[REF TEST] Refactor data handling #1045
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* Add error handling to caller of center_nifti_origin * start refactoring * continue refactoring and add tests * add test * refactor _create_merge_file_from_bids (BROKEN...) * better names and more tests * improve tests and code * refactor further * remove duplicate and broken tests * refactor pipeline handling * port changes from PR 1052 * port changes from PR 1055 * port changes from PR 1062 * fixes * fix broken test * some fixes and enhancements * fix broken exception
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This PR proposes to refactor the utilities in the
clinica.iotools.utilsmodule.