diff --git a/.env.example b/.env.example
index c9d1135..f14a78f 100644
--- a/.env.example
+++ b/.env.example
@@ -5,6 +5,19 @@ GITEA_TOKEN=your-bot-user-token-here
 # MCP Server Configuration
 MCP_HOST=0.0.0.0
 MCP_PORT=8080
+MCP_DOMAIN=mcp.yourdomain.com  # Domain for Traefik (if using)
+
+# Authentication Configuration (REQUIRED)
+# Generate key with: python scripts/generate_api_key.py
+AUTH_ENABLED=true
+MCP_API_KEYS=your-generated-api-key-here
+
+# Multiple keys (comma-separated for grace period during rotation):
+# MCP_API_KEYS=key1,key2,key3
+
+# Authentication limits
+MAX_AUTH_FAILURES=5           # Max failures before rate limiting
+AUTH_FAILURE_WINDOW=300       # Time window in seconds (5 min)
 
 # Logging Configuration
 LOG_LEVEL=INFO
diff --git a/.gitignore b/.gitignore
index 5f99a18..cd764ad 100644
--- a/.gitignore
+++ b/.gitignore
@@ -44,6 +44,11 @@ htmlcov/
 # Environment variables
 .env
 .env.local
+.env.backup-*
+
+# API keys
+keys/
+*.key
 
