Fix calibration logic by removing error and multiconformer output in csv

[rodvrees]

Changed

• Updated write_output in im2deep/_io_helpers.py to handle multi-output predictions, enabling output of both low and high CCS predictions together with their corresponding ion mobility values.
• Improved CCS metadata extraction in im2deep/calibration.py by populating the CCS column from metadata when it is absent from the source DataFrame.
• Simplified calibration fitting in im2deep/core.py by passing psm_df_reference directly to fit(), allowing the method to resolve None values and load the default reference internally.
• Removed redundant assignment of calibration_reference during calibration fitting in im2deep/core.py to streamline the logic.

Removed

• Removed an unnecessary debug logging statement from the legacy format parser in im2deep/_io_helpers.py to reduce log verbosity.