **Query Optimization** | Speed up slow database queries | `npx ruflo@latest performance benchmark --suite all` |
+| **Memory Analysis** | Reduce memory usage and fix leaks | `npx ruflo@latest performance metrics` |
 
 ### 🔄 GitHub & DevOps
 
 | Scenario | What It Solves | How To Do It |
 |----------|----------------|--------------|
-| **PR Management** | Review, approve, and merge PRs efficiently | `npx ruflo@v3alpha --agent pr-manager --task "Review open PRs"` |
-| **Issue Triage** | Categorize, prioritize, and assign issues automatically | `npx ruflo@v3alpha --agent issue-tracker --task "Triage new issues"` |
-| **Release Management** | Coordinate releases with changelogs and versioning | `npx ruflo@v3alpha --agent release-manager --task "Prepare v2.0 release"` |
-| **CI/CD Optimization** | Speed up pipelines and reduce flaky tests | `npx ruflo@v3alpha --agent cicd-engineer --task "Optimize GitHub Actions workflow"` |
+| **PR Management** | Review, approve, and merge PRs efficiently | `npx ruflo@latest hive-mind spawn "Review open PRs"` |
+| **Issue Triage** | Categorize, prioritize, and assign issues automatically | `npx ruflo@latest hive-mind spawn "Triage new issues"` |
+| **Release Management** | Coordinate releases with changelogs and versioning | `npx ruflo@latest hive-mind spawn "Prepare v2.0 release"` |
+| **CI/CD Optimization** | Speed up pipelines and reduce flaky tests | `npx ruflo@latest hive-mind spawn "Optimize GitHub Actions workflow"` |
 
 ### 📋 Spec-Driven Development
 
 | Scenario | What It Solves | How To Do It |
 |----------|----------------|--------------|
-| **Generate Specs** | Create complete specifications before coding | `npx ruflo@v3alpha --agent architect --task "Create ADR for authentication system"` |
-| **Validate Implementation** | Ensure code matches specifications | `npx ruflo@v3alpha hooks progress --detailed` |
-| **Track Compliance** | Monitor spec adherence across the team | `npx ruflo@v3alpha progress sync` |
+| **Generate Specs** | Create complete specifications before coding | `npx ruflo@latest hive-mind spawn "Create ADR for authentication system"` |
+| **Validate Implementation** | Ensure code matches specifications | `npx ruflo@latest hooks progress --detailed` |
+| **Track Compliance** | Monitor spec adherence across the team | `npx ruflo@latest progress sync` |
 
 ### 🧠 Learning & Intelligence
 
 | Scenario | What It Solves | How To Do It |
 |----------|----------------|--------------|
-| **Bootstrap Intelligence** | Train the system on your codebase patterns | `npx ruflo@v3alpha hooks pretrain --depth deep` |
-| **Optimize Routing** | Improve task-to-agent matching over time | `npx ruflo@v3alpha hooks route "<task>" --include-explanation` |
-| **Transfer Learning** | Apply patterns learned from other projects | `npx ruflo@v3alpha hooks transfer <sourceProject>` |
+| **Bootstrap Intelligence** | Train the system on your codebase patterns | `npx ruflo@latest hooks pretrain --depth deep` |
+| **Optimize Routing** | Improve task-to-agent matching over time | `npx ruflo@latest hooks route "<task>" --include-explanation` |
+| **Transfer Learning** | Apply patterns learned from other projects | `npx ruflo@latest hooks transfer <sourceProject>` |
 
 </details>
 
@@ -3214,7 +3217,7 @@ When hooks run, they emit signals that guide routing decisions. Watch for these
 
 **Example Hook Output:**
 ```bash
-$ npx ruflo@v3alpha hooks pre-task --description "convert var to const in utils.ts"
+$ npx ruflo@latest hooks pre-task --description "convert var to const in utils.ts"
 
 [AGENT_BOOSTER_AVAILABLE] Intent: var-to-const
 Recommendation: Use Edit tool directly
@@ -3332,8 +3335,8 @@ The stats command shows:
 
