[ENH][TEST] Move logic for file checking and add tests in center_nifti

[AliceJoubert]

In this PR :

• All the logic for file checking is moved in the private function for centering files
• Unit tests are added
• File overwriting was renewed :
  • Before : it copied only files at the root level (ex : description json) but not nifti files nested in folders if both directories had folders with same names. That is a bit misleading because it looks like it will preserve what is inside the BIDS input and actually... does not.
  • Now : will completely remove files inside the output folder.
    → This is a bit radical and could be changed for a solution that iteratively checks files from both folders in a follow-up PR

In another PR : non-regressions tests should look inside nifti files and check option for overwriting