Move tool configs to pyproject.toml

[Mr-Pepe]

Resolves #586.

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Please make sure to check for the following items:

• Add unit tests and integration tests where applicable.
  If you've added an error code or changed an error code behavior,
  you should probably add or change a test case file under tests/test_cases/ and add
  it to the list under tests/test_definitions.py.
  If you've added or changed a command line option,
  you should probably add or change a test in tests/test_integration.py.
• Add a line to the release notes (docs/release_notes.rst) under "Current Development Version".
  Make sure to include the PR number after you open and get one.

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