fix: v3.5.5-v3.5.7 platform parity, branding, stdin timeout (#1301)

* fix: v3.5.5–v3.5.7 platform parity, branding, stdin timeout, settings completeness

Covers three releases published to npm:

v3.5.5 — Complete branding sweep
- Replace all "Claude Flow V3" with "RuFlo V3" across 30+ CLI source and helper files
- Fix Windows PS1 daemon manager, BAT wrapper, statusline branding
- Fix config.yaml header, CAPABILITIES.md, JSDoc, SQL schema comments

v3.5.6 — Platform parity and settings completeness
- Fix macOS daemon death on terminal close (SIGHUP handler in foreground mode)
- Fix Windows daemon spawn (shell:true, windowsHide:true, no detached flag)
- Fix PID file write order (write after child.unref() + 100ms delay)
- Add 4 missing hooks to settings-generator: PostToolUse:Bash, PreToolUse:Write|Edit|MultiEdit, SubagentEnd, Notification
- Rename "Worker Daemon" to "RuFlo Daemon"

v3.5.7 — Hook stdin timeout fix
- Replace `for await` stdin with event-based + 500ms timeout in hook-handler.cjs
- Prevents hanging when Claude Code leaves stdin in ambiguous state (not TTY, not pipe)
- Update helpers-generator.ts template with same fix

Also:
- Add Nginx reverse proxy service to ruflo docker-compose for Chat UI branding
- Update ADR-060: 13/24 items fixed, all P0/P1 resolved

Co-Authored-By: claude-flow <ruv@ruv.net>

* fix: update pnpm-lock.yaml for agentic-flow dependency

The lockfile specifiers were out of sync with @claude-flow/cli/package.json
after agentic-flow was added, causing CI frozen-lockfile failures.

Co-Authored-By: claude-flow <ruv@ruv.net>

Author: ruvnet

.claude/helpers/README.md

@@ -1,4 +1,4 @@
-# Claude Flow V3 Helpers
+# RuFlo V3 Helpers
 
 This directory contains helper scripts and utilities for V3 development.
 

.claude/helpers/adr-compliance.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# Claude Flow V3 - ADR Compliance Checker Worker
+# RuFlo V3 - ADR Compliance Checker Worker
 # Checks compliance with Architecture Decision Records
 
 set -euo pipefail

.claude/helpers/daemon-manager.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# Claude Flow V3 - Daemon Manager
+# RuFlo V3 - Daemon Manager
 # Manages background services for real-time statusline updates
 
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
@@ -155,7 +155,7 @@ restart_all() {
 show_status() {
     echo ""
     echo -e "${CYAN}═══════════════════════════════════════════════════${RESET}"
-    echo -e "${CYAN}       Claude Flow V3 Daemon Status${RESET}"
+    echo -e "${CYAN}       RuFlo V3 Daemon Status${RESET}"
     echo -e "${CYAN}═══════════════════════════════════════════════════${RESET}"
     echo ""
 
@@ -225,7 +225,7 @@ case "${1:-status}" in
         start_metrics_daemon "${2:-60}"
         ;;
     "help"|"-h"|"--help")
-        echo "Claude Flow V3 Daemon Manager"
+        echo "RuFlo V3 Daemon Manager"
         echo ""
         echo "Usage: $0 [command] [options]"
         echo ""

.claude/helpers/ddd-tracker.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# Claude Flow V3 - DDD Progress Tracker Worker
+# RuFlo V3 - DDD Progress Tracker Worker
 # Tracks Domain-Driven Design implementation progress
 
 set -euo pipefail

.claude/helpers/guidance-hooks.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# Guidance Hooks for Claude Flow V3
+# Guidance Hooks for RuFlo V3
 # Provides context and routing for Claude Code operations
 
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"

.claude/helpers/health-monitor.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# Claude Flow V3 - Health Monitor Worker
+# RuFlo V3 - Health Monitor Worker
 # Checks disk space, memory pressure, process health
 
 set -euo pipefail

.claude/helpers/hook-handler.cjs

@@ -38,14 +38,23 @@ const intelligence = safeRequire(path.join(helpersDir, 'intelligence.cjs'));
 const [,, command, ...args] = process.argv;
 
 // Read stdin — Claude Code sends hook data as JSON via stdin
+// Uses a timeout to prevent hanging when stdin is in an ambiguous state
+// (not TTY, not a proper pipe) which happens with Claude Code hook invocations.
 async function readStdin() {
   if (process.stdin.isTTY) return '';
-  let data = '';
-  process.stdin.setEncoding('utf8');
-  for await (const chunk of process.stdin) {
-    data += chunk;
-  }
-  return data;
+  return new Promise((resolve) => {
+    let data = '';
+    const timer = setTimeout(() => {
+      process.stdin.removeAllListeners();
+      process.stdin.pause();
+      resolve(data);
+    }, 500);
+    process.stdin.setEncoding('utf8');
+    process.stdin.on('data', (chunk) => { data += chunk; });
+    process.stdin.on('end', () => { clearTimeout(timer); resolve(data); });
+    process.stdin.on('error', () => { clearTimeout(timer); resolve(data); });
+    process.stdin.resume();
+  });
 }
 
 async function main() {

.claude/helpers/learning-hooks.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# Claude Flow V3 - Learning Hooks
+# RuFlo V3 - Learning Hooks
 # Integrates learning-service.mjs with session lifecycle
 
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
@@ -300,7 +300,7 @@ case "${1:-help}" in
     ;;
   "help"|"-h"|"--help")
     cat << 'EOF'
-Claude Flow V3 Learning Hooks
+RuFlo V3 Learning Hooks
 
 Usage: learning-hooks.sh <command> [args]
 

.claude/helpers/learning-optimizer.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# Claude Flow V3 - Learning Optimizer Worker
+# RuFlo V3 - Learning Optimizer Worker
 # Runs SONA micro-LoRA optimization on patterns
 
 set -euo pipefail

.claude/helpers/learning-service.mjs

@@ -1,6 +1,6 @@
 #!/usr/bin/env node
 /**
- * Claude Flow V3 - Persistent Learning Service
+ * RuFlo V3 - Persistent Learning Service
  *
  * Connects ReasoningBank to AgentDB with HNSW indexing and ONNX embeddings.
  *
@@ -1112,7 +1112,7 @@ async function main() {
       case 'help':
       default:
         console.log(`
-Claude Flow V3 Learning Service
+RuFlo V3 Learning Service
 
 Usage: learning-service.mjs <command> [args]