Merge main branch and resolve conflicts

- Merge latest changes from main branch
- Adopt Pino structured logger from main (replaces simple logger)
- Integrate backup system with new request tracking middleware
- Maintain all backup functionality with improved logging
- Server now uses Pino logger for structured output
- Backup system compatible with production logging standards

Co-authored-by: clduab11 <185000089+clduab11@users.noreply.github.com>

Author: Copilot

DOCKER.md

@@ -29,7 +29,7 @@ gemini-flow is now available as an official Gemini CLI extension, packaging:
 
 ```bash
 # Install from GitHub
-gemini extensions install github:clduab11/gemini-flow
+gemini extensions install https://github.com/clduab11/gemini-flow
 
 # Install from local clone
 cd /path/to/gemini-flow
@@ -39,6 +39,8 @@ gemini extensions install .
 gemini extensions enable gemini-flow
 ```
 
+> **⚠️ Important**: Use the full GitHub URL (`https://github.com/clduab11/gemini-flow`). The shorthand syntax `github:username/repo` is **not supported** and will cause installation errors.
+
 ### Using gemini-flow Commands
 
 Once enabled, use gemini-flow commands directly in Gemini CLI:
@@ -100,7 +102,7 @@ gemini-flow also includes its own extension management commands:
 
 ```bash
 # Using gem-extensions command
-gemini-flow gem-extensions install github:user/extension
+gemini-flow gem-extensions install https://github.com/user/extension
 gemini-flow gem-extensions list
 gemini-flow gem-extensions enable extension-name
 gemini-flow gem-extensions info extension-name
@@ -157,7 +159,7 @@ This documentation is specifically engineered for **Gemini Code Assist** using G
 gemini-flow is now available as an official Gemini CLI extension. Install it with:
 
 ```bash
-gemini extensions install github:clduab11/gemini-flow
+gemini extensions install https://github.com/clduab11/gemini-flow
 ```
 
 ---

GEMINI.md

@@ -36,9 +36,9 @@ gemini-flow init --protocols a2a,mcp --topology hierarchical
 gemini-flow agents spawn --count 50 --specialization "enterprise-ready"
 
 # NEW: Official Gemini CLI Extension (October 8, 2025)
-gemini extensions install github:clduab11/gemini-flow  # Install as Gemini extension
-gemini extensions enable gemini-flow                   # Enable the extension
-gemini hive-mind spawn "Build AI application"         # Use commands in Gemini CLI
+gemini extensions install https://github.com/clduab11/gemini-flow  # Install as Gemini extension
+gemini extensions enable gemini-flow                                # Enable the extension
+gemini hive-mind spawn "Build AI application"                      # Use commands in Gemini CLI
 ```
 
 **🚀 Modern Protocol Support**: Native A2A and MCP integration for seamless inter-agent communication and model coordination  
@@ -489,7 +489,7 @@ gemini-flow is now available as an **official Gemini CLI extension**, providing
 
 ```bash
 # Install from GitHub
-gemini extensions install github:clduab11/gemini-flow
+gemini extensions install https://github.com/clduab11/gemini-flow
 
 # Install from local clone
 cd /path/to/gemini-flow
@@ -499,6 +499,8 @@ gemini extensions install .
 gemini extensions enable gemini-flow
 ```
 
+> **Note**: Always use the full GitHub URL format (`https://github.com/username/repo`). The shorthand syntax `github:username/repo` is **not supported** by Gemini CLI and will result in "Install source not found" errors.
+
 ### What's Included
 
