chore: upgrade all Python packages and fix linting issues

- Update all dependencies to latest versions (fastmcp, httpx, packaging, etc.)
- Downgrade click from yanked 8.2.2 to stable 8.1.7
- Fix code formatting and linting issues with ruff
- Most tests passing (2 test failures in dependency resolver need investigation)

pypi_query_mcp/tools/dependency_resolver.py

@@ -35,7 +35,7 @@ class DependencyResolver:
         Args:
             package_name: Name of the package to resolve
             python_version: Target Python version (e.g., "3.10")
-            include_extras: List of extra dependency groups to include (e.g., ['socks'] for requests, 
+            include_extras: List of extra dependency groups to include (e.g., ['socks'] for requests,
                 ['test', 'doc'] for setuptools). These are optional dependencies defined by the package.
             include_dev: Whether to include development dependencies
             max_depth: Maximum recursion depth (overrides instance default)
@@ -243,7 +243,7 @@ async def resolve_package_dependencies(
     Args:
         package_name: Name of the package to resolve
         python_version: Target Python version (e.g., "3.10")
-        include_extras: List of extra dependency groups to include (e.g., ['socks'] for requests, 
+        include_extras: List of extra dependency groups to include (e.g., ['socks'] for requests,
             ['test', 'doc'] for setuptools). These are optional dependencies defined by the package.
         include_dev: Whether to include development dependencies
         max_depth: Maximum recursion depth