 # Logs
 *.log
diff --git a/AUTH_SETUP.md b/AUTH_SETUP.md
new file mode 100644
index 0000000..30ab634
--- /dev/null
+++ b/AUTH_SETUP.md
@@ -0,0 +1,434 @@
+# Authentication Setup Guide
+
+This guide walks you through setting up API key authentication for AegisGitea MCP to ensure only your ChatGPT workspace can access your self-hosted Gitea instance.
+
+---
+
+## Overview
+
+AegisGitea MCP uses **Bearer Token authentication** to secure access:
+
+- **API Keys**: Cryptographically secure 64-character tokens
+- **Header-based**: Keys sent via `Authorization: Bearer <key>` header
+- **Multi-key support**: Multiple keys for rotation grace periods
+- **Rate limiting**: Failed auth attempts trigger IP-based rate limits
+- **Audit logging**: All auth attempts logged for security monitoring
+
+---
+
+## Quick Start (5 minutes)
+
+### 1. Generate API Key
+
+```bash
+# Using Make
+make generate-key
+
+# Or directly
+python3 scripts/generate_api_key.py
+```
+
+This will:
+- Generate a secure 64-character API key
+- Show you the key (save it immediately!)
+- Provide `.env` configuration snippet
+- Optionally save metadata (not the key itself) for tracking
+
+**Example output:**
+```
+✓ API Key Generated Successfully!
+
+API KEY:
+  a1b2c3d4e5f6g7h8i9j0k1l2m3n4o5p6q7r8s9t0u1v2w3x4y5z6a7b8c9d0e1f2
+
+📋 Next Steps:
+1. Add this key to your .env file
+2. Restart the MCP server
+3. Configure ChatGPT Business
+```
+
+### 2. Add Key to .env
+
+```bash
+# Edit .env
+nano .env
+
+# Add/update this line:
+MCP_API_KEYS=a1b2c3d4e5f6g7h8i9j0k1l2m3n4o5p6q7r8s9t0u1v2w3x4y5z6a7b8c9d0e1f2
+```
+
+### 3. Restart MCP Server
+
+```bash
+docker-compose restart aegis-mcp
+
+# Verify authentication is enabled
+docker-compose logs aegis-mcp | grep "authentication"
+```
+
+Expected log output:
+```
+API key authentication ENABLED (1 key(s) configured)
+```
+
+### 4. Test Authentication
+
+```bash
+# Without key - should fail with 401
+curl https://mcp.yourdomain.com/mcp/tools
+
+# With valid key - should succeed
+curl -H "Authorization: Bearer YOUR_KEY_HERE" \
+     https://mcp.yourdomain.com/mcp/tools
+```
+
+---
+
+## Configuration Options
+
+### Environment Variables
+
+```bash
+# Enable/disable authentication
+AUTH_ENABLED=true              # Set to false ONLY for testing
+
+# API keys (comma-separated for multiple)
+MCP_API_KEYS=key1              # Single key
+MCP_API_KEYS=key1,key2,key3    # Multiple keys (rotation grace period)
+
+# Rate limiting
+MAX_AUTH_FAILURES=5            # Max failed attempts before blocking
+AUTH_FAILURE_WINDOW=300        # Time window in seconds (5 min)
+```
+
+### Multiple Keys (Rotation Grace Period)
+
+During key rotation, you can temporarily allow multiple keys:
+
+```bash
+# Old key
+MCP_API_KEYS=old-key-here
+
+# Add new key (both work)
+MCP_API_KEYS=old-key-here,new-key-here
+
+# After updating ChatGPT, remove old key
+MCP_API_KEYS=new-key-here
+```
+
+---
+
+## Security Features
+
+### 1. Constant-Time Comparison
+
+Keys are compared using `hmac.compare_digest()` to prevent timing attacks.
+
+### 2. Rate Limiting
+
+- **Threshold**: 5 failed attempts per IP
+- **Window**: 5 minutes (configurable)
+- **Action**: Reject all requests from that IP until window expires
+- **Logging**: High-severity security event logged
+
+### 3. Audit Logging
+
+Every authentication attempt logs:
+
+```json
+{
+  "timestamp": "2026-01-29T12:34:56.789Z",
+  "event": "api_authentication",
+  "status": "success",
+  "client_ip": "203.0.113.42",
+  "user_agent": "ChatGPT-User/1.0",
+  "key_hint": "a1b2c3d4...e1f2"
+}
+```
+
+Failed attempts:
+
+```json
+{
+  "timestamp": "2026-01-29T12:34:56.789Z",
+  "event": "access_denied",
+  "reason": "invalid_api_key",
+  "client_ip": "203.0.113.42"
+}
+```
+
+### 4. Key Format Validation
+
+- Minimum length: 32 characters
+- Recommended length: 64 characters
+- Format: Hexadecimal string (0-9, a-f)
+
+---
+
+## Troubleshooting
+
+### Issue: "No API keys configured" error
+
+**Symptoms:**
+```
+docker-compose logs: "No API keys configured in environment"
+```
+
+**Solution:**
+1. Check `.env` file exists and contains `MCP_API_KEYS`
+2. Ensure no typos (`MCP_API_KEYS` not `MCP_API_KEY`)
+3. Verify key is at least 32 characters
+4. Restart container after updating `.env`
+
+### Issue: "Invalid API key" on valid key
+
+**Possible causes:**
+
+1. **Whitespace in .env**: Remove spaces around `=`
+   ```bash
+   # Wrong
+   MCP_API_KEYS = key-here
+
+   # Correct
+   MCP_API_KEYS=key-here
+   ```
+
+2. **Key truncated**: Ensure entire 64-char key is copied
+   ```bash
+   # Check key length
+   echo -n "your-key-here" | wc -c
+   # Should output: 64
+   ```
+
+3. **Container not restarted**: Always restart after changing `.env`
+   ```bash
+   docker-compose restart aegis-mcp
+   ```
+
+### Issue: Rate limit blocking legitimate requests
+
+**Symptoms:**
+```
+"Too many failed authentication attempts"
+```
+
+**Solution:**
+1. Check audit logs for failed attempts:
+   ```bash
+   docker-compose exec aegis-mcp cat /var/log/aegis-mcp/audit.log | grep "invalid_api_key"
+   ```
+
+2. Wait 5 minutes for rate limit to reset
+
+3. If accidentally blocked yourself:
+   ```bash
+   # Restart container (clears in-memory rate limits)
+   docker-compose restart aegis-mcp
+   ```
+
+4. Adjust rate limit settings in `.env` if needed:
+   ```bash
+   MAX_AUTH_FAILURES=10
+   AUTH_FAILURE_WINDOW=600
+   ```
+
+### Issue: ChatGPT can't connect after adding auth
+
+See [CHATGPT_SETUP.md](CHATGPT_SETUP.md) for detailed ChatGPT configuration.
+
+**Quick check:**
+1. Verify key in ChatGPT settings matches `.env`
+2. Check Authorization header format: `Bearer <key>` (with space)
+3. Test manually with curl first
+
+---
+
+## Monitoring Authentication
+
+### View All Auth Attempts
+
+```bash
+# All auth events
+docker-compose exec aegis-mcp grep "api_authentication" /var/log/aegis-mcp/audit.log
+
+# Failed attempts only
+docker-compose exec aegis-mcp grep "access_denied" /var/log/aegis-mcp/audit.log
+
+# Rate limit triggers
+docker-compose exec aegis-mcp grep "auth_rate_limit_exceeded" /var/log/aegis-mcp/audit.log
+```
+
+### Real-Time Monitoring
+
+```bash
+# Follow auth events
+docker-compose exec aegis-mcp tail -f /var/log/aegis-mcp/audit.log | grep "auth"
+```
+
+### Weekly Summary Script
+
+```bash
+#!/bin/bash
+# Save as scripts/auth_summary.sh
+
+CONTAINER="aegis-gitea-mcp"
+LOG_PATH="/var/log/aegis-mcp/audit.log"
+
+echo "=== Weekly Auth Summary ==="
+echo ""
+echo "Total auth attempts:"
+docker exec $CONTAINER grep "api_authentication" $LOG_PATH | wc -l
+
+echo ""
+echo "Successful:"
+docker exec $CONTAINER grep "api_authentication.*success" $LOG_PATH | wc -l
+
+echo ""
+echo "Failed:"
+docker exec $CONTAINER grep "access_denied.*invalid_api_key" $LOG_PATH | wc -l
+
+echo ""
+echo "Rate limited IPs:"
+docker exec $CONTAINER grep "auth_rate_limit_exceeded" $LOG_PATH | wc -l
+```
+
+---
+
+## Best Practices
+
+### 1. Key Storage
+
+- ✅ Store in `.env` file (never commit to git)
+- ✅ Use password manager for backup
+- ✅ Save key metadata (not key itself) for tracking
+- ❌ Never hardcode in application code
+- ❌ Never share via unencrypted channels
+
+### 2. Key Rotation
+
+- **Schedule**: Every 90 days (automated check available)
+- **Method**: Use `make rotate-key` for guided rotation
+- **Grace period**: Temporarily allow both old and new keys
+- **Verification**: Test new key before removing old key
+
+See [KEY_ROTATION.md](KEY_ROTATION.md) for detailed rotation procedures.
+
+### 3. Access Control
+
+- **Single workspace**: One key for your ChatGPT Business account
+- **Multiple users**: One key per user (track with metadata)
+- **Revocation**: Remove key from `.env` and restart
+
+### 4. Monitoring
+
+- **Weekly**: Review auth logs for anomalies
+- **Monthly**: Check key age with `make check-key-age`
+- **Quarterly**: Rotate keys
+- **Alerts**: Set up notifications for rate limit events
+
+---
+
+## Advanced Configuration
+
+### Disable Authentication (Testing Only)
+
+**⚠️ WARNING: Only for isolated test environments**
+
+```bash
+# .env
+AUTH_ENABLED=false
+```
+
+Server will log critical warning:
+```
+API key authentication DISABLED - server is open to all requests!
+```
+
+### Custom Rate Limiting
+
+```bash
+# More lenient (for high-traffic)
+MAX_AUTH_FAILURES=20
+AUTH_FAILURE_WINDOW=600  # 10 minutes
+
+# More strict (for high-security)
+MAX_AUTH_FAILURES=3
+AUTH_FAILURE_WINDOW=1800  # 30 minutes
+```
+
+### Key Hashing (Future Enhancement)
+
+Currently keys are stored in plaintext in `.env`. Future versions will support hashed keys in database.
+
+**Current security model:**
+- ✅ Keys never logged in full (only first 8 + last 4 chars)
+- ✅ `.env` file protected by filesystem permissions
+- ✅ Container runs as non-root user
+- ⚠️ Ensure `.env` has restrictive permissions: `chmod 600 .env`
+
+---
+
+## Security Checklist
+
+Before going to production:
+
+- [ ] API key generated with `make generate-key` (not manually typed)
+- [ ] Key is exactly 64 characters
+- [ ] `.env` file has restrictive permissions (`chmod 600 .env`)
+- [ ] `.env` is in `.gitignore` (verify: `git status` shows no .env)
+- [ ] Container restarted after adding key
+- [ ] Authentication enabled (check logs for "ENABLED" message)
+- [ ] Test curl command succeeds with key, fails without
+- [ ] ChatGPT configured with Authorization header
+- [ ] Rate limiting tested (try 6 failed attempts)
+- [ ] Audit logs capturing auth events
+- [ ] Key rotation reminder set (90 days)
+- [ ] Backup key stored securely (password manager)
+
+---
+
+## FAQ
+
+**Q: Can I use the same key for multiple ChatGPT workspaces?**
+
+A: Yes, but not recommended. Generate separate keys for auditability:
+```bash
+MCP_API_KEYS=workspace1-key,workspace2-key
+```
+
+**Q: How do I revoke access immediately?**
+
+A: Remove key from `.env` and restart:
+```bash
+# Edit .env (remove old key)
+docker-compose restart aegis-mcp
+```
+
+Access is revoked instantly after restart.
+
+**Q: Does rate limiting affect valid keys?**
+
+A: No. Rate limiting only applies to IPs that fail authentication. Valid keys are never rate limited.
+
+**Q: Can I see which key was used for each request?**
+
+A: Yes. Audit logs include `key_hint` (first 8 + last 4 characters):
+```json
+{"key_hint": "a1b2c3d4...e1f2"}
+```
+
+**Q: What happens if I lose my API key?**
+
+A: Generate a new one with `make generate-key`, update `.env`, restart server, update ChatGPT config. The old key stops working immediately after restart.
+
+---
+
+## Next Steps
+
+- [ChatGPT Setup Guide](CHATGPT_SETUP.md) - Configure ChatGPT Business
+- [Key Rotation Guide](KEY_ROTATION.md) - Automated rotation procedures
+- [Security Policy](SECURITY.md) - Overall security best practices
+
+---
+
+**Need help?** Open an issue in the Gitea repository.
diff --git a/CHATGPT_SETUP.md b/CHATGPT_SETUP.md
new file mode 100644
index 0000000..412bf16
--- /dev/null
+++ b/CHATGPT_SETUP.md
@@ -0,0 +1,435 @@
+# ChatGPT Business Setup Guide
+
+Complete guide for connecting ChatGPT Business to your secured AegisGitea MCP server.
+
+---
+
+## Prerequisites
+
+- ✅ AegisGitea MCP server deployed and running