 ```bash
 # Example: Edit with pattern learning
-npx ruflo@v3alpha hooks pre-edit ./src/auth.ts
-npx ruflo@v3alpha hooks post-edit ./src/auth.ts --success true --train-patterns
+npx ruflo@latest hooks pre-edit ./src/auth.ts
+npx ruflo@latest hooks post-edit ./src/auth.ts --success true --train-patterns
 ```
 
 #### 🧠 Intelligence & Routing Hooks (8 hooks)
@@ -3351,10 +3354,10 @@ npx ruflo@v3alpha hooks post-edit ./src/auth.ts --success true --train-patterns
 
 ```bash
 # Route a task with explanation
-npx ruflo@v3alpha hooks route "refactor authentication to use JWT" --include-explanation
+npx ruflo@latest hooks route "refactor authentication to use JWT" --include-explanation
 
 # Bootstrap intelligence from your codebase
-npx ruflo@v3alpha hooks pretrain --depth deep --model-type moe
+npx ruflo@latest hooks pretrain --depth deep --model-type moe
 ```
 
 #### 📅 Session Management Hooks (4 hooks)
@@ -3368,10 +3371,10 @@ npx ruflo@v3alpha hooks pretrain --depth deep --model-type moe
 
 ```bash
 # Start session with auto-daemon
-npx ruflo@v3alpha hooks session-start --session-id "feature-auth" --start-daemon
+npx ruflo@latest hooks session-start --session-id "feature-auth" --start-daemon
 
 # End session and export learnings
-npx ruflo@v3alpha hooks session-end --export-metrics --persist-patterns
+npx ruflo@latest hooks session-end --export-metrics --persist-patterns
 ```
 
 #### 🤖 Intelligence System Hooks (9 hooks)
@@ -3390,13 +3393,13 @@ npx ruflo@v3alpha hooks session-end --export-metrics --persist-patterns
 
 ```bash
 # Start trajectory for complex task
-npx ruflo@v3alpha hooks intelligence trajectory-start --task "implement OAuth2"
+npx ruflo@latest hooks intelligence trajectory-start --task "implement OAuth2"
 
 # Record successful action
-npx ruflo@v3alpha hooks intelligence trajectory-step --action "created token service" --quality 0.9
+npx ruflo@latest hooks intelligence trajectory-step --action "created token service" --quality 0.9
 
 # End trajectory and trigger learning
-npx ruflo@v3alpha hooks intelligence trajectory-end --success true
+npx ruflo@latest hooks intelligence trajectory-end --success true
 
 # View intelligence diagnostics and improvement trends (ADR-050)
 node .claude/helpers/hook-handler.cjs stats
@@ -3424,13 +3427,13 @@ Workers run automatically based on context, or dispatch manually.
 
 ```bash
 # List all workers
-npx ruflo@v3alpha hooks worker list
+npx ruflo@latest hooks worker list
 
 # Manually dispatch security audit
-npx ruflo@v3alpha hooks worker dispatch --trigger audit --context "./src/auth"
+npx ruflo@latest hooks worker dispatch --trigger audit --context "./src/auth"
 
 # Check worker status
-npx ruflo@v3alpha hooks worker status
+npx ruflo@latest hooks worker status
 ```
 
 ### Model Routing Hooks (3 hooks)
@@ -3445,10 +3448,10 @@ Automatically selects haiku/sonnet/opus based on task complexity.
 
 ```bash
 # Get model recommendation
-npx ruflo@v3alpha hooks model-route --task "fix typo in README"
+npx ruflo@latest hooks model-route --task "fix typo in README"
 # → Recommends: haiku (simple task, low complexity)
 
-npx ruflo@v3alpha hooks model-route --task "design distributed consensus system"
+npx ruflo@latest hooks model-route --task "design distributed consensus system"
 # → Recommends: opus (complex architecture, high reasoning)
 ```
 
@@ -3469,15 +3472,15 @@ npx ruflo@v3alpha hooks model-route --task "design distributed consensus system"
 # ══════════════════════════════════════════════════════════════════
 
 # Route task to best agent (with intelligence context injection)
-npx ruflo@v3alpha hooks route "<task>" --include-explanation
+npx ruflo@latest hooks route "<task>" --include-explanation
 
