feat: harden MCP capability discovery and agent usability

[josbeir]

Summary

• Align the server identity, default protocol version, and initialization instructions with MCP SDK 0.7 so agents receive actionable capability guidance.
• Add MCP safety annotations for read-only and destructive tools.
• Redact environment and sensitive CakePHP configuration values before they cross the MCP boundary.
• Fix prompt references and percent-encode documentation resource URI variables so search and document resources work through protocol discovery.
• Add repository agent guidance and protocol-level capability discovery/invocation coverage.

Compatibility

• MCP_PROTOCOL_VERSION remains available for clients requiring an older protocol version.
• Existing tool names are preserved.
• Environment/config inspection now intentionally redacts values that may contain secrets.