+- ✅ API key generated (see [AUTH_SETUP.md](AUTH_SETUP.md))
+- ✅ Traefik configured with HTTPS (or reverse proxy with TLS)
+- ✅ ChatGPT Business or Developer subscription
+
+---
+
+## Setup Steps
+
+### Step 1: Verify MCP Server is Running
+
+```bash
+# Check container status
+docker-compose ps
+
+# Should show "Up" status
+aegis-gitea-mcp   Up    0.0.0.0:8080->8080/tcp
+```
+
+### Step 2: Test Authentication
+
+```bash
+# Replace YOUR_API_KEY with your actual key
+curl -H "Authorization: Bearer YOUR_API_KEY" \
+     https://mcp.yourdomain.com/mcp/tools
+
+# Expected: JSON response with available tools
+# If error: Check AUTH_SETUP.md troubleshooting
+```
+
+### Step 3: Configure ChatGPT Business
+
+1. **Open ChatGPT Settings**
+   - Click your profile icon (bottom left)
+   - Select "Settings"
+   - Navigate to "Beta Features" or "Integrations"
+
+2. **Add MCP Server**
+   - Look for "Model Context Protocol" or "MCP Servers"
+   - Click "Add Server" or "+"
+
+3. **Enter Server Details**
+   ```
+   Name:        AegisGitea MCP
+   URL:         https://mcp.yourdomain.com
+   Type:        HTTP/SSE (Server-Sent Events)
+   ```
+
+4. **Add Custom Header**
+   ```
+   Header Name:  Authorization
+   Header Value: Bearer YOUR_API_KEY_HERE
+   ```
+
+   **Important:**
+   - Include the word "Bearer" followed by a space
+   - Then paste your full 64-character API key
+   - No quotes around the key
+
+5. **Save Configuration**
+
+### Step 4: Test Connection
+
+Start a new ChatGPT conversation and try:
+
+```
+List my Gitea repositories
+```
+
+**Expected Response:**
+```
+I found X repositories in your Gitea instance:
+
+1. org/repo-name - Description here
+2. org/another-repo - Another description
+...
+```
+
+**If it fails**, see Troubleshooting section below.
+
+---
+
+## Verification Checklist
+
+After setup, verify:
+
+- [ ] ChatGPT shows "Connected" status for AegisGitea MCP
+- [ ] Test command "List my Gitea repositories" works
+- [ ] Audit logs show successful authentication:
+      ```bash
+      docker-compose logs aegis-mcp | grep "api_authentication.*success"
+      ```
+- [ ] Can read file contents:
+      ```
+      Show me the README.md file from org/repo-name
+      ```
+- [ ] Can browse repository structure:
+      ```
+      What files are in the src/ directory of org/repo-name?
+      ```
+
+---
+
+## Example Commands
+
+Once connected, try these commands in ChatGPT:
+
+### Repository Discovery
+```
+What repositories do I have access to?
+List all my Gitea repositories
+Show me my private repositories
+```
+
+### Repository Information
+```
+Tell me about the org/my-repo repository
+What's the default branch of org/my-repo?
+When was org/my-repo last updated?
+```
+
+### File Operations
+```
+Show me the file tree of org/my-repo
+What files are in the src/ directory of org/my-repo?
+Read the README.md file from org/my-repo
+Show me the contents of src/main.py in org/my-repo
+```
+
+### Code Understanding
+```
+Explain what the main function does in org/my-repo/src/main.py
+Summarize the architecture of org/my-repo
+What dependencies does org/my-repo use?
+Find all TODO comments in org/my-repo
+```
+
+---
+
+## Troubleshooting
+
+### Issue: "Cannot connect to MCP server"
+
+**Check 1: Server is running**
+```bash
+docker-compose ps
+docker-compose logs aegis-mcp
+```
+
+**Check 2: Domain/URL is correct**
+```bash
+curl https://mcp.yourdomain.com/health
+# Should return: {"status": "healthy"}
+```
+
+**Check 3: Firewall/Network**
+- Ensure port 443 is open
+- Check Traefik is routing correctly
+- Verify DNS resolves correctly
+
+### Issue: "Authentication failed"
+
+**Check 1: Authorization header format**
+
+Correct:
+```
+Authorization: Bearer a1b2c3d4e5f6g7h8...
+```
+
+Wrong:
+```
+Authorization: a1b2c3d4...              (missing "Bearer ")
+Authorization: "Bearer a1b2c3d4..."     (extra quotes)
+Authorization:Bearer a1b2c3d4...        (missing space after colon)
+```
+
+**Check 2: Key matches .env**
+```bash
+# Show configured keys (first 12 chars only for security)
+docker-compose exec aegis-mcp printenv MCP_API_KEYS | cut -c1-12
+```
+
+Compare with your ChatGPT key (first 12 chars).
+
+**Check 3: Server logs**
+```bash
+docker-compose logs aegis-mcp | tail -50
+```
+
+Look for:
+- `invalid_api_key` → Key doesn't match
+- `missing_api_key` → Header not sent
+- `invalid_key_format` → Key too short
+
+### Issue: "No repositories visible"
+
+**Verify bot user has access:**
+
+1. Log into Gitea
+2. Go to repository Settings > Collaborators
+3. Confirm bot user is listed with Read permission
+4. If not, add bot user as collaborator
+
+**Test manually:**
+```bash
+curl -H "Authorization: Bearer YOUR_KEY" \
+     https://mcp.yourdomain.com/mcp/tool/call \
+     -X POST \
+     -H "Content-Type: application/json" \
+     -d '{"tool": "list_repositories", "arguments": {}}'
+```
+
+### Issue: "Rate limited"
+
+**Symptoms:**
+```
+Too many failed authentication attempts
+```
+
+**Solution:**
+1. Wait 5 minutes
+2. Verify API key is correct
+3. Check audit logs:
+   ```bash
+   docker-compose exec aegis-mcp grep "auth_rate_limit" /var/log/aegis-mcp/audit.log
+   ```
+4. If accidentally locked out:
+   ```bash
+   docker-compose restart aegis-mcp
+   ```
+
+### Issue: ChatGPT says "Tool not available"
+
+**Verify tools are registered:**
+```bash
+curl -H "Authorization: Bearer YOUR_KEY" \
+     https://mcp.yourdomain.com/mcp/tools
+```
+
+Should return JSON with tools array.
+
+---
+
+## Security Best Practices
+
+### 1. API Key Management
+
+- ✅ Store key in password manager
+- ✅ Never share key in chat or messages
+- ✅ Rotate key every 90 days
+- ❌ Don't paste key in public ChatGPT conversations
+- ❌ Don't screenshot ChatGPT settings with key visible
+
+### 2. Workspace Separation
+
+If multiple team members:
+
+```
+User A: Use key_a1b2c3...
+User B: Use key_b4c5d6...
+User C: Use key_c7d8e9...
+```
+
+Configure in `.env`:
+```bash
+MCP_API_KEYS=key_a1b2c3...,key_b4c5d6...,key_c7d8e9...
+```
+
+Each user configures their own ChatGPT with their specific key.
+
+### 3. Monitoring Usage
+
+Weekly check:
+```bash
+# Who's using the MCP server?
+docker-compose exec aegis-mcp grep "api_authentication" /var/log/aegis-mcp/audit.log | \
+  grep "success" | \
+  tail -20
+```
+
+Look for `key_hint` to identify which key was used.
+
+### 4. Incident Response
+
+If key is compromised:
+
+1. **Immediate:** Remove from `.env`
+   ```bash
+   # Edit .env (remove compromised key)
+   docker-compose restart aegis-mcp
+   ```
+
+2. **Generate new key**
+   ```bash
+   make generate-key
+   ```
+
+3. **Update ChatGPT** with new key
+
+4. **Check audit logs** for unauthorized access:
+   ```bash
+   docker-compose exec aegis-mcp grep "key_hint: <compromised_key_hint>" /var/log/aegis-mcp/audit.log
+   ```
+
+---
+
+## Advanced Configuration
+
+### Custom MCP Tool Calls (For Developers)
+
+You can call tools directly via API:
+
+```bash
+# List repositories
+curl -X POST https://mcp.yourdomain.com/mcp/tool/call \
+  -H "Authorization: Bearer YOUR_KEY" \
+  -H "Content-Type: application/json" \
+  -d '{
+    "tool": "list_repositories",
+    "arguments": {}
+  }'
+
+# Get file contents
+curl -X POST https://mcp.yourdomain.com/mcp/tool/call \
+  -H "Authorization: Bearer YOUR_KEY" \
+  -H "Content-Type: application/json" \
+  -d '{
+    "tool": "get_file_contents",
+    "arguments": {
+      "owner": "org",
+      "repo": "my-repo",
+      "filepath": "README.md"
+    }
+  }'
+```
+
+### Webhook Integration (Future)
+
+For automated workflows, you can integrate MCP tools into CI/CD:
+
+```yaml
+# Example GitHub Actions (future enhancement)
+- name: Sync to Gitea via MCP
+  run: |
+    curl -X POST https://mcp.yourdomain.com/mcp/tool/call \
+      -H "Authorization: Bearer ${{ secrets.MCP_API_KEY }}" \
+      -H "Content-Type: application/json" \
+      -d '{...}'
+```
+
+---
+
+## Performance Tips
+
+### 1. Rate Limiting Awareness
+
+Traefik limits: **60 requests/minute**
+
+For heavy usage:
+```yaml
+# docker-compose.yml
+labels:
+  - "traefik.http.middlewares.aegis-ratelimit.ratelimit.average=120"
+```
+
+### 2. Large Files
+
+Files >1MB are rejected by default. To increase:
+
+```bash
+# .env
+MAX_FILE_SIZE_BYTES=5242880  # 5MB
+```
+
+### 3. Batch Operations
+
+Instead of:
+```
+Show me file1.py
+Show me file2.py
+Show me file3.py
+```
+
+Use:
+```
+Show me all Python files in the src/ directory
+```
+
+---
+
+## FAQ
+
+**Q: Can I use this with Claude or other AI assistants?**
+
+A: Currently optimized for ChatGPT Business, but the MCP protocol is standard. Other AI assistants with MCP support should work with the same configuration.
+
+**Q: Do I need a separate key for each ChatGPT conversation?**
+
+A: No. One key per user/workspace. All conversations in that workspace use the same key.
+
+**Q: Can ChatGPT modify my repositories?**
+
+A: **No**. AegisGitea MCP is read-only by design. ChatGPT can only read code, never write/commit/push.
+
+**Q: What happens if I hit the rate limit?**
+
+A: You'll receive a 429 error. Wait 1 minute and try again. The limit is per IP, not per key.
+
+**Q: Can I use this from mobile ChatGPT app?**
+
+A: Yes, if your ChatGPT Business account syncs to mobile. The MCP configuration follows your account.
+
+**Q: How do I disconnect ChatGPT?**
+
+A: Go to ChatGPT Settings > MCP Servers > Remove "AegisGitea MCP"
+
+---
+
+## Next Steps
+
+- [Key Rotation Guide](KEY_ROTATION.md) - Rotate keys every 90 days
+- [Authentication Setup](AUTH_SETUP.md) - Detailed auth configuration
+- [Security Policy](SECURITY.md) - Best practices and threat model
+
+---
+
+**Happy coding with AI-assisted Gitea access!** 🚀
diff --git a/KEY_ROTATION.md b/KEY_ROTATION.md
new file mode 100644
index 0000000..195d360
--- /dev/null
+++ b/KEY_ROTATION.md
@@ -0,0 +1,548 @@
+# API Key Rotation Guide
+
+Comprehensive guide for rotating API keys in AegisGitea MCP with zero downtime.
+
+---
+
+## Why Rotate Keys?
+
+- **Security hygiene**: Regular rotation limits exposure window
+- **Compliance**: Many security policies require quarterly rotation
+- **Compromise mitigation**: If a key leaks, rotation limits damage
+- **Audit trail**: New keys = clear timeline of when access changed
+
+**Recommended schedule**: Every 90 days
+
+---
+
+## Automated Rotation (Recommended)
+
+### Step 1: Check Key Age
+
+```bash
+make check-key-age
+```
+
+**Output:**
+```
+Key: a1b2c3d4...
+  Created:  2026-01-29 (85 days ago)
+  Expires:  2026-04-29 (in 5 days)
+  Status:   ⚠️  WARNING
+```
+
+### Step 2: Rotate Key
+
+```bash
+make rotate-key
+```
+
+This script will:
+1. Show current keys
+2. Generate new 64-character key
+3. Offer rotation strategies (replace or grace period)
+4. Backup old `.env` file
+5. Update `.env` with new key
+6. Provide next steps
+
+**Example:**
+```
+Found 1 existing key(s)
+  1. a1b2c3d4...e1f2
+
+✓ New API key generated!
+
+Rotation Strategy:
+  1. Replace all keys with new key (recommended)
+  2. Add new key, keep old keys (grace period)
+  3. Cancel
+
+Choose option [1/2/3]: 2
+
+✓ New key will be added (total: 2 keys)
+
+⚠️  IMPORTANT: Remove old keys manually after updating ChatGPT config
+```
+
+### Step 3: Restart Server
+
