[feat] Use ruff for formatting and linting new files by default

- Updated pre-commit configuration and pyproject.toml for improved file inclusion.
- Removed exclusions from `pyproject.toml` related to `isort`, `yapf` and `autoflake`.
- Instead, explicitly specified the files to be included in the `isort`, `yapf` and `autoflake` hooks in pre-commit config.
- Updated `ruff` settings to exclude the files that are already linted by `isort`, `yapf` and `autoflake`.

Signed-off-by: Robin Kobus <[email protected]>

Author: Funatiq