Close the MCP lifecycle gap from config to runtime tool execution

This wires configured MCP servers into the CLI/runtime path so discovered
MCP tools, resource wrappers, search visibility, shutdown handling, and
best-effort discovery all work together instead of living as isolated
runtime primitives.

Constraint: Keep non-MCP startup flows working without new required config
Constraint: Preserve partial availability when one configured MCP server fails discovery
Rejected: Fail runtime startup on any MCP discovery error | too brittle for mixed healthy/broken server configs
Rejected: Keep MCP support runtime-only without registry wiring | left discovery and invocation unreachable from the CLI tool lane
Confidence: high
Scope-risk: moderate
Reversibility: clean
Directive: Runtime MCP tools are registry-backed but executed through CliToolExecutor state; keep future tool-registry changes aligned with that split
Tested: cargo test -p runtime mcp -- --nocapture; cargo test -p tools -- --nocapture; cargo test -p rusty-claude-cli -- --nocapture; cargo test --workspace -- --nocapture
Not-tested: Live remote MCP transports (http/sse/ws/sdk) remain unsupported in the CLI execution path

rust/Cargo.lock

@@ -1198,6 +1198,7 @@ dependencies = [
  "pulldown-cmark",
  "runtime",
  "rustyline",
+ "serde",
  "serde_json",
  "syntect",
  "tokio",