 # Start/end session with learning
-npx ruflo@v3alpha hooks session-start --start-daemon
-npx ruflo@v3alpha hooks session-end --persist-patterns
+npx ruflo@latest hooks session-start --start-daemon
+npx ruflo@latest hooks session-end --persist-patterns
 
 # View what the system has learned
-npx ruflo@v3alpha hooks metrics
-npx ruflo@v3alpha hooks intelligence stats
+npx ruflo@latest hooks metrics
+npx ruflo@latest hooks intelligence stats
 
 # Intelligence diagnostics — see if intelligence is improving
 node .claude/helpers/hook-handler.cjs stats          # Human-readable
@@ -3485,10 +3488,10 @@ node .claude/helpers/hook-handler.cjs stats --json   # JSON for scripting
 node .claude/helpers/intelligence.cjs stats           # Direct access
 
 # Bootstrap on new project
-npx ruflo@v3alpha hooks pretrain --depth deep
+npx ruflo@latest hooks pretrain --depth deep
 
 # Dispatch background worker
-npx ruflo@v3alpha hooks worker dispatch --trigger audit
+npx ruflo@latest hooks worker dispatch --trigger audit
 ```
 
 </details>
@@ -3514,38 +3517,38 @@ Share learned patterns across projects, teams, and the community via the decentr
 
 ```bash
 # Export learned patterns to file
-npx ruflo@v3alpha memory export --format json --output ./patterns.json
+npx ruflo@latest memory export --format json --output ./patterns.json
 
 # Export specific namespace
-npx ruflo@v3alpha memory export --namespace "security" --output ./security-patterns.json
+npx ruflo@latest memory export --namespace "security" --output ./security-patterns.json
 
 # Export with embeddings (larger file, faster import)
-npx ruflo@v3alpha memory export --include-embeddings --output ./full-export.json
+npx ruflo@latest memory export --include-embeddings --output ./full-export.json
 
 # Export agent configurations
-npx ruflo@v3alpha config export --scope project --output ./agent-configs.json
+npx ruflo@latest config export --scope project --output ./agent-configs.json
 
 # Export session state
-npx ruflo@v3alpha session export --session-id "my-session" --output ./session.json
+npx ruflo@latest session export --session-id "my-session" --output ./session.json
 ```
 
 ### Import Commands
 
 ```bash
 # Import patterns from file
-npx ruflo@v3alpha memory import --input ./patterns.json
+npx ruflo@latest memory import --input ./patterns.json
 
 # Import and merge with existing (don't overwrite)
-npx ruflo@v3alpha memory import --input ./patterns.json --merge
+npx ruflo@latest memory import --input ./patterns.json --merge
 
 # Import from another project
-npx ruflo@v3alpha hooks transfer --source-path ../other-project
+npx ruflo@latest hooks transfer --source-path ../other-project
 
 # Import agent configurations
-npx ruflo@v3alpha config import --input ./agent-configs.json --scope project
+npx ruflo@latest config import --input ./agent-configs.json --scope project
 
 # Restore session
-npx ruflo@v3alpha session restore --session-id "my-session"
+npx ruflo@latest session restore --session-id "my-session"
 ```
 
 ### Pattern Store (IPFS Marketplace)
@@ -3563,13 +3566,13 @@ Decentralized pattern marketplace for sharing and discovering community patterns
 
 ```bash
 # Search for authentication patterns
-npx ruflo@v3alpha transfer-store search --query "authentication" --min-rating 4.0
+npx ruflo@latest transfer-store search --query "authentication" --min-rating 4.0
 
 # Download a pattern
-npx ruflo@v3alpha transfer-store download --id "auth-jwt-patterns-v2" --verify
+npx ruflo@latest transfer-store download --id "auth-jwt-patterns-v2" --verify
 
 # Publish your patterns
-npx ruflo@v3alpha transfer-store publish --input ./my-patterns.json --category "security"
+npx ruflo@latest transfer-store publish --input ./my-patterns.json --category "security"
 ```
 
 ### Plugin Store
@@ -3587,22 +3590,22 @@ Discover and install community plugins from the **live IPFS registry** with 19 o
 
