Add SDRF input support with parameter translation

## Summary
Replace CSV samplesheet input with SDRF. Use sdrf-pipelines `convert-relink` converter to extract per-file metadata and XL-MS specific columns (crosslinker, enrichment, tolerances). Add parameter translator (`bin/generate_engine_config.py`) to generate xiSEARCH XML or Scout JSON configs from SDRF-derived parameters.

## Tasks
- [ ] Create SDRF_PARSING module (modules/local/sdrf_parsing/)
- [ ] Create GENERATE_ENGINE_CONFIG module
- [ ] Create bin/generate_engine_config.py
- [ ] Wire SDRF parsing into pipeline input

## Dependencies
- Requires convert-relink in sdrf-pipelines

Start by reviewing the sdrf-pipelines convert-relink dependency and the existing pipeline input path. Then examine modules/local/sdrf_parsing/, GENERATE_ENGINE_CONFIG, and bin/generate_engine_config.py; the work is done when SDRF-derived metadata and XL-MS parameters flow through the pipeline and produce xiSEARCH XML or Scout JSON configurations.

Written by the indexing model from the issue text.