feat: repository list tree

What does this merge request do and why?

Include list_repository_tree into the list of read-only tools for chat.

It doesn't collide with list_dir and it is still preferably called from IDE, but it would make the Web Agentic Chat more powerful. For example, the queries like explain this project would benefit from the project structure and sometimes a model hallucinates and starts calling list_commits or list_issues to get this information.

Screenshot

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