feat(config): move from hydra to pydantic models - #1221

- Create config/ package with SessionDefaults (Pydantic frozen model)
- Move all legacy step config dataclasses to config/defaults.py
- Rewrite test_config.py for Pydantic SessionDefaults model
- All 15 existing step config dataclasses remain importable from gentropy.config

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

- Add BiosampleIndexDefaults Pydantic model (all fields required)
- Update BiosampleIndexStep constructor to accept (config, session)
- Rewrite test to construct config and validate step initialization
- Add config validation test

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

- Add ColocalisationDefaults Pydantic model with 3 required + 3 optional fields
- Update ColocalisationStep constructor to accept (config, session)
- Add config validation tests and update existing tests to use config

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Migrate the following steps from dataclass StepConfig to Pydantic
config models: credible_set_qc, decode_ingestion (4 configs),
intervals (2 configs), study_locus_validation, study_validation,
sumstat_qc_step, variant_index (2 configs).

Fix duplicate class definition bugs caused by sequential Write tool
operations in 4 files: sumstat_qc_step, study_validation,
variant_index, intervals.

Update all corresponding test files to use (config=Defaults(...),
session=...) pattern and add config validation tests.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Add co-located Pydantic config models and update step classes to
accept (config, session) parameters for:

- eqtl_catalogue, finngen_finemapping_ingestion, finngen_studies,
  finngen_sumstat_preprocess, finngen_ukb_mvp_meta, foldx_ingestion
- gnomad_ingestion
- gwas_catalog_study_curation, gwas_catalog_study_index,
  gwas_catalog_sumstat_preprocess, gwas_catalog_top_hits
- l2g (4 configs: evidence, associations, feature_matrix, model)
- ld_based_clumping, locus_breaker_clumping
- lof_curation_ingestion, molecular_complex, pics, pqtl_study
- ukb_ppp_eur_sumstat_preprocess, window_based_clumping

All files pass ruff check, ruff format, and mypy. 8 test failures
are pre-existing (unrelated to these changes).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

…ation_method

- Replace mutable list[] defaults with Field(default_factory=list) in:
  - study_validation.py (StudyValidationDefaults.invalid_qc_reasons)
  - study_locus_validation.py (StudyLocusValidationDefaults.invalid_qc_reasons)
  - intervals.py (IntervalE2GDefaults.invalid_qc_reasons)
  - intervals.py (IntervalEpiractionDefaults.invalid_qc_reasons)
- Add field_validator for colocalisation_method in colocalisation.py
  to reject invalid values at config validation time (case-insensitive)
- Simplify step body normalization code since fields are now always list[str]

Agent-Logs-Url: https://github.com/project-defiant/gentropy/sessions/25062353-a56a-4286-a077-a67a6c204c94

Co-authored-by: project-defiant <69353402+project-defiant@users.noreply.github.com>