chore: cleanup dead code warnings and apply clippy fixes for v1.1.1

- Add #![allow(dead_code)] to deprecated tool modules (kept for
  backwards compatibility but not exposed in MCP tool list)
- Mark unused functions with #[allow(dead_code)] annotations
- Fix unused variable warnings (prefix with _)
- Apply clippy auto-fixes for redundant closures and derives
- Fix test to account for protocol version negotiation
- Reorganize tools/mod.rs to clarify active vs deprecated tools

Security review: LOW RISK - no critical vulnerabilities found
Dead code review: deprecated tools properly annotated

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

crates/vestige-mcp/src/protocol/types.rs

@@ -127,6 +127,7 @@ impl JsonRpcError {
         Self::new(ErrorCode::ServerNotInitialized, "Server not initialized")
     }
 
+    #[allow(dead_code)] // Reserved for future resource handling
     pub fn resource_not_found(uri: &str) -> Self {
         Self::new(ErrorCode::ResourceNotFound, &format!("Resource not found: {}", uri))
     }