Replace rubydex_mcp server with Ruby implementation

[st0012]

Summary

Adds a Ruby implementation of rubydex_mcp with a small internal MCP/JSON-RPC protocol layer.

The existing Rust MCP crate and build plumbing are left in place. If this PR is accepted, I'll remove it in a follow up PR.

Parity with the Rust MCP server

Matches the existing Rust MCP server for:

• tool names and schemas: search_declarations, get_declaration, get_descendants, find_constant_references, get_file_declarations, codebase_stats
• startup indexing behavior and indexing-in-progress / indexing-failed responses
• JSON payload shapes, pagination defaults and caps, kind filtering, exact/fuzzy search modes, relative path formatting, declaration details, descendants, file declarations, and stats
• constant-reference behavior for classes/modules/constants, with methods returning an empty reference list

Manually checked against rust/target/debug/rubydex_mcp using the same fixture and tool calls for the six tools.

Known difference:

• unresolved partial ancestors are not exposed by the current Ruby API, so the Ruby MCP server only reports resolved ancestors. The manual parity check confirmed this as the expected mismatch.

Follow-up work

• Remove the Rust MCP implementation in a separate PR.
• Open a follow-up PR for Bundler integration.