Dev/tools logging

[EzicStar]

Some new features that I found necessary after new experiments with STAMP agent:

• Table Analysis tools.
• Server runs _run_cli() method directly instead of creating a subprocess for running the CLI command.
• Logging improvements to avoid flooding agents.
• Heatmaps tool and context improvements.
• List files now summarizes the list in case it exceeds a given amount of items.

These improvements reduce the risk of exceeding the context length of a model, while improving its quality.

[mducducd]

I will merge this PR to #142 (comment) to avoid conflics. Thank you.