 ```bash
 # List plugins with live ratings from Cloud Function
-npx ruflo@v3alpha plugins list
+npx ruflo@latest plugins list
 
 # Filter by type
-npx ruflo@v3alpha plugins list --type integration
+npx ruflo@latest plugins list --type integration
 
 # Rate a plugin
-npx ruflo@v3alpha plugins rate --name @claude-flow/embeddings --rating 5
+npx ruflo@latest plugins rate --name @claude-flow/embeddings --rating 5
 
 # Search for MCP tool plugins
-npx ruflo@v3alpha transfer plugin-search --type "mcp-tool" --verified
+npx ruflo@latest transfer plugin-search --type "mcp-tool" --verified
 
 # Get plugin info
-npx ruflo@v3alpha transfer plugin-info --name "semantic-code-search"
+npx ruflo@latest transfer plugin-info --name "semantic-code-search"
 
 # List official plugins
-npx ruflo@v3alpha transfer plugin-official
+npx ruflo@latest transfer plugin-official
 ```
 
 #### Live IPFS Plugin Registry
@@ -3635,10 +3638,10 @@ Patterns and models are distributed via IPFS for decentralization and integrity.
 
 ```bash
 # Resolve IPNS name to CID
-npx ruflo@v3alpha transfer ipfs-resolve --name "/ipns/patterns.ruflo.io"
+npx ruflo@latest transfer ipfs-resolve --name "/ipns/patterns.ruflo.io"
 
 # Detect PII before publishing
-npx ruflo@v3alpha transfer detect-pii --content "$(cat ./patterns.json)"
+npx ruflo@latest transfer detect-pii --content "$(cat ./patterns.json)"
 ```
 
 ### Model & Learning Pattern Import/Export
@@ -3703,13 +3706,13 @@ Import pre-trained learning patterns for common tasks. **90.5% average accuracy*
 curl -s "https://gateway.pinata.cloud/ipfs/QmNr1yYMKi7YBaL8JSztQyuB5ZUaTdRMLxJC1pBpGbjsTc" | jq '.models[].name'
 
 # Import all models
-npx ruflo@v3alpha transfer import --cid QmNr1yYMKi7YBaL8JSztQyuB5ZUaTdRMLxJC1pBpGbjsTc
+npx ruflo@latest transfer import --cid QmNr1yYMKi7YBaL8JSztQyuB5ZUaTdRMLxJC1pBpGbjsTc
 
 # Import specific category
-npx ruflo@v3alpha neural import --model security-review-patterns --source ipfs
+npx ruflo@latest neural import --model security-review-patterns --source ipfs
 
 # Use patterns in routing
-npx ruflo@v3alpha hooks route --task "review authentication code" --use-patterns
+npx ruflo@latest hooks route --task "review authentication code" --use-patterns
 ```
 
 #### Benefits vs Fresh Install
@@ -3734,7 +3737,7 @@ npx ruflo@v3alpha hooks route --task "review authentication code" --use-patterns
 
 ```bash
 # Install a pattern pack
-npx ruflo@v3alpha transfer-store download --id "security-essentials" --apply
+npx ruflo@latest transfer-store download --id "security-essentials" --apply
 ```
 
 ### RuVector WASM Neural Training
@@ -3752,25 +3755,25 @@ Real WASM-accelerated neural training using `@ruvector/learning-wasm` and `@ruve
 
 ```bash
 # List available pre-trained models from IPFS registry
-npx ruflo@v3alpha neural list
+npx ruflo@latest neural list
 
 # List models by category
-npx ruflo@v3alpha neural list --category security
+npx ruflo@latest neural list --category security
 
 # Train with WASM acceleration
-npx ruflo@v3alpha neural train -p coordination -e 100 --wasm --flash --contrastive
+npx ruflo@latest neural train -p coordination -e 100 --wasm --flash --contrastive
 
 # Train security patterns
-npx ruflo@v3alpha neural train -p security --wasm --contrastive
+npx ruflo@latest neural train -p security --wasm --contrastive
 
 # Benchmark WASM performance
-npx ruflo@v3alpha neural benchmark -d 256 -i 1000
+npx ruflo@latest neural benchmark -d 256 -i 1000
 
 # Import pre-trained models
-npx ruflo@v3alpha neural import --cid QmNr1yYMKi7YBaL8JSztQyuB5ZUaTdRMLxJC1pBpGbjsTc
+npx ruflo@latest neural import --cid QmNr1yYMKi7YBaL8JSztQyuB5ZUaTdRMLxJC1pBpGbjsTc
 
 # Export trained patterns to IPFS
-npx ruflo@v3alpha neural export --ipfs --sign
+npx ruflo@latest neural export --ipfs --sign
 ```
 
