chore: update dependencies and bump version to 0.11.3

[shinpr]

Summary

• update production and development dependencies, excluding Node.js types and TypeScript
• resolve vulnerable transitive dependencies through standard semver resolution without package overrides
• bump the package and MCP server metadata versions to 0.11.3

Security

• update hono from 4.12.23 to 4.12.29
• update protobufjs from 7.6.2 to 7.6.5
• confirm npm audit reports 0 vulnerabilities

Validation

• npm run check:all
• 234 tests passed