refactor: make tool registration object-based

[mplemay]

Summary

Refactor tool registration to be object-first, matching resource registration, and fix structured-output inference for list[Any] so mixed media tool results continue to serialize correctly.

Motivation and Context

This makes MCPServer.add_tool() consistent with add_resource() and ToolManager.add_tool(). It also prevents list[Any] return annotations from advertising structured output when they can include Image / Audio helpers that only serialize correctly through the unstructured conversion path.

How Has This Been Tested?

• UV_CACHE_DIR=/tmp/uv-cache uv run --frozen pytest tests/server/mcpserver/tools/test_base.py tests/server/mcpserver/test_tool_manager.py tests/server/mcpserver/test_server.py
• UV_CACHE_DIR=/tmp/uv-cache uv run --frozen pytest tests/server/mcpserver/test_func_metadata.py tests/server/mcpserver/test_server.py -q
• UV_CACHE_DIR=/tmp/uv-cache uv run --frozen ruff check src/mcp/server/mcpserver/tools/base.py src/mcp/server/mcpserver/tools/tool_manager.py src/mcp/server/mcpserver/server.py src/mcp/server/mcpserver/utilities/func_metadata.py tests/server/mcpserver/test_tool_manager.py tests/server/mcpserver/test_server.py tests/server/mcpserver/test_func_metadata.py
• UV_CACHE_DIR=/tmp/uv-cache uv run --frozen pyright src/mcp/server/mcpserver/tools/base.py src/mcp/server/mcpserver/tools/tool_manager.py src/mcp/server/mcpserver/server.py src/mcp/server/mcpserver/utilities/func_metadata.py tests/server/mcpserver/test_tool_manager.py tests/server/mcpserver/test_server.py tests/server/mcpserver/test_func_metadata.py

Breaking Changes

Yes. MCPServer.add_tool() and ToolManager.add_tool() now expect prebuilt Tool instances instead of callables. Callers should use Tool.from_function(...) or @mcp.tool().

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation update

Checklist

• I have read the MCP Documentation
• My code follows the repository's style guidelines
• New and existing tests pass locally
• I have added appropriate error handling
• I have added or updated documentation as needed

Additional context

Tool registration now follows the same object-first pattern as resources. The list[Any] guard keeps mixed-content tool results unstructured so Image and Audio helpers stay on the legacy content conversion path and CI no longer fails on JSON serialization.