 #### Benchmark Results
@@ -4109,9 +4112,9 @@ Skills are **reusable workflows** that combine agents, hooks, and patterns into
 /v3-security-overhaul
 
 # Via CLI
-npx ruflo@v3alpha skill run github-code-review
-npx ruflo@v3alpha skill list
-npx ruflo@v3alpha skill info sparc-methodology
+npx ruflo@latest skill run github-code-review
+npx ruflo@latest skill list
+npx ruflo@latest skill info sparc-methodology
 ```
 
 ### Creating Custom Skills
@@ -4168,21 +4171,21 @@ The Claims system manages **who is working on what** — whether human or agent.
 
 | Command | What It Does | Example |
 |---------|--------------|---------|
-| `issues list` | See all issues and their status | `npx ruflo@v3alpha issues list` |
-| `issues claim` | Claim an issue for yourself/agent | `npx ruflo@v3alpha issues claim #123 --as coder-1` |
-| `issues release` | Release your claim | `npx ruflo@v3alpha issues release #123` |
-| `issues handoff` | Hand off to another worker | `npx ruflo@v3alpha issues handoff #123 --to reviewer` |
-| `issues status` | Update progress on claimed work | `npx ruflo@v3alpha issues status #123 --progress 75` |
-| `issues stealable` | List abandoned/stuck issues | `npx ruflo@v3alpha issues stealable` |
-| `issues steal` | Take over stealable issue | `npx ruflo@v3alpha issues steal #123` |
-| `issues load` | View agent workloads | `npx ruflo@v3alpha issues load` |
-| `issues rebalance` | Redistribute work evenly | `npx ruflo@v3alpha issues rebalance --dry-run` |
-| `issues board` | Visual board view | `npx ruflo@v3alpha issues board` |
+| `issues list` | See all issues and their status | `npx ruflo@latest issues list` |
+| `issues claim` | Claim an issue for yourself/agent | `npx ruflo@latest issues claim #123 --as coder-1` |
+| `issues release` | Release your claim | `npx ruflo@latest issues release #123` |
+| `issues handoff` | Hand off to another worker | `npx ruflo@latest issues handoff #123 --to reviewer` |
+| `issues status` | Update progress on claimed work | `npx ruflo@latest issues status #123 --progress 75` |
+| `issues stealable` | List abandoned/stuck issues | `npx ruflo@latest issues stealable` |
+| `issues steal` | Take over stealable issue | `npx ruflo@latest issues steal #123` |
+| `issues load` | View agent workloads | `npx ruflo@latest issues load` |
+| `issues rebalance` | Redistribute work evenly | `npx ruflo@latest issues rebalance --dry-run` |
+| `issues board` | Visual board view | `npx ruflo@latest issues board` |
 
 ### Visual Board View
 
 ```bash
-npx ruflo@v3alpha issues board
+npx ruflo@latest issues board
 ```
 
 ```
@@ -4204,13 +4207,13 @@ When you need to pass work to someone else:
 
 ```bash
 # 1. Request handoff with context
-npx ruflo@v3alpha issues handoff #123 \
+npx ruflo@latest issues handoff #123 \
   --to security-architect \
   --reason "Needs security review" \
   --progress 80
 
 # 2. Target accepts handoff
-npx ruflo@v3alpha issues accept #123 --as security-architect
+npx ruflo@latest issues accept #123 --as security-architect
 
 # 3. Work continues with full context
 ```
@@ -4219,7 +4222,7 @@ npx ruflo@v3alpha issues accept #123 --as security-architect
 
 ```bash
 # View current load
-npx ruflo@v3alpha issues load
+npx ruflo@latest issues load
 
 # Output:
 # Agent          | Claims | Load  | Status
@@ -4230,7 +4233,7 @@ npx ruflo@v3alpha issues load
 # security-arch  | 0      | 0%    | 🟢 Available
 
 # Auto-rebalance
-npx ruflo@v3alpha issues rebalance
+npx ruflo@latest issues rebalance
 ```
 
