Fix alignment fine-tune option and alignment archive path bug

[zuazo]

Hello!

This PR fixes two related issues affecting the --fine_tune functionality:

• Fine-tuning not triggered: The PretrainedAligner.__init__() method was incorrectly assigning fine_tune_boundary_tolerance to self.fine_tune, effectively disabling fine-tuning even when the flag was passed. This is now fixed, and a regression test ensures the fine-tuning process is properly invoked.
  The issue has been present since Add remap alignments functionality #912 (v3.3.5).

• Incorrect alignment archive path: The construction of .ark file paths during fine-tuning included an unintended leading dot in the extension (..ark), which caused a FileNotFoundError.
  Example traceback:

"~/.anaconda3/envs/aligner/lib/python3.11/site-packages/montreal_forced_aligner/alignment/multiprocessing.py", line 961, in _run
    alignment_archive = AlignmentArchive(ali_path)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "~/.anaconda3/envs/aligner/lib/python3.11/site-packages/kalpy/gmm/data.py", line 296, in __init__
    raise OSError(f"Specified file does not exist: {file_name}")
OSError: Specified file does not exist: ~/Documents/MFA/test/alignment/ali.spanish_spain_mfa.2..ark 

This second issue remained hidden because the fine-tuning was never activated. But the test suite already fails if the ..ark bug resurfaces, so no extra assertion was added for that specific case.

To confirm that fine-tuning is now active, check that the aligner prints:

 INFO     Fine tuning alignments...

These changes are minimal and maintain backward compatibility with current usage.