staging: add directory tool

[vrtornisiello]

• Refactored tools.py module as a package.
• Add directory table IDs to columns metadata.
• Create new get_table_details tool for context management.
• Update codebase to work with Gemini 3 models, with thinking enabled.
• Parse Gemini 3 model thinking blocks on streaming.
• Update system prompt for Gemini 3 Flash.