Update README.md with Secured Agent Examples

[alexheifetz]

This pull request enhances the documentation to introduce and explain a new "Secured MCP Server Mode" for the Embabel agent platform. It details how to run JWT-secured agents with per-agent access control using the @SecureAgentTool annotation, and provides step-by-step instructions for generating JWT tokens and connecting clients. The changes also update directory listings to reflect new example code and scripts related to secured agents.

Secured MCP Server Mode and Access Control:

• Added a new section explaining how to run agents with JWT-based security using @SecureAgentTool, including class-level access control, JWT validation, and two-layer security enforcement. Example agents (NewsDigestAgent and MarketIntelligenceAgent) and their required authorities are described, with code snippets and usage instructions.
• Introduced a comprehensive guide for generating JWT tokens, setting up the secured server, and connecting with MCP Inspector, including details on key generation and token usage.

Documentation and Directory Updates:

• Updated the quick-start instructions and directory structure to include new scripts (mcp_secured_server.sh) and application entrypoints (KotlinAgentSecuredMcpServerApplication.kt) for running the secured MCP server mode. [1] [2]
• Clarified Maven profiles and usage commands for both standard and secured server modes, ensuring users know how to enable each mode.