Align python-best-practices scripts and references with SKILL.md

[Copilot]

• Update scripts/lint.sh: replace black --check with ruff format --check, replace mypy with ty check
• Update scripts/setup-project.sh: replace manual scaffold with uv init --lib
• Update references/pyproject-template.toml: remove black/mypy deps and tool sections; add ty>=0.0.21 dev dependency
• Update SKILL.md: fix "(Black default)" note, update scripts/references tables to reflect new tools

Original prompt

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This section details on the original issue you should resolve

<issue_title>python-best-practices references and scripts should be aligned with the updated SKILL.md</issue_title>
<issue_description>Currently the references and scripts implement outdated practices that are not aligned with the current version of SKILL.md.
For example, mypy is used for type checking, black for formatting, while we should be using ty check and ruff format.
Furthermore, the init script should use uv init --lib to instantiate a fresh project.</issue_description>

<agent_instructions>Keep the implementation light. Less code is better. Remove anything that is not strictly aligned with the SKILL.md.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes python-best-practices references and scripts should be aligned with the updated SKILL.md #4

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[VMinB12]

We are

[VMinB12]

We are missing the ty 0.0.21 dev dependency.

[Copilot]

Added ty>=0.0.21 to the dev dependencies in d7b0bb5.

[VMinB12]

@hugodendievelb12 Can you make sure all tech experts have write access?