When `python -m arcade_mcp_server` was executed, we would get the
following Runtime Warning:
```
<frozen runpy>:128: RuntimeWarning: 'arcade_mcp_server.__main__' found in sys.modules after import of package 'arcade_mcp_server', but prior to execution of 'arcade_mcp_server.__main__'; this may result in unpredictable behaviour
```
This PR resolves this. This PR is mainly just moving existing functions
to new locations; a refactor
<!-- CURSOR_SUMMARY -->
---
> [!NOTE]
> **Low Risk**
> Primarily a module-organization refactor with minimal behavior change;
main risk is import-path regressions for internal callers and stdio/CLI
startup wiring.
>
> **Overview**
> Fixes the `python -m arcade_mcp_server` runtime warning by refactoring
`arcade_mcp_server.__main__` to be a thin CLI entrypoint and moving its
reusable logic into import-safe modules.
>
> Extracts stdio execution and tool discovery into a new
`arcade_mcp_server.stdio_runner` (`initialize_tool_catalog`,
`run_stdio_server`) and moves `setup_logging` into `logging_utils`,
updating `MCPApp`, the FastAPI `worker`, and tests to import from the
new locations. Bumps package version to `1.17.3`.
>
> <sup>Written by [Cursor
Bugbot](https://cursor.com/dashboard?tab=bugbot) for commit
210475acea7c5df44fc66be2bde06f1f0c806c4e. This will update automatically
on new commits. Configure
[here](https://cursor.com/dashboard?tab=bugbot).</sup>
<!-- /CURSOR_SUMMARY -->
