feat: update reporting process for qc reads and assembly pipelines

[emilylm]

📌 Summary

This PR updates the assembly reporting workflow to better match the current assembly pipeline process.

It introduces explicit assembly_run records for repo/commit-scoped pipeline invocations, links stage results to those runs, adds assembly-scoped QC read reporting, removes assembly-level status tracking, and aligns the QC-read model with the latest reporting contract by storing source_read_file_checksums and validating them against the experiment resolved from bpa_package_id.

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🔄 Type of Change

• 🐛 Bug fix (non-breaking change that fixes an issue)
• ✨ New feature (non-breaking change that adds functionality)
• 💥 Breaking change (fix or feature that would cause existing functionality to change)
• 📚 Documentation update

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🧩 Key Changes

• Added assembly_run as the explicit pipeline invocation model (assembly_id + github_repo + git_commit) and linked assembly_stage_run records to assembly_run_id instead of directly to assembly_id.
• Added assembly-scoped QC read reporting via POST /api/v1/assemblies/{assembly_id}/qc-reads/report, including qc_read_assembly, source_read_file_checksums, updated QC file classification, and ENA prepared payload generation.
• Removed assembly.status, updated manifest retrieval behaviour, added forward migrations for the schema changes, and updated docs/tests/Postman examples to match the new API shape.

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✅ Checklist

• Tests are passing locally / in CI
• New tests have been added for new or changed functionality
• Self-review completed
• Documentation updated (if needed)
• No sensitive data or secrets included

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🔍 Review Notes

• This PR includes breaking API and schema changes:
  • stage-run routes are now nested under /assemblies/{assembly_id}/runs/{run_id}/stage-runs
  • QC reporting moved to the assembly-scoped route
  • assembly.status has been removed
  • QC provenance now uses source_read_file_checksums rather than source BPA resource IDs
• Please review the Alembic migration chain closely, especially:
  • 0003_assembly_run_github
  • 0004_qc_reads_assembly_refs
  • 0005_remove_assembly_status
• QC reporting now validates:
  • bpa_package_id resolves to an existing experiment
  • the resolved experiment belongs to the target assembly specimen lineage
  • the resolved experiment is present in the target assembly manifest inputs
  • each submitted source_read_file_checksums value matches a read.file_checksum for that experiment

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📎 Related Issues / Tickets

• Closes #
• Related to #

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