build: simplify dependency setup and CI workflows

[Pymetheus]

Description

Replace verbose uv sync usage across CI and PR workflows with a simpler uv sync invocation and update security workflow accordingly. Update README and docs/CHECKLIST to reflect the new install instructions (pip install -e . --group dev, uv sync, poetry install). Rework pyproject.toml to use dependency-groups (test, quality) and include those groups in the dev group, tidy dependencies and formatting. These changes unify dependency installation patterns and simplify CI setup.

Type of Change

• Bug fix (non-breaking change that fixes an issue)
• New feature (non-breaking change that adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Code refactoring
• Performance improvement
• Test addition or update

Related Issue

#12

Changes Made

• Rework pyproject.toml to use dependency-groups
• Unify dependency installation patterns and simplify CI setup
• Update README and docs/CHECKLIST to reflect the new install instructions

Testing

Describe how you tested your changes:

• Unit tests pass
• Integration tests pass
• Manual testing performed

Screenshots (if applicable)

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Checklist

• My code follows the project's style guidelines
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have updated the documentation accordingly
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes

Additional Context

Add any other context about the PR here.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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