 The extension packages gemini-flow's complete AI orchestration platform:
@@ -560,7 +562,7 @@ gemini-flow also includes its own extension management commands:
 
 ```bash
 # Using gem-extensions command
-gemini-flow gem-extensions install github:user/extension
+gemini-flow gem-extensions install https://github.com/user/extension
 gemini-flow gem-extensions list
 gemini-flow gem-extensions enable extension-name
 gemini-flow gem-extensions info extension-name

README.md

@@ -0,0 +1,60 @@
+# Dependencies
+node_modules
+npm-debug.log
+yarn-error.log
+pnpm-debug.log
+
+# Environment files
+.env
+.env.*
+!.env.example
+
+# Git
+.git
+.gitignore
+
+# Data directories (should be volume mounted)
+.data
+.data-test
+.data/*
+backups
+logs
+
+# Testing
+coverage
+*.test.js
+*.spec.js
+__tests__
+
+# Documentation (except README)
+*.md
+!README.md
+
+# IDE
+.vscode
+.idea
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+.Spotlight-V100
+.Trashes
+
+# Build artifacts
+dist
+build
+*.tgz
+
+# Temporary files
+tmp
+temp
+*.tmp
+*.cache
+
+# Development
+nodemon.json
+.eslintrc*
+.prettierrc*

backend/.dockerignore

@@ -11,4 +11,13 @@ GOOGLE_AI_API_KEY=your_google_ai_api_key_here
 PORT=3001
 
 # CORS Origins (for development)
-CORS_ORIGINS=http://localhost:5173,http://localhost:3000
+CORS_ORIGINS=http://localhost:5173,http://localhost:3000
+
+# Logging Configuration
+# Log levels: trace, debug, info, warn, error, fatal
+# Recommended: 'debug' for development, 'info' for production
+LOG_LEVEL=info
+
+# Environment (affects log formatting)
+# 'development' enables pretty printing, 'production' uses JSON
+NODE_ENV=development

backend/.env.example

@@ -0,0 +1,67 @@
+# =============================================================================
+# Stage 1: Builder - Install dependencies and prepare application
+# =============================================================================
+FROM node:18-alpine AS builder
+
+WORKDIR /app
+
+# Copy package files first (for better caching)
+COPY package*.json ./
+
+# Install ALL dependencies (including devDependencies for potential build steps)
+RUN npm ci && npm cache clean --force
+
+# Copy application source
+COPY . .
+
+# Remove development dependencies
+RUN npm prune --production
+
+# =============================================================================
+# Stage 2: Production - Minimal runtime image
+# =============================================================================
+FROM node:18-alpine
+
+# Install dumb-init to handle PID 1 responsibilities
+RUN apk add --no-cache dumb-init
+
+# Create non-root user and group
+RUN addgroup -g 1001 -S nodejs && \
+    adduser -S geminiflow -u 1001 -G nodejs
+
+WORKDIR /app
+
+# Create data directory with correct permissions
+RUN mkdir -p .data logs && \
+    chown -R geminiflow:nodejs .data logs
+
+# Copy dependencies from builder stage
+COPY --from=builder --chown=geminiflow:nodejs /app/node_modules ./node_modules
+
+# Copy application code with correct ownership
+COPY --chown=geminiflow:nodejs package*.json ./
+COPY --chown=geminiflow:nodejs src ./src
+
+# Switch to non-root user
+USER geminiflow
+
+# Expose port
+EXPOSE 3001
+
+# Health check (runs as non-root user)
+HEALTHCHECK --interval=30s --timeout=10s --start-period=40s --retries=3 \
+  CMD node -e "require('http').get('http://localhost:3001/health', (r) => {process.exit(r.statusCode === 200 ? 0 : 1)})" || exit 1
+
+# Use dumb-init to handle signals properly
+ENTRYPOINT ["dumb-init", "--"]
+
+# Start server
+CMD ["node", "src/server.js"]
+
+# Metadata
+LABEL org.opencontainers.image.title="Gemini Flow Backend" \
+      org.opencontainers.image.description="Backend API and WebSocket server for Gemini Flow" \
+      org.opencontainers.image.version="1.0.0" \
+      org.opencontainers.image.vendor="Gemini Flow" \
+      org.opencontainers.image.source="https://github.com/clduab11/gemini-flow" \
+      maintainer="clduab11"