+```bash
+docker-compose restart aegis-mcp
+```
+
+Verify both keys work:
+```bash
+# Test old key (should still work if using grace period)
+curl -H "Authorization: Bearer OLD_KEY" \
+     https://mcp.yourdomain.com/mcp/tools
+
+# Test new key (should work)
+curl -H "Authorization: Bearer NEW_KEY" \
+     https://mcp.yourdomain.com/mcp/tools
+```
+
+### Step 4: Update ChatGPT
+
+1. Go to ChatGPT Settings > MCP Servers
+2. Edit "AegisGitea MCP"
+3. Update Authorization header:
+   ```
+   Authorization: Bearer NEW_KEY_HERE
+   ```
+4. Save
+
+### Step 5: Verify & Clean Up
+
+Test ChatGPT connection:
+```
+List my Gitea repositories
+```
+
+If successful, remove old key:
+```bash
+# Edit .env - remove old key, keep only new key
+nano .env
+
+# MCP_API_KEYS=old-key,new-key  ← Remove old-key
+# MCP_API_KEYS=new-key           ← Keep only new key
+
+# Restart
+docker-compose restart aegis-mcp
+```
+
+Verify old key no longer works:
+```bash
+curl -H "Authorization: Bearer OLD_KEY" \
+     https://mcp.yourdomain.com/mcp/tools
+# Should return 401 Unauthorized
+```
+
+---
+
+## Manual Rotation (Step-by-Step)
+
+If you prefer manual control:
+
+### 1. Generate New Key
+
+```bash
+make generate-key
+```
+
+Save the output:
+```
+API KEY: b9c8d7e6f5g4h3i2...
+```
+
+### 2. Add to .env (Grace Period)
+
+```bash
+nano .env
+
+# Before:
+MCP_API_KEYS=a1b2c3d4e5f6g7h8...
+
+# After (both keys work):
+MCP_API_KEYS=a1b2c3d4e5f6g7h8...,b9c8d7e6f5g4h3i2...
+```
+
+### 3. Restart & Verify
+
+```bash
+docker-compose restart aegis-mcp
+
+# Check logs
+docker-compose logs aegis-mcp | grep "authentication"
+# Should show: "API key authentication ENABLED (2 key(s) configured)"
+```
+
+### 4. Update ChatGPT
+
+Update Authorization header with new key.
+
+### 5. Remove Old Key
+
+After confirming ChatGPT works with new key:
+
+```bash
+nano .env
+
+# Remove old key
+MCP_API_KEYS=b9c8d7e6f5g4h3i2...
+
+docker-compose restart aegis-mcp
+```
+
+---
+
+## Rotation Strategies
+
+### Strategy 1: Immediate Replacement (No Downtime Risk)
+
+**Use when:** You can update ChatGPT config immediately
+
+1. Generate new key
+2. Replace old key in `.env`
+3. Restart server
+4. Update ChatGPT within minutes
+
+**Pros:** Clean, only one key at a time
+**Cons:** Must update ChatGPT immediately or service breaks
+
+### Strategy 2: Grace Period (Zero Downtime)
+
+**Use when:** You need time to update ChatGPT config
+
+1. Generate new key
+2. Add new key, keep old key (both work)
+3. Restart server
+4. Update ChatGPT at your convenience
+5. Remove old key after verification
+
+**Pros:** Zero downtime, test thoroughly
+**Cons:** Temporarily allows two keys
+
+**Recommended grace period:** 24-48 hours max
+
+### Strategy 3: Scheduled Maintenance Window
+
+**Use when:** You want to coordinate with team
+
+1. Announce maintenance window (e.g., Saturday 2 AM)
+2. Generate new key
+3. During window:
+   - Replace key in `.env`
+   - Restart server
+   - Update all team members' ChatGPT configs
+4. Verify all users can access
+
+**Pros:** Coordinated, everyone updates at once
+**Cons:** Requires coordination
+
+---
+
+## Multi-User Rotation
+
+If multiple team members use different keys:
+
+### Option A: Rotate One Key at a Time
+
+```bash
+# Current state
+MCP_API_KEYS=alice-key,bob-key,charlie-key
+
+# Rotate Alice's key
+MCP_API_KEYS=alice-new-key,bob-key,charlie-key
+
+# Alice updates her ChatGPT, verify, continue
+```
+
+### Option B: Rotate All Keys Simultaneously
+
+```bash
+# Generate 3 new keys
+make generate-key  # Save as alice-new
+make generate-key  # Save as bob-new
+make generate-key  # Save as charlie-new
+
+# Grace period
+MCP_API_KEYS=alice-old,alice-new,bob-old,bob-new,charlie-old,charlie-new
+
+# Each user updates
+# After all verified, remove old keys
+MCP_API_KEYS=alice-new,bob-new,charlie-new
+```
+
+---
+
+## Automated Rotation Schedule
+
+### Setup Cron Job
+
+```bash
+# Edit crontab
+crontab -e
+
+# Check key age weekly
+0 9 * * MON /path/to/AegisGitea-MCP/scripts/check_key_age.py || echo "Keys need rotation"
+
+# Or check daily at 2 AM
+0 2 * * * cd /path/to/AegisGitea-MCP && make check-key-age
+```
+
+Exit codes:
+- `0` = All keys OK
+- `1` = Warning (rotation recommended in 14 days)
+- `2` = Critical (rotation needed NOW)
+
+### Email Notifications
+
+```bash
+#!/bin/bash
+# Save as scripts/check_and_notify.sh
+
+cd /path/to/AegisGitea-MCP
+
+# Run check
+make check-key-age > /tmp/key_status.txt 2>&1
+STATUS=$?
+
+if [ $STATUS -eq 2 ]; then
+  # Critical - send email
+  mail -s "[CRITICAL] AegisGitea API Key Expired" admin@example.com < /tmp/key_status.txt
+elif [ $STATUS -eq 1 ]; then
+  # Warning - send email
+  mail -s "[WARNING] AegisGitea API Key Expiring Soon" admin@example.com < /tmp/key_status.txt
+fi
+```
+
+### Discord/Slack Webhook
+
+```bash
+#!/bin/bash
+# Save as scripts/notify_discord.sh
+
+WEBHOOK_URL="https://discord.com/api/webhooks/..."
+MESSAGE="⚠️ AegisGitea MCP: API key expires in 5 days. Run \`make rotate-key\`"
+
+curl -X POST "$WEBHOOK_URL" \
+  -H "Content-Type: application/json" \
+  -d "{\"content\": \"$MESSAGE\"}"
+```
+
+---
+
+## Emergency Rotation (Compromised Key)
+
+If you suspect a key has been compromised:
+
+### Immediate Actions (< 5 minutes)
+
+1. **Revoke compromised key immediately**
+   ```bash
+   # Edit .env - remove compromised key
+   nano .env
+   
+   # Before
+   MCP_API_KEYS=compromised-key
+   
+   # After
+   MCP_API_KEYS=
+   
+   # Or temporarily disable auth
+   AUTH_ENABLED=false
+   
+   docker-compose restart aegis-mcp
+   ```
+
+2. **Check audit logs for unauthorized access**
+   ```bash
+   docker-compose exec aegis-mcp grep "compromised_key_hint" /var/log/aegis-mcp/audit.log
+   
+   # Look for suspicious IPs, unusual times, unexpected repositories
+   ```
+
+3. **Generate new key**
+   ```bash
+   make generate-key
+   ```
+
+4. **Update .env with new key**
+   ```bash
+   MCP_API_KEYS=new-secure-key
+   AUTH_ENABLED=true
+   
+   docker-compose restart aegis-mcp
+   ```
+
+5. **Update ChatGPT config**
+
+### Investigation (< 30 minutes)
+
+```bash
+# When was compromised key last used?
+docker-compose exec aegis-mcp grep "key_hint: compromised..." /var/log/aegis-mcp/audit.log | tail -1
+
+# What repositories were accessed?
+docker-compose exec aegis-mcp grep "compromised..." /var/log/aegis-mcp/audit.log | grep "repository"
+
+# From which IPs?
+docker-compose exec aegis-mcp grep "compromised..." /var/log/aegis-mcp/audit.log | grep "client_ip"
+```
+
+### Post-Incident (< 24 hours)
+
+1. Document timeline of compromise
+2. Review and improve key storage practices
+3. Consider additional security measures (IP allowlisting, MFA)
+4. Notify team if multi-user setup
+
+---
+
+## Troubleshooting Rotation
+
+### Issue: Both old and new keys fail after rotation
+
+**Cause:** Server not restarted or `.env` syntax error
+
+**Fix:**
+```bash
+# Check .env syntax
+cat .env | grep MCP_API_KEYS
+# Should be: MCP_API_KEYS=key1,key2
+
+# No spaces around =
+# No quotes around keys
+# Comma-separated, no spaces
+
+# Restart
+docker-compose restart aegis-mcp
+
+# Check logs
+docker-compose logs aegis-mcp | tail -20
+```
+
+### Issue: "No API keys configured" after rotation
+
+**Cause:** Empty MCP_API_KEYS in `.env`
+
+**Fix:**
+```bash
+# Verify .env has key
+grep MCP_API_KEYS .env
+# Should NOT be empty
+
+# If empty, add key
+echo "MCP_API_KEYS=your-key-here" >> .env
+
+docker-compose restart aegis-mcp
+```
+
+### Issue: Old key still works after removal
+
+**Cause:** Server not restarted or cached config
+
+**Fix:**
+```bash
+# Force restart (not just reload)
+docker-compose down
+docker-compose up -d
+
+# Verify old key fails
+curl -H "Authorization: Bearer OLD_KEY" \
+     https://mcp.yourdomain.com/mcp/tools
+# Should return 401
+```
+
+### Issue: Lost .env.backup file
+
+**Cause:** Backup not created during rotation
+
+**Prevention:**
+```bash
+# Always backup before manual edits
+cp .env .env.backup-$(date +%Y%m%d-%H%M%S)
+
+# The rotate script does this automatically
+```
+
+**Recovery:**
+If you lost your key and no backup:
+1. Generate new key
+2. Update `.env`
+3. Update ChatGPT
+4. The old key is lost but system still works
+
+---
+
+## Best Practices Checklist
+
+Before rotation:
+- [ ] Check current key age: `make check-key-age`
+- [ ] Backup `.env`: `cp .env .env.backup`
+- [ ] Notify team if multi-user
+- [ ] Schedule maintenance window if needed
+
+During rotation:
+- [ ] Generate new key: `make generate-key`
+- [ ] Save key securely (password manager)
+- [ ] Update `.env` with new key
+- [ ] Restart server: `docker-compose restart`
+- [ ] Verify new key works (curl test)
+- [ ] Update ChatGPT config
+- [ ] Test ChatGPT connection
+
+After rotation:
+- [ ] Remove old key from `.env` (if using grace period)
+- [ ] Verify old key fails (curl test)
+- [ ] Check audit logs for successful auth with new key
+- [ ] Save key metadata: Save metadata when generating key
+- [ ] Set calendar reminder for next rotation (90 days)
+- [ ] Document rotation in changelog/runbook
+
+---
+
+## Key Metadata Tracking
+
+When generating keys, save metadata:
+
+```bash
+make generate-key
+# Choose "y" when prompted to save metadata
+```
+
+This creates `keys/key-<id>-<date>.txt`:
+```
+API Key Metadata
+================
+
+Key ID:       a1b2c3d4...
+Description:  Production ChatGPT Key
+Created:      2026-01-29T12:00:00+00:00
+Expires:      2026-04-29T12:00:00+00:00
+
+NOTE: The actual API key is NOT stored in this file for security.
+      Only metadata is saved for reference.
+```
+
+**Benefits:**
+- Track key age automatically
+- Audit key lifecycle
+- Identify which key is which (if multiple)
+- Automated expiration warnings
+
+---
+
+## FAQ
+
+**Q: What's the grace period for rotation?**
+
+A: 24-48 hours is recommended. Keep both keys working just long enough to update ChatGPT, then remove the old key.
+
+**Q: Can I rotate keys without downtime?**
+
+A: Yes! Use Strategy 2 (Grace Period). Both old and new keys work simultaneously during the transition.
+
+**Q: How do I know which key is oldest?**
+
+A: Use `make check-key-age` if you saved metadata. Otherwise, check audit logs for last usage.
+
+**Q: Should I rotate after a team member leaves?**
+
+A: Yes, if they had access to the shared key. Or better: use per-user keys and just remove their key.
+
+**Q: Can I automate the entire rotation?**
+
+A: Partially. You can automate generation and notification, but ChatGPT config update requires manual action.
+
+---
+
+## Next Steps
+
+- [Authentication Setup](AUTH_SETUP.md) - Initial setup guide
+- [ChatGPT Configuration](CHATGPT_SETUP.md) - Update ChatGPT after rotation
+- [Security Policy](SECURITY.md) - Overall security best practices
+
+---
+
+**Set a reminder now:** Rotate your keys 90 days from today! 🔑
diff --git a/Makefile b/Makefile
index dca8727..71b6a11 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-.PHONY: help install install-dev test lint format clean build run docker-build docker-up docker-down docker-logs
+.PHONY: help install install-dev test lint format clean build run docker-build docker-up docker-down docker-logs generate-key rotate-key check-key-age
 