 ### MCP Tools
@@ -4291,14 +4294,14 @@ The Route system uses **Q-Learning** to automatically assign tasks to the best a
 
 | Command | What It Does | Example |
 |---------|--------------|---------|
-| `route task` | Get agent recommendation | `npx ruflo@v3alpha route task "implement OAuth2"` |
-| `route explain` | Understand routing decision | `npx ruflo@v3alpha route explain "task"` |
-| `route coverage` | Route based on test coverage | `npx ruflo@v3alpha route coverage` |
+| `route task` | Get agent recommendation | `npx ruflo@latest route task "implement OAuth2"` |
+| `route explain` | Understand routing decision | `npx ruflo@latest route explain "task"` |
+| `route coverage` | Route based on test coverage | `npx ruflo@latest route coverage` |
 
 ### Example: Route a Task
 
 ```bash
-npx ruflo@v3alpha route task "refactor authentication to use JWT"
+npx ruflo@latest route task "refactor authentication to use JWT"
 
 # Output:
 # ╔══════════════════════════════════════════════════════════════╗
@@ -4325,7 +4328,7 @@ npx ruflo@v3alpha route task "refactor authentication to use JWT"
 Routes tasks to agents based on **test coverage gaps**:
 
 ```bash
-npx ruflo@v3alpha route coverage
+npx ruflo@latest route coverage
 
 # Finds untested code and routes to tester agent:
 # • src/auth/jwt.ts - 23% coverage → tester
@@ -4337,10 +4340,10 @@ npx ruflo@v3alpha route coverage
 
 ```bash
 # Route via hooks (preferred)
-npx ruflo@v3alpha hooks route "implement caching layer" --include-explanation
+npx ruflo@latest hooks route "implement caching layer" --include-explanation
 
 # Record outcome for learning
-npx ruflo@v3alpha hooks post-task --task-id "task-123" --success true --agent coder
+npx ruflo@latest hooks post-task --task-id "task-123" --success true --agent coder
 ```
 
 ### How Q-Learning Improves Over Time
@@ -4374,7 +4377,7 @@ Use Ruflo packages directly in your TypeScript/JavaScript applications.
 npm install @claude-flow/cli @claude-flow/memory @claude-flow/swarm
 
 # Or install everything
-npm install ruflo@v3alpha
+npm install ruflo@latest
 ```
 
 ### Quick Examples
@@ -5685,7 +5688,7 @@ Flow Nexus is a **cloud platform** for deploying and scaling Ruflo beyond your l
 /flow-nexus-swarm
 
 # Or via CLI
-npx ruflo@v3alpha nexus swarm deploy \
+npx ruflo@latest nexus swarm deploy \
   --topology hierarchical \
   --max-agents 50 \
   --region us-east-1
@@ -5697,13 +5700,13 @@ Isolated execution environments for running untrusted code:
 
 ```bash
 # Create sandbox
-npx ruflo@v3alpha nexus sandbox create --language python
+npx ruflo@latest nexus sandbox create --language python
 
 # Execute code safely
-npx ruflo@v3alpha nexus sandbox exec --code "print('Hello')"
+npx ruflo@latest nexus sandbox exec --code "print('Hello')"
 
 # Cleanup
-npx ruflo@v3alpha nexus sandbox destroy
+npx ruflo@latest nexus sandbox destroy
 ```
 
 ### Event-Driven Workflows
@@ -5729,10 +5732,10 @@ steps:
 # 1. Sign up at flow-nexus.io
 # 2. Get API key
 # 3. Configure
-npx ruflo@v3alpha nexus configure --api-key <key>
+npx ruflo@latest nexus configure --api-key <key>
 
 # 4. Deploy
-npx ruflo@v3alpha nexus swarm deploy
+npx ruflo@latest nexus swarm deploy
 ```
 
