Add ellmer examples for mcp-repl

[t-kalinowski]

Summary

Adds runnable ellmer starter examples for using mcp-repl as an R-backed MCP server, including both pager overflow mode and files-mode output bundles.

Public-facing changes:

• Adds examples/README.md with setup instructions and usage notes.
• Adds a short pager-mode ellmer example.
• Adds a files-mode ellmer example with simple bundle inspection tools.
• Cleans up the published repl tool schema so optional timeout_ms is omitted from required without advertising a null default.

Internal-only changes:

• Adds docs-contract coverage to keep the examples present, short, and focused.
• Adds a server unit test for the timeout_ms schema shape.