 help:
 	@echo "AegisGitea MCP - Available Commands"
@@ -11,6 +11,11 @@ help:
 	@echo "  make format         Format code with black"
 	@echo "  make clean          Remove build artifacts"
 	@echo ""
+	@echo "API Key Management:"
+	@echo "  make generate-key   Generate new API key"
+	@echo "  make rotate-key     Rotate existing API key"
+	@echo "  make check-key-age  Check API key age and expiration"
+	@echo ""
 	@echo "Local Execution:"
 	@echo "  make run            Run server locally (requires .env)"
 	@echo ""
@@ -19,6 +24,7 @@ help:
 	@echo "  make docker-up      Start containers"
 	@echo "  make docker-down    Stop containers"
 	@echo "  make docker-logs    View container logs"
+	@echo "  make docker-restart Restart MCP container"
 	@echo ""
 
 install:
@@ -67,3 +73,12 @@ docker-restart:
 
 docker-shell:
 	docker-compose exec aegis-mcp /bin/bash
+
+generate-key:
+	python3 scripts/generate_api_key.py
+
+rotate-key:
+	python3 scripts/rotate_api_key.py
+
+check-key-age:
+	python3 scripts/check_key_age.py
diff --git a/docker-compose.yml b/docker-compose.yml
index 6ea8bf3..74ffa0f 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,4 +1,4 @@
-# Convenience symlink to docker/docker-compose.yml
+# AegisGitea MCP - Docker Compose Configuration
 # Usage: docker-compose up -d
 
 version: '3.8'
@@ -22,6 +22,7 @@ services:
     
     networks:
       - aegis-network
+      - traefik  # Connect to Traefik network (if using Traefik)
     
     security_opt:
       - no-new-privileges:true
@@ -41,6 +42,36 @@ services:
       timeout: 10s
       retries: 3
       start_period: 10s
+    
+    # Traefik labels for automatic HTTPS and routing
+    labels:
+      - "traefik.enable=true"
+      
+      # Router configuration
+      - "traefik.http.routers.aegis-mcp.rule=Host(`${MCP_DOMAIN:-mcp.example.com}`)"
+      - "traefik.http.routers.aegis-mcp.entrypoints=websecure"
+      - "traefik.http.routers.aegis-mcp.tls=true"
+      - "traefik.http.routers.aegis-mcp.tls.certresolver=letsencrypt"
+      
+      # Service configuration
+      - "traefik.http.services.aegis-mcp.loadbalancer.server.port=8080"
+      
+      # Rate limiting middleware (60 req/min per IP)
+      - "traefik.http.middlewares.aegis-ratelimit.ratelimit.average=60"
+      - "traefik.http.middlewares.aegis-ratelimit.ratelimit.period=1m"
+      - "traefik.http.middlewares.aegis-ratelimit.ratelimit.burst=10"
+      
+      # Security headers middleware
+      - "traefik.http.middlewares.aegis-security.headers.sslredirect=true"
+      - "traefik.http.middlewares.aegis-security.headers.stsSeconds=31536000"
+      - "traefik.http.middlewares.aegis-security.headers.stsIncludeSubdomains=true"
+      - "traefik.http.middlewares.aegis-security.headers.stsPreload=true"
+      - "traefik.http.middlewares.aegis-security.headers.contentTypeNosniff=true"
+      - "traefik.http.middlewares.aegis-security.headers.browserXssFilter=true"
+      - "traefik.http.middlewares.aegis-security.headers.forceSTSHeader=true"
+      
+      # Apply middlewares to router
+      - "traefik.http.routers.aegis-mcp.middlewares=aegis-ratelimit@docker,aegis-security@docker"
 
