docs: replace black references with ruff across docs and Makefile

[SemTiOne]

🔗 Related Issue

Closes #5248

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📝 Summary

Removes stale references to black formatter across documentation and Makefile.
The project has migrated to ruff format but several files still referenced black
in comments, help text, and coding standards. This is a documentation-only cleanup.

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📏 Reviewability

• This PR has one clear purpose
• The linked issue is not labeled triage
• Unrelated bugs or improvements are tracked in separate issues/PRs
• Tests are included with the code they validate
• If AI-assisted, I understand and can explain the generated changes

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🏷️ Type of Change

• Documentation

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🧪 Verification

No functional changes — documentation and comments only. No tests required.

Check	Command	Status
Lint suite	make lint	CI
Unit tests	make test	CI

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✅ Checklist

• Tests added/updated for changes
• Documentation updated (if applicable)
• No secrets or credentials committed

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📓 Notes

Changes cover:

• Makefile: update comments, help text, FILE_AWARE_LINTERS, .PHONY, lint-quick, lint-fix, pre-commit targets, remove deprecated black-check target
• pyproject.toml: update tool configuration comment
• AGENTS.md: update coding standards, code quality, and CLI tools sections
• llms/*.md: update black references to ruff format