Switch spectral format from MGF to mzML

## Summary
Update ThermoRawFileParser to output mzML (`-f=2`), adapt xiSEARCH module to accept mzML input, adapt mass recalibration script (`recalibrate_mgf.py` -> `recalibrate_spectra.py`) to read/write mzML via pyopenms, remove FORMAT_CORRECTION step (MGF-specific). Both xiSEARCH and Scout support mzML natively.

## Motivation
Standardize on mzML as the intermediate spectral format. This enables both xiSEARCH and Scout to share the same conversion step.

## Tasks
- [ ] Change ThermoRawFileParser `-f=0` (MGF) to `-f=2` (mzML) in modules.config
- [ ] Update xiSEARCH module to accept mzML
- [ ] Adapt recalibrate_mgf.py for mzML I/O (rename to recalibrate_spectra.py)
- [ ] Remove FORMAT_CORRECTION step from workflow
- [ ] Update all channel variable names (ch_mgf -> ch_mzml)

Start with modules.config and the xiSEARCH module, then inspect recalibrate_mgf.py and the workflow steps that use FORMAT_CORRECTION. Trace the current MGF channels and conversion path before changing them. Done means ThermoRawFileParser emits mzML, xiSEARCH and recalibration use mzML, FORMAT_CORRECTION is removed, and channel names are updated consistently.

Written by the indexing model from the issue text.