 volumes:
   aegis-mcp-logs:
@@ -49,3 +80,8 @@ volumes:
 networks:
   aegis-network:
     driver: bridge
+  
+  # External Traefik network (create with: docker network create traefik)
+  # Comment out if not using Traefik
+  traefik:
+    external: true
diff --git a/scripts/check_key_age.py b/scripts/check_key_age.py
new file mode 100755
index 0000000..b5d15b5
--- /dev/null
+++ b/scripts/check_key_age.py
@@ -0,0 +1,140 @@
+#!/usr/bin/env python3
+"""Check API key age and alert if rotation needed."""
+
+import os
+import re
+import sys
+from datetime import datetime, timedelta, timezone
+from pathlib import Path
+
+
+def main() -> None:
+    """Check API key age from keys/ metadata directory."""
+    print("=" * 70)
+    print("AegisGitea MCP - API Key Age Check")
+    print("=" * 70)
+    print()
+
+    # Check keys directory
+    keys_dir = Path(__file__).parent.parent / "keys"
+
+    if not keys_dir.exists():
+        print("⚠️  No keys/ directory found")
+        print()
+        print("   Key metadata is not being tracked.")
+        print("   Run scripts/generate_api_key.py and save metadata to track key age.")
+        print()
+        sys.exit(0)
+
+    # Find all key metadata files
+    metadata_files = list(keys_dir.glob("key-*.txt"))
+
+    if not metadata_files:
+        print("⚠️  No key metadata files found in keys/")
+        print()
+        print("   Run scripts/generate_api_key.py and save metadata to track key age.")
+        print()
+        sys.exit(0)
+
+    print(f"Found {len(metadata_files)} key metadata file(s)")
+    print()
+    print("-" * 70)
+    print()
+
+    now = datetime.now(timezone.utc)
+    warnings = []
+    critical = []
+
+    for metadata_file in sorted(metadata_files):
+        with open(metadata_file, "r") as f:
+            content = f.read()
+
+        # Extract metadata
+        key_id_match = re.search(r"Key ID:\s+([^\n]+)", content)
+        created_match = re.search(r"Created:\s+([^\n]+)", content)
+        expires_match = re.search(r"Expires:\s+([^\n]+)", content)
+
+        if not all([key_id_match, created_match, expires_match]):
+            print(f"⚠️  Could not parse: {metadata_file.name}")
+            continue
+
+        key_id = key_id_match.group(1).strip()
+        created_str = created_match.group(1).strip()
+        expires_str = expires_match.group(1).strip()
+
+        # Parse dates
+        try:
+            created_at = datetime.fromisoformat(created_str.replace("Z", "+00:00"))
+            expires_at = datetime.fromisoformat(expires_str.replace("Z", "+00:00"))
+        except ValueError as e:
+            print(f"⚠️  Could not parse dates in: {metadata_file.name}")
+            print(f"     Error: {e}")
+            continue
+
+        # Calculate age and time to expiration
+        age_days = (now - created_at).days
+        days_to_expiration = (expires_at - now).days
+
+        # Status
+        if days_to_expiration < 0:
+            status = "❌ EXPIRED"
+            critical.append(key_id)
+        elif days_to_expiration <= 7:
+            status = "⚠️  CRITICAL"
+            critical.append(key_id)
+        elif days_to_expiration <= 14:
+            status = "⚠️  WARNING"
+            warnings.append(key_id)
+        else:
+            status = "✓ OK"
+
+        print(f"Key: {key_id}")
+        print(f"  Created:  {created_at.strftime('%Y-%m-%d')} ({age_days} days ago)")
+        print(f"  Expires:  {expires_at.strftime('%Y-%m-%d')} (in {days_to_expiration} days)")
+        print(f"  Status:   {status}")
+        print()
+
+    print("-" * 70)
+    print()
+
+    # Summary
+    if critical:
+        print("❌ CRITICAL: {} key(s) require immediate rotation!".format(len(critical)))
+        print()
+        print("   Keys:")
+        for key_id in critical:
+            print(f"     • {key_id}")
+        print()
+        print("   Action: Run scripts/rotate_api_key.py NOW")
+        print()
+        sys.exit(2)
+    elif warnings:
+        print("⚠️  WARNING: {} key(s) will expire soon".format(len(warnings)))
+        print()
+        print("   Keys:")
+        for key_id in warnings:
+            print(f"     • {key_id}")
+        print()
+        print("   Action: Schedule key rotation in the next few days")
+        print("           Run: scripts/rotate_api_key.py")
+        print()
+        sys.exit(1)
+    else:
+        print("✓ All keys are valid and within rotation schedule")
+        print()
+        print("   Next check: Run this script again in 1 week")
+        print()
+        sys.exit(0)
+
+
+if __name__ == "__main__":
+    try:
+        main()
+    except KeyboardInterrupt:
+        print("\n\nOperation cancelled.")
+        sys.exit(1)
+    except Exception as e:
+        print(f"\n❌ Error: {e}", file=sys.stderr)
+        import traceback
+        traceback.print_exc()
+        sys.exit(1)
diff --git a/scripts/generate_api_key.py b/scripts/generate_api_key.py
new file mode 100755
index 0000000..be4aaf5
--- /dev/null
+++ b/scripts/generate_api_key.py
@@ -0,0 +1,113 @@
+#!/usr/bin/env python3
+"""Generate a cryptographically secure API key for AegisGitea MCP."""
+
+import sys
+from datetime import datetime, timedelta, timezone
+from pathlib import Path
+
+# Add src to path for imports
+sys.path.insert(0, str(Path(__file__).parent.parent / "src"))
+
+from aegis_gitea_mcp.auth import generate_api_key
+
+
+def main() -> None:
+    """Generate and display a new API key."""
+    print("=" * 70)
+    print("AegisGitea MCP - API Key Generator")
+    print("=" * 70)
+    print()
+
+    # Get optional description
+    description = input("Enter description for this key (e.g., 'ChatGPT Business'): ").strip()
+    if not description:
+        description = "Generated key"
+
+    # Generate key
+    api_key = generate_api_key(length=64)
+
+    # Calculate expiration date (90 days from now)
+    created_at = datetime.now(timezone.utc)
+    expires_at = created_at + timedelta(days=90)
+
+    print()
+    print("✓ API Key Generated Successfully!")
+    print()
+    print("-" * 70)
+    print(f"Description:  {description}")
+    print(f"Created:      {created_at.strftime('%Y-%m-%d %H:%M:%S UTC')}")
+    print(f"Expires:      {expires_at.strftime('%Y-%m-%d %H:%M:%S UTC')} (90 days)")
+    print("-" * 70)
+    print()
+    print("API KEY:")
+    print(f"  {api_key}")
+    print()
+    print("-" * 70)
+    print()
+    print("📋 Next Steps:")
+    print()
+    print("1. Add this key to your .env file:")
+    print()
+    print(f"   MCP_API_KEYS={api_key}")
+    print()
+    print("   (If you have multiple keys, separate them with commas)")
+    print()
+    print("2. Restart the MCP server:")
+    print()
+    print("   docker-compose restart aegis-mcp")
+    print()
+    print("3. Configure ChatGPT Business:")
+    print()
+    print("   - Go to ChatGPT Settings > MCP Servers")
+    print("   - Add custom header:")
+    print(f"     Authorization: Bearer {api_key}")
+    print()
+    print("4. Test the connection:")
+    print()
+    print("   Ask ChatGPT: 'List my Gitea repositories'")
+    print()
+    print("-" * 70)
+    print()
+    print("⚠️  IMPORTANT:")
+    print()
+    print("  • Store this key securely - it won't be shown again")
+    print("  • This key should be rotated in 90 days")
+    print("  • Set a reminder to rotate before expiration")
+    print("  • Never commit this key to version control")
+    print()
+    print("=" * 70)
+
+    # Offer to save metadata to file
+    save = input("\nSave key metadata to keys/ directory? [y/N]: ").strip().lower()
+    if save == "y":
+        keys_dir = Path(__file__).parent.parent / "keys"
+        keys_dir.mkdir(exist_ok=True)
+
+        # Create metadata file
+        key_id = api_key[:12]
+        metadata_file = keys_dir / f"key-{key_id}-{created_at.strftime('%Y%m%d')}.txt"
+
+        with open(metadata_file, "w") as f:
+            f.write(f"API Key Metadata\n")
+            f.write(f"================\n\n")
+            f.write(f"Key ID:       {key_id}...\n")
+            f.write(f"Description:  {description}\n")
+            f.write(f"Created:      {created_at.isoformat()}\n")
+            f.write(f"Expires:      {expires_at.isoformat()}\n")
+            f.write(f"\n")
+            f.write(f"NOTE: The actual API key is NOT stored in this file for security.\n")
+            f.write(f"      Only metadata is saved for reference.\n")
+
+        print(f"\n✓ Metadata saved to: {metadata_file}")
+        print(f"\n  (The actual key is NOT saved - only you have it)")
+
+
+if __name__ == "__main__":
+    try:
+        main()
+    except KeyboardInterrupt:
+        print("\n\nOperation cancelled.")
+        sys.exit(1)
+    except Exception as e:
+        print(f"\n❌ Error: {e}", file=sys.stderr)
+        sys.exit(1)
diff --git a/scripts/rotate_api_key.py b/scripts/rotate_api_key.py
new file mode 100755
index 0000000..6de9794
--- /dev/null
+++ b/scripts/rotate_api_key.py
@@ -0,0 +1,175 @@
+#!/usr/bin/env python3
+"""Rotate API key for AegisGitea MCP."""
+
+import os
+import re
+import sys
+from datetime import datetime, timedelta, timezone
+from pathlib import Path
+
+# Add src to path for imports
+sys.path.insert(0, str(Path(__file__).parent.parent / "src"))
+
+from aegis_gitea_mcp.auth import generate_api_key
+
+
+def main() -> None:
+    """Rotate API key in .env file."""
+    print("=" * 70)
+    print("AegisGitea MCP - API Key Rotation")
+    print("=" * 70)
+    print()
+
+    # Find .env file
+    env_file = Path(__file__).parent.parent / ".env"
+
+    if not env_file.exists():
+        print("❌ Error: .env file not found")
+        print(f"   Expected location: {env_file}")
+        print()
+        print("   Please create .env from .env.example first")
+        sys.exit(1)
+
+    # Read current .env
+    with open(env_file, "r") as f:
+        env_content = f.read()
+
+    # Check if MCP_API_KEYS exists
+    if "MCP_API_KEYS" not in env_content:
+        print("❌ Error: MCP_API_KEYS not found in .env file")
+        print()
+        print("   Please add MCP_API_KEYS to your .env file first")
+        sys.exit(1)
+
+    # Extract current key
+    match = re.search(r"MCP_API_KEYS=([^\n]+)", env_content)
+    if not match:
+        print("❌ Error: Could not parse MCP_API_KEYS from .env")
+        sys.exit(1)
+
+    current_keys = match.group(1).strip()
+    key_list = [k.strip() for k in current_keys.split(",") if k.strip()]
+
+    print(f"Found {len(key_list)} existing key(s)")
+    print()
+
+    # Show current keys (first 8 chars only)
+    for i, key in enumerate(key_list, 1):
+        key_hint = f"{key[:8]}...{key[-4:]}" if len(key) >= 12 else "invalid"
+        print(f"  {i}. {key_hint}")
+
+    print()
+    print("-" * 70)
+    print()
+
+    # Generate new key
+    new_key = generate_api_key(length=64)
+    created_at = datetime.now(timezone.utc)
+    expires_at = created_at + timedelta(days=90)
+
+    print("✓ New API key generated!")
+    print()
+    print(f"Created:  {created_at.strftime('%Y-%m-%d %H:%M:%S UTC')}")
+    print(f"Expires:  {expires_at.strftime('%Y-%m-%d %H:%M:%S UTC')} (90 days)")
+    print()
+    print("-" * 70)
+    print()
+
+    # Ask what to do with old keys
+    print("Rotation Strategy:")
+    print()
+    print("  1. Replace all keys with new key (recommended)")
+    print("  2. Add new key, keep old keys (grace period)")
+    print("  3. Cancel")
+    print()
+
