chore: migrate Ruff lint configuration

[njzjz-bot]

Summary

• Move Ruff select and ignore settings under [tool.ruff.lint].
• Move the pydocstyle convention under [tool.ruff.lint.pydocstyle].
• Remove the deprecated ignore-init-module-imports option.

Tests

• ruff check dpgen tests --select F821,F822,F823 --output-format=concise
• ruff check pyproject.toml

Both commands complete without the prior Ruff configuration warnings.

Fixes #1895

Coding agent: Codex
Codex version: codex-cli 0.149.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

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Reviewing files that changed from the base of the PR and between d5ce577 and 55c8da7.

📒 Files selected for processing (1)

• pyproject.toml

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 49.80%. Comparing base (d5ce577) to head (55c8da7).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1946   +/-   ##
=======================================
  Coverage   49.80%   49.80%           
=======================================
  Files          83       83           
  Lines       14986    14986           
=======================================
  Hits         7464     7464           
  Misses       7522     7522           

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