Issue 897: Reduce EpiAutoGP to a script

[SamuelBrand1]

This pull request can close #897 by removing the standalone EpiAutoGP Julia package from the repository and adds a script runner for the pipeline located at pipelines/epiautogp instead. It also adjusts CI workflows and pre-commit hooks to reflect this change, and removes related documentation and test configuration for the old package.

Changes

• Removed the entire EpiAutoGP directory/
• Updated all references in GitHub Actions workflows to use --project=pipelines/epiautogp when installing Julia dependencies, instead of the now-removed EpiAutoGP directory.
• Rather than a pkg the epiautogp runner has a script environment and we pin deps with a committed Manifest.toml
• Removed Julia-specific test steps and coverage reporting for the standalone EpiAutoGP package from .github/workflows/test.yaml. Instead, added direct calls to run the relevant parquet interop and parquet tests for pipelines/epiautogp.
• Updated .pre-commit-config.yaml to exclude pipelines/epiautogp/Manifest.toml from secret detection and typo checks.

[codecov]

Codecov Report

❌ Patch coverage is 0% with 45 lines in your changes missing coverage. Please review.
✅ Project coverage is 56.13%. Comparing base (d66ebd4) to head (ba74099).

Files with missing lines	Patch %	Lines
pipelines/tests/test_epiautogp_parquet.py	0.00%	33 Missing ⚠️
pipelines/tests/test_epiautogp_parquet_interop.py	0.00%	12 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1070      +/-   ##
==========================================
- Coverage   59.50%   56.13%   -3.38%     
==========================================
  Files          32       29       -3     
  Lines        2109     1997     -112     
==========================================
- Hits         1255     1121     -134     
- Misses        854      876      +22     

Flag	Coverage Δ
epiautogp	?
hewr	76.98% <ø> (ø)
pipelines	53.29% <0.00%> (-1.06%)	⬇️

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[SamuelBrand1]

@damonbayer I think this is the safer/easier/better direction than #1068 although I'm sad because juliacall looks slick in many ways (especially the julia dep handling)

[damonbayer]

Thanks @SamuelBrand1!