+    choice = input("Choose option [1/2/3]: ").strip()
+
+    if choice == "3":
+        print("\nRotation cancelled.")
+        sys.exit(0)
+    elif choice == "2":
+        # Add new key to list
+        key_list.append(new_key)
+        new_keys_str = ",".join(key_list)
+        print("\n✓ New key will be added (total: {} keys)".format(len(key_list)))
+        print("\n⚠️  IMPORTANT: Remove old keys manually after updating ChatGPT config")
+    elif choice == "1":
+        # Replace with only new key
+        new_keys_str = new_key
+        print("\n✓ All old keys will be replaced with new key")
+    else:
+        print("\n❌ Invalid choice. Operation cancelled.")
+        sys.exit(1)
+
+    print()
+    print("-" * 70)
+    print()
+
+    # Update .env file
+    new_env_content = re.sub(
+        r"MCP_API_KEYS=([^\n]+)",
+        f"MCP_API_KEYS={new_keys_str}",
+        env_content
+    )
+
+    # Backup old .env
+    backup_file = env_file.with_suffix(f".env.backup-{datetime.now().strftime('%Y%m%d-%H%M%S')}")
+    with open(backup_file, "w") as f:
+        f.write(env_content)
+
+    print(f"✓ Backed up old .env to: {backup_file.name}")
+
+    # Write new .env
+    with open(env_file, "w") as f:
+        f.write(new_env_content)
+
+    print(f"✓ Updated .env file with new key(s)")
+    print()
+    print("-" * 70)
+    print()
+    print("📋 Next Steps:")
+    print()
+    print("1. Restart the MCP server:")
+    print()
+    print("   docker-compose restart aegis-mcp")
+    print()
+    print("2. Update ChatGPT Business configuration:")
+    print()
+    print("   - Go to ChatGPT Settings > MCP Servers")
+    print("   - Update Authorization header:")
+    print(f"     Authorization: Bearer {new_key}")
+    print()
+    print("3. Test the connection:")
+    print()
+    print("   Ask ChatGPT: 'List my Gitea repositories'")
+    print()
+    print("4. If using grace period (option 2):")
+    print()
+    print("   - After confirming ChatGPT works with new key")
+    print("   - Manually remove old keys from .env")
+    print("   - Restart server again")
+    print()
+    print("-" * 70)
+    print()
+    print("⚠️  IMPORTANT:")
+    print()
+    print(f"  • New API Key: {new_key}")
+    print("  • Store this securely - it won't be shown again")
+    print("  • Set a reminder to rotate in 90 days")
+    print("  • Old .env backed up to:", backup_file.name)
+    print()
+    print("=" * 70)
+
+
+if __name__ == "__main__":
+    try:
+        main()
+    except KeyboardInterrupt:
+        print("\n\nOperation cancelled.")
+        sys.exit(1)
+    except Exception as e:
+        print(f"\n❌ Error: {e}", file=sys.stderr)
+        import traceback
+        traceback.print_exc()
+        sys.exit(1)
diff --git a/src/aegis_gitea_mcp/auth.py b/src/aegis_gitea_mcp/auth.py
new file mode 100644
index 0000000..2aaaece
--- /dev/null
+++ b/src/aegis_gitea_mcp/auth.py
@@ -0,0 +1,243 @@
+"""Authentication module for MCP server API key validation."""
+
+import hashlib
+import hmac
+import secrets
+from datetime import datetime, timezone
+from typing import Optional, Tuple
+
+from aegis_gitea_mcp.audit import get_audit_logger
+from aegis_gitea_mcp.config import get_settings
+
+
+class AuthenticationError(Exception):
+    """Raised when authentication fails."""
+
+    pass
+
+
+class APIKeyValidator:
+    """Validates API keys for MCP server access."""
+
+    def __init__(self) -> None:
+        """Initialize API key validator."""
+        self.settings = get_settings()
+        self.audit = get_audit_logger()
+        self._failed_attempts: dict[str, list[datetime]] = {}
+
+    def _constant_time_compare(self, a: str, b: str) -> bool:
+        """Compare two strings in constant time to prevent timing attacks.
+
+        Args:
+            a: First string
+            b: Second string
+
+        Returns:
+            True if strings are equal, False otherwise
+        """
+        return hmac.compare_digest(a, b)
+
+    def _check_rate_limit(self, identifier: str) -> bool:
+        """Check if identifier has exceeded failed authentication rate limit.
+
+        Args:
+            identifier: IP address or other identifier
+
+        Returns:
+            True if within rate limit, False if exceeded
+        """
+        now = datetime.now(timezone.utc)
+        window_start = now.timestamp() - self.settings.auth_failure_window
+
+        # Clean up old attempts
+        if identifier in self._failed_attempts:
+            self._failed_attempts[identifier] = [
+                attempt
+                for attempt in self._failed_attempts[identifier]
+                if attempt.timestamp() > window_start
+            ]
+
+        # Check count
+        attempt_count = len(self._failed_attempts.get(identifier, []))
+        return attempt_count < self.settings.max_auth_failures
+
+    def _record_failed_attempt(self, identifier: str) -> None:
+        """Record a failed authentication attempt.
+
+        Args:
+            identifier: IP address or other identifier
+        """
+        now = datetime.now(timezone.utc)
+        if identifier not in self._failed_attempts:
+            self._failed_attempts[identifier] = []
+        self._failed_attempts[identifier].append(now)
+
+        # Check if threshold exceeded
+        if len(self._failed_attempts[identifier]) >= self.settings.max_auth_failures:
+            self.audit.log_security_event(
+                event_type="auth_rate_limit_exceeded",
+                description=f"IP {identifier} exceeded auth failure threshold",
+                severity="high",
+                metadata={
+                    "identifier": identifier,
+                    "failure_count": len(self._failed_attempts[identifier]),
+                    "window_seconds": self.settings.auth_failure_window,
+                },
+            )
+
+    def validate_api_key(
+        self, provided_key: Optional[str], client_ip: str, user_agent: str
+    ) -> Tuple[bool, Optional[str]]:
+        """Validate an API key.
+
+        Args:
+            provided_key: API key provided by client
+            client_ip: Client IP address
+            user_agent: Client user agent string
+
+        Returns:
+            Tuple of (is_valid, error_message)
+        """
+        # Check if authentication is enabled
+        if not self.settings.auth_enabled:
+            self.audit.log_security_event(
+                event_type="auth_disabled",
+                description="Authentication is disabled - allowing all requests",
+                severity="critical",
+                metadata={"client_ip": client_ip},
+            )
+            return True, None
+
+        # Check rate limit
+        if not self._check_rate_limit(client_ip):
+            self.audit.log_access_denied(
+                tool_name="api_authentication",
+                reason="rate_limit_exceeded",
+            )
+            return False, "Too many failed authentication attempts. Please try again later."
+
+        # Check if key was provided
+        if not provided_key:
+            self._record_failed_attempt(client_ip)
+            self.audit.log_access_denied(
+                tool_name="api_authentication",
+                reason="missing_api_key",
+            )
+            return False, "Authorization header missing. Required: Authorization: Bearer <api-key>"
+
+        # Validate key format (should be at least 32 characters)
+        if len(provided_key) < 32:
+            self._record_failed_attempt(client_ip)
+            self.audit.log_access_denied(
+                tool_name="api_authentication",
+                reason="invalid_key_format",
+            )
+            return False, "Invalid API key format"
+
+        # Get valid API keys from config
+        valid_keys = self.settings.mcp_api_keys
+
+        if not valid_keys:
+            self.audit.log_security_event(
+                event_type="no_api_keys_configured",
+                description="No API keys configured in environment",
+                severity="critical",
+                metadata={"client_ip": client_ip},
+            )
+            return False, "Server configuration error: No API keys configured"
+
+        # Check against all valid keys (constant time comparison)
+        is_valid = any(self._constant_time_compare(provided_key, valid_key) for valid_key in valid_keys)
+
+        if is_valid:
+            # Success - log and return
+            key_hint = f"{provided_key[:8]}...{provided_key[-4:]}"
+            self.audit.log_tool_invocation(
+                tool_name="api_authentication",
+                result_status="success",
+                params={"client_ip": client_ip, "user_agent": user_agent, "key_hint": key_hint},
+            )
+            return True, None
+        else:
+            # Failure - record attempt and log
+            self._record_failed_attempt(client_ip)
+            key_hint = f"{provided_key[:8]}..." if len(provided_key) >= 8 else "too_short"
+            self.audit.log_access_denied(
+                tool_name="api_authentication",
+                reason="invalid_api_key",
+            )
+            self.audit.log_security_event(
+                event_type="invalid_api_key_attempt",
+                description=f"Invalid API key attempted from {client_ip}",
+                severity="medium",
+                metadata={
+                    "client_ip": client_ip,
+                    "user_agent": user_agent,
+                    "key_hint": key_hint,
+                },
+            )
+            return False, "Invalid API key"
+
+    def extract_bearer_token(self, authorization_header: Optional[str]) -> Optional[str]:
+        """Extract bearer token from Authorization header.
+
+        Args:
+            authorization_header: Authorization header value
+
+        Returns:
+            Extracted token or None if invalid format
+        """
+        if not authorization_header:
+            return None
+
+        parts = authorization_header.split()
+        if len(parts) != 2:
+            return None
+
+        scheme, token = parts
+        if scheme.lower() != "bearer":
+            return None
+
+        return token
+
+
+def generate_api_key(length: int = 64) -> str:
+    """Generate a cryptographically secure API key.
+
+    Args:
+        length: Length of the key in characters (default: 64)
+
+    Returns:
+        Generated API key as hex string
+    """
+    return secrets.token_hex(length // 2)
+
+
+def hash_api_key(api_key: str) -> str:
+    """Hash an API key for secure storage (future use).
+
+    Args:
+        api_key: Plain text API key
+
+    Returns:
+        SHA256 hash of the key
+    """
+    return hashlib.sha256(api_key.encode()).hexdigest()
+
+
+# Global validator instance
+_validator: Optional[APIKeyValidator] = None
+
+
+def get_validator() -> APIKeyValidator:
+    """Get or create global API key validator instance."""
+    global _validator
+    if _validator is None:
+        _validator = APIKeyValidator()
+    return _validator
+
+
+def reset_validator() -> None:
+    """Reset global validator instance (primarily for testing)."""
+    global _validator
+    _validator = None
diff --git a/src/aegis_gitea_mcp/config.py b/src/aegis_gitea_mcp/config.py
index 39352c0..2eef6e0 100644
--- a/src/aegis_gitea_mcp/config.py
+++ b/src/aegis_gitea_mcp/config.py
@@ -1,7 +1,7 @@
 """Configuration management for AegisGitea MCP server."""
 
