Create comprehensive docs/cognito.md guide and fix file references

- Add complete Amazon Cognito setup guide covering both user identity and agent identity authentication modes
- Include step-by-step Cognito User Pool creation and App Client configuration
- Document OAuth 2.0 PKCE flow setup and M2M authentication
- Provide complete .env.user and .env.agent configuration examples
- Add comprehensive testing and troubleshooting section
- Fix file references throughout codebase:
  - Update agent_w_auth.py references to agent.py
  - Update auth_server/cli_auth.py references to agents/cli_user_auth.py
- Address GitHub issue #16 requirements

Resolves #16

Author: aarora79

agents/agent.py

@@ -21,11 +21,11 @@
 - AWS_REGION: AWS region for Cognito
 
 Usage:
-    python agent_w_auth.py --mcp-registry-url URL --model model_id --message "your question" \
+    python agent.py --mcp-registry-url URL --model model_id --message "your question" \
         --client-id CLIENT_ID --client-secret CLIENT_SECRET --user-pool-id USER_POOL_ID --region REGION
 
 Example with command line arguments:
-    python agent_w_auth.py --mcp-registry-url http://localhost/mcpgw/sse \
+    python agent.py --mcp-registry-url http://localhost/mcpgw/sse \
         --model anthropic.claude-3-haiku-20240307-v1:0 --message "current time in new delhi" \
         --client-id [REDACTED] --client-secret [REDACTED] \
         --user-pool-id [REDACTED] --region us-east-1
@@ -36,7 +36,7 @@
     COGNITO_USER_POOL_ID=your_user_pool_id
     AWS_REGION=us-east-1
     
-    python agent_w_auth.py --message "current time in new delhi"
+    python agent.py --message "current time in new delhi"
 """
 
 import asyncio
@@ -248,7 +248,7 @@ def parse_arguments() -> argparse.Namespace:
         cookie_path = os.path.expanduser(args.session_cookie_file)
         if not os.path.exists(cookie_path):
             parser.error(f"Session cookie file not found: {cookie_path}\n"
-                        f"Run 'python auth_server/cli_auth.py' to authenticate first")
+                        f"Run 'python agents/cli_user_auth.py' to authenticate first")
     else:
         # For M2M auth, validate Cognito parameters
         missing_params = []

agents/cli_user_auth.py

@@ -408,7 +408,7 @@ def main():
                 print("✓ Authentication successful!")
                 print(f"✓ Session cookie saved to: {Path(args.cookie_file).expanduser()}")
                 print("\nYou can now use this cookie with agents:")
-                print(f"  python agents/agent_w_auth.py --use-session-cookie")
+                print(f"  python agents/agent.py --use-session-cookie")
                 print("="*50 + "\n")
                 return 0
             else:

docs/auth.md

@@ -144,7 +144,7 @@ sequenceDiagram
         IdP->>Agent: Return JWT token + scopes
     else Session Cookie (On-behalf of User)
         participant CLIAuth as CLI Auth Tool
-        User->>CLIAuth: Run cli_auth.py
+        User->>CLIAuth: Run cli_user_auth.py
         CLIAuth->>IdP: OAuth PKCE flow
         IdP->>CLIAuth: Auth code + user info
         CLIAuth->>CLIAuth: Create session cookie
@@ -227,15 +227,15 @@ The auth server provides dual authentication support:
 - **Group Mapping**: Maps Cognito groups to MCP scopes via `scopes.yml` configuration
   - Both M2M and session cookie auth use the same scope definitions
 
-#### 2. CLI Authentication Tool (`auth_server/cli_auth.py`)
+#### 2. CLI Authentication Tool (`agents/cli_user_auth.py`)
 A standalone tool for user-based authentication:
 - Implements OAuth 2.0 PKCE flow with Cognito hosted UI
 - Opens browser for user authentication
 - Runs local callback server on port 8080
 - Creates session cookie compatible with registry format
 - Saves to `~/.mcp/session_cookie` with secure permissions (0600)
 
-#### 3. Agent (`agents/agent_w_auth.py`)
+#### 3. Agent (`agents/agent.py`)
 The agent supports both authentication methods:
 - `--use-session-cookie` flag for session-based auth
 - `--session-cookie-file` parameter (default: `~/.mcp/session_cookie`)
@@ -254,7 +254,7 @@ Cognito supports machine-to-machine authentication, enabling Agents to have thei
 #### Authentication Flow:
 Run the Agent with the following command:
 ```{.bash}
-python agents/agent_w_auth.py
+python agents/agent.py
 ```
 1. Copy `agents/.env.template` to `agents/.env.agent` and set the environment variables (`COGNITO_CLIENT_ID`, `COGNITO_CLIENT_SECRET`, `COGNITO_USER_POOL_ID`) as appropriate for your setup. For detailed Cognito configuration steps, see [`docs/cognito.md`](cognito.md).
 1. Agent startup:
@@ -283,13 +283,13 @@ Session cookie authentication enables agents to act on behalf of users, using th
 
 #### Implementation Components
 
-##### a. CLI Authentication Tool (`auth_server/cli_auth.py`)
+##### a. CLI Authentication Tool (`agents/cli_user_auth.py`)
 
 The CLI tool handles the OAuth flow with Cognito and saves the session cookie locally:
 
 ```bash
 # Run the CLI authentication tool
-python agents/cli_auth.py
+python agents/cli_user_auth.py
 
 # This will:
 # 1. Open your browser to Cognito hosted UI
@@ -307,11 +307,11 @@ Required environment variables:
 
 Copy `agents/.env.template` to `agents/.env.user` and set the environment variables (`COGNITO_CLIENT_ID`, `COGNITO_CLIENT_SECRET`, `COGNITO_USER_POOL_ID`, `SECRET_KEY`) as appropriate for your setup. For detailed Cognito configuration steps, see [`docs/cognito.md`](cognito.md).
 
-The agent (`agents/agent_w_auth.py`) supports session cookie authentication:
+The agent (`agents/agent.py`) supports session cookie authentication:
 
 ```bash
 # Use agent with session cookie
-python agent_w_auth.py \
+python agent.py \
   --use-session-cookie \
   --message "What time is it in Tokyo?" \
   --mcp-registry-url http://localhost/mcpgw/sse