Add support for passing tools through the Configuration

[Thomvis]

This PR adds support for passing tools through the Configuration. I built this because I wanted to run Open Deep Research from within my own Python application and give it my own tools, without the overhead of MCP.

[rlancemartin]

@Thomvis thank you! we recently merged some updates. you can please resolve conflicts? we also may want the ability to update the research system prompt here with configurable instructions re: the new tools.

[Thomvis]

I've rebased my work on top of main and added a custom_tools_prompt property to Configuration that can be used to add info about the custom tools to the research system prompt.