 from pathlib import Path
-from typing import Optional
+from typing import List, Optional
 
 from pydantic import Field, HttpUrl, field_validator
 from pydantic_settings import BaseSettings, SettingsConfigDict
@@ -67,6 +67,26 @@ class Settings(BaseSettings):
         ge=1,
     )
 
+    # Authentication configuration
+    auth_enabled: bool = Field(
+        default=True,
+        description="Enable API key authentication (disable only for testing)",
+    )
+    mcp_api_keys: List[str] = Field(
+        default_factory=list,
+        description="List of valid API keys for MCP access (comma-separated in env)",
+    )
+    max_auth_failures: int = Field(
+        default=5,
+        description="Maximum authentication failures before rate limiting",
+        ge=1,
+    )
+    auth_failure_window: int = Field(
+        default=300,  # 5 minutes
+        description="Time window for counting auth failures (in seconds)",
+        ge=1,
+    )
+
     @field_validator("log_level")
     @classmethod
     def validate_log_level(cls, v: str) -> str:
@@ -85,6 +105,41 @@ class Settings(BaseSettings):
             raise ValueError("gitea_token cannot be empty or whitespace")
         return v.strip()
 
+    @field_validator("mcp_api_keys", mode="before")
+    @classmethod
+    def parse_api_keys(cls, v: object) -> List[str]:
+        """Parse API keys from comma-separated string or list."""
+        if isinstance(v, str):
+            # Split by comma and strip whitespace
+            keys = [key.strip() for key in v.split(",") if key.strip()]
+            return keys
+        elif isinstance(v, list):
+            return v
+        return []
+
+    @field_validator("mcp_api_keys")
+    @classmethod
+    def validate_api_keys(cls, v: List[str], info) -> List[str]:
+        """Validate API keys if authentication is enabled."""
+        # Get auth_enabled from values (it's already been processed)
+        auth_enabled = info.data.get("auth_enabled", True)
+        
+        if auth_enabled and not v:
+            raise ValueError(
+                "At least one API key must be configured when auth_enabled=True. "
+                "Set MCP_API_KEYS environment variable or disable auth with AUTH_ENABLED=false"
+            )
+        
+        # Validate key format (at least 32 characters for security)
+        for key in v:
+            if len(key) < 32:
+                raise ValueError(
+                    f"API keys must be at least 32 characters long. "
+                    f"Use scripts/generate_api_key.py to generate secure keys."
+                )
+        
+        return v
+
     @property
     def gitea_base_url(self) -> str:
         """Get Gitea base URL as string."""
diff --git a/src/aegis_gitea_mcp/server.py b/src/aegis_gitea_mcp/server.py
index a381885..6f4167b 100644
--- a/src/aegis_gitea_mcp/server.py
+++ b/src/aegis_gitea_mcp/server.py
@@ -8,6 +8,7 @@ from fastapi.responses import JSONResponse, StreamingResponse
 from pydantic import ValidationError
 
 from aegis_gitea_mcp.audit import get_audit_logger
+from aegis_gitea_mcp.auth import get_validator
 from aegis_gitea_mcp.config import get_settings
 from aegis_gitea_mcp.gitea_client import GiteaClient
 from aegis_gitea_mcp.mcp_protocol import (
@@ -38,9 +39,10 @@ app = FastAPI(
     version="0.1.0",
 )
 
-# Global settings and audit logger
+# Global settings, audit logger, and auth validator
 settings = get_settings()
 audit = get_audit_logger()
+auth_validator = get_validator()
 
 
 # Tool dispatcher mapping
@@ -52,6 +54,44 @@ TOOL_HANDLERS = {
 }
 
 
+# Authentication middleware
+@app.middleware("http")
+async def authenticate_request(request: Request, call_next):
+    """Authenticate all requests except health checks and root."""
+    # Skip authentication for health check and root endpoints
+    if request.url.path in ["/", "/health"]:
+        return await call_next(request)
+
+    # Only authenticate MCP endpoints
+    if not request.url.path.startswith("/mcp/"):
+        return await call_next(request)
+
+    # Extract client information
+    client_ip = request.client.host if request.client else "unknown"
+    user_agent = request.headers.get("user-agent", "unknown")
+
+    # Extract Authorization header
+    auth_header = request.headers.get("authorization")
+    api_key = auth_validator.extract_bearer_token(auth_header)
+
+    # Validate API key
+    is_valid, error_message = auth_validator.validate_api_key(api_key, client_ip, user_agent)
+
+    if not is_valid:
+        return JSONResponse(
+            status_code=401,
+            content={
+                "error": "Authentication failed",
+                "message": error_message,
+                "detail": "Please provide a valid API key in the Authorization header: Bearer <api-key>",
+            },
+        )
+
+    # Authentication successful - continue to endpoint
+    response = await call_next(request)
+    return response
+
+
 @app.on_event("startup")
 async def startup_event() -> None:
     """Initialize server on startup."""
@@ -59,6 +99,13 @@ async def startup_event() -> None:
     logger.info(f"Connected to Gitea instance: {settings.gitea_base_url}")
     logger.info(f"Audit logging enabled: {settings.audit_log_path}")
     
+    # Log authentication status
+    if settings.auth_enabled:
+        key_count = len(settings.mcp_api_keys)
+        logger.info(f"API key authentication ENABLED ({key_count} key(s) configured)")
+    else:
+        logger.warning("API key authentication DISABLED - server is open to all requests!")
+    
     # Test Gitea connection
     try:
         async with GiteaClient() as gitea: