py-scikit-build-core: updated to 0.9.4

Version 0.9.4

This version supports the newly available free-threading variant of Python
3.13b1 (mostly related to skipping the stable ABI). We test this via the
manylinux/musllinux images. There's also a new feature requested by third-party
packagers; the ability to pass args directly to the build tool

Features:

- Add `build.tool-args`

Fixes:

- Support free-threaded builds of Python 3.13+
- Slightly better stable ABI behavior using PyPy

Documentation:

- Fix example of configuration overrides in configuration.md
- Update stable ABI instructions

CI and testing:

- Use pylint 3.2, gha reporter
- Some minor improvements to running tests on some systems

(adam)