Switch spectral format from MGF to mzML

Update ThermoRawFileParser to output mzML, adapt xiSEARCH module, adapt mass recalibration script, remove FORMAT_CORRECTION step.

Start by locating the ThermoRawFileParser output step, the xiSEARCH module, the mass recalibration script, and the FORMAT_CORRECTION step in the Nextflow workflow. Trace how MGF is produced and consumed, then update each named component for mzML and confirm that FORMAT_CORRECTION is no longer used. Done means the workflow runs with mzML through xiSEARCH and mass recalibration without the removed step.

Written by the indexing model from the issue text.