 </details>
@@ -5766,7 +5769,7 @@ Stream-Chain enables **sequential processing** where the output of one agent bec
 /stream-chain
 
 # Define pipeline
-npx ruflo@v3alpha stream-chain create \
+npx ruflo@latest stream-chain create \
   --name "feature-pipeline" \
   --stages "researcher,architect,coder,tester,reviewer"
 ```
@@ -5808,11 +5811,11 @@ stages:
 
 ```bash
 # Run the pipeline
-npx ruflo@v3alpha stream-chain run feature-pipeline \
+npx ruflo@latest stream-chain run feature-pipeline \
   --input '{"requirements": "Add user dashboard with analytics"}'
 
 # Monitor progress
-npx ruflo@v3alpha stream-chain status feature-pipeline
+npx ruflo@latest stream-chain status feature-pipeline
 ```
 
 ### Use Cases
@@ -5852,7 +5855,7 @@ The Pair Programming skill provides **human-AI collaborative coding** with role
 /pair-programming --mode tdd
 
 # Via CLI
-npx ruflo@v3alpha pair start --mode navigator
+npx ruflo@latest pair start --mode navigator
 ```
 
 ### TDD Mode Workflow
@@ -5892,16 +5895,16 @@ npx ruflo@v3alpha pair start --mode navigator
 
 ```bash
 # Switch roles mid-session
-npx ruflo@v3alpha pair switch
+npx ruflo@latest pair switch
 
 # Get AI explanation
-npx ruflo@v3alpha pair explain
+npx ruflo@latest pair explain
 
 # Run tests
-npx ruflo@v3alpha pair test
+npx ruflo@latest pair test
 
 # End session with summary
-npx ruflo@v3alpha pair end
+npx ruflo@latest pair end
 ```
 
 </details>
@@ -5958,22 +5961,22 @@ Detection Time: 0.04ms | 50+ Patterns | Self-Learning | HNSW Vector Search
 
 ```bash
 # Basic threat scan
-npx ruflo@v3alpha security defend -i "ignore previous instructions"
+npx ruflo@latest security defend -i "ignore previous instructions"
 
 # Scan a file
-npx ruflo@v3alpha security defend -f ./user-prompts.txt
+npx ruflo@latest security defend -f ./user-prompts.txt
 
 # Quick scan (faster)
-npx ruflo@v3alpha security defend -i "some text" --quick
+npx ruflo@latest security defend -i "some text" --quick
 
 # JSON output
-npx ruflo@v3alpha security defend -i "test" -o json
+npx ruflo@latest security defend -i "test" -o json
 
 # View statistics
-npx ruflo@v3alpha security defend --stats
+npx ruflo@latest security defend --stats
 
 # Full security audit
-npx ruflo@v3alpha security scan --depth full
+npx ruflo@latest security scan --depth full
 ```
 
 ### MCP Tools
@@ -6564,10 +6567,10 @@ npm run bench:attention
 npm run bench:startup
 
 # Performance report
-npx ruflo@v3alpha performance report
+npx ruflo@latest performance report
 
 # Benchmark specific suite
-npx ruflo@v3alpha performance benchmark --suite memory
+npx ruflo@latest performance benchmark --suite memory
 ```
 
 </details>
@@ -7244,25 +7247,25 @@ Ruflo looks for configuration in this order:
 
 ```bash
 # View current configuration
-npx ruflo@v3alpha config list
+npx ruflo@latest config list
 
 # Get specific value
-npx ruflo@v3alpha config get --key memory.type
+npx ruflo@latest config get --key memory.type
 
 # Set configuration value
-npx ruflo@v3alpha config set --key swarm.maxAgents --value 10
+npx ruflo@latest config set --key swarm.maxAgents --value 10
 
 # Export configuration
-npx ruflo@v3alpha config export > my-config.json
+npx ruflo@latest config export > my-config.json
 
 # Import configuration
-npx ruflo@v3alpha config import --file my-config.json
+npx ruflo@latest config import --file my-config.json
 
