SBP-487: workflow input staging

[vtnphan]

Pull Request

Summary

SBP-487 Stages all workflow input files from S3 to Gadi via Globus before a run executes, instead of assuming Nextflow can read S3 URIs directly on Gadi.

Changes

• New Globus service (globus_client.py, globus_transfer.py, globus_errors.py, DataTransfer model): submits/polls Globus transfers per run and gates execution — a queued job stays "staging" until every input DataTransfer reports "completed".
• Per-workflow staging (routes/workflows.py): the samplesheet is always staged; bindcraft's starting_pdb, proteinfold's fasta, and WISPS's aggregated FASTA each get their own additional transfer, with samplesheet columns rewritten from S3 URIs to local Gadi paths where needed.
• Executors (bindflow_, proteindj_, proteinfold_, wisps_executor.py): consume the already-staged local path instead of building an S3 URI; prerun scripts no longer carry AWS credentials — WISPS's now receives its staged FASTA path/split dir as inline shell vars instead.
• Scheduler: new sync_data_transfers job (every 2 min) drives submission/polling.
• DataTransfer.provider_metadata (JSON) replaced with reusing transfer_id for both the pre-submission Globus submission id and the post-submission task id (removes a redundant column).
• New migration for the above; .env.example documents the new Globus env vars.

How to Test

.venv/bin/python -m pytest -q
.venv/bin/ruff check app tests
.venv/bin/python -m mypy app --ignore-missing-imports

Manually: launch a run, confirm its DataTransfer row(s) reach Globus SUCCEEDED, the job flips "staging" → "pending", and staged files land on Gadi as local paths (not s3://).

Type of change

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

Checklist

• I have added tests that prove my fix is effective or that my feature works
• I have added or updated documentation where necessary
• I have run linting and unit tests locally
• The code follows the project's style guidelines

[marius-mather]

Closing, will be merged via #132