RFD-008: Ordered Tool Directives

[JeanMertz]

Tracking issue for RFD-008: Ordered Tool Directives.

This issue tracks the progress towards the complete implementation of RFD-008.

Tasks

• Add ToolDirective enum and ToolDirectives struct with manual clap::Args + FromArgMatches.
• Replace tools/no_tools fields on Query with #[command(flatten)] tool_directives.
• Rewrite apply_enable_tools to iterate directives sequentially.
• Update existing tests; add new tests for interleaved ordering.