 # Reset to defaults
-npx ruflo@v3alpha config reset --key swarm
+npx ruflo@latest config reset --key swarm
 
 # Initialize with wizard
-npx ruflo@v3alpha init --wizard
+npx ruflo@latest init --wizard
 ```
 
 </details>
@@ -7286,7 +7289,7 @@ lsof -i :3000
 # Kill existing process
 kill -9 <PID>
 # Restart MCP server
-npx ruflo@v3alpha mcp start
+npx ruflo@latest mcp start
 ```
 
 **Agent spawn failures**
@@ -7300,9 +7303,9 @@ export CLAUDE_FLOW_MAX_AGENTS=5
 **Pattern search returning no results**
 ```bash
 # Verify patterns are stored
-npx ruflo@v3alpha hooks metrics
+npx ruflo@latest hooks metrics
 # Re-run pretraining if empty
-npx ruflo@v3alpha hooks pretrain
+npx ruflo@latest hooks pretrain
 ```
 
 **Windows path issues**
@@ -7370,20 +7373,20 @@ cp -r ./data ./data-backup-v2
 cp -r ./.ruflo ./.ruflo-backup-v2
 
 # STEP 2: Check migration status
-npx ruflo@v3alpha migrate status
+npx ruflo@latest migrate status
 
 # STEP 3: Run migration with dry-run first
-npx ruflo@v3alpha migrate run --dry-run
+npx ruflo@latest migrate run --dry-run
 
 # STEP 4: Execute migration
-npx ruflo@v3alpha migrate run --from v2
+npx ruflo@latest migrate run --from v2
 
 # STEP 5: Verify migration
-npx ruflo@v3alpha migrate verify
+npx ruflo@latest migrate verify
 
 # STEP 6: Initialize V3 learning
-npx ruflo@v3alpha hooks pretrain
-npx ruflo@v3alpha doctor --fix
+npx ruflo@latest hooks pretrain
+npx ruflo@latest doctor --fix
 ```
 
 ### Command Changes Reference
@@ -7450,10 +7453,10 @@ If migration fails, you can rollback:
 
 ```bash
 # Check rollback options
-npx ruflo@v3alpha migrate rollback --list
+npx ruflo@latest migrate rollback --list
 
 # Rollback to V2
-npx ruflo@v3alpha migrate rollback --to v2
+npx ruflo@latest migrate rollback --to v2
 
 # Restore backup manually if needed
 rm -rf ./data
@@ -7462,12 +7465,12 @@ cp -r ./data-backup-v2 ./data
 
 ### Post-Migration Checklist
 
-- [ ] Verify all agents spawn correctly: `npx ruflo@v3alpha agent list`
-- [ ] Check memory search works: `npx ruflo@v3alpha memory search -q "test"`
-- [ ] Confirm MCP server starts: `npx ruflo@v3alpha mcp start`
-- [ ] Run doctor diagnostics: `npx ruflo@v3alpha doctor`
-- [ ] Test a simple swarm: `npx ruflo@v3alpha swarm init --topology mesh`
-- [ ] Bootstrap learning: `npx ruflo@v3alpha hooks pretrain`
+- [ ] Verify all agents spawn correctly: `npx ruflo@latest agent list`
+- [ ] Check memory search works: `npx ruflo@latest memory search -q "test"`
+- [ ] Confirm MCP server starts: `npx ruflo@latest mcp start`
+- [ ] Run doctor diagnostics: `npx ruflo@latest doctor`
+- [ ] Test a simple swarm: `npx ruflo@latest swarm init --topology mesh`
+- [ ] Bootstrap learning: `npx ruflo@latest hooks pretrain`
 
 ### Common Migration Issues
 
@@ -7511,7 +7514,7 @@ cp -r ./data-backup-v2 ./data
 ### Additional Resources
 
 - [V2 Documentation](./v2/README.md)
-- [Architecture Decisions (ADRs)](./v3/docs/adr/)
+- [Architecture Decisions (ADRs)](./v3/implementation/adrs/)
 - [API Reference](./v2/docs/technical/)
 - [Examples](./v2/examples/)