Add --continue_upload flag

[rajeee]

Pull Request Description

Add --continue_upload flag so that if files are partially uploaded to s3, one can continue from that.

Verified operation by deleting some files from s3 and letting BSQ initialization flag it.

Then I ran --continue_upload to get the missing files uploaded.

The error is then resolved.

--upload_only will still error out and suggest using --continue_upload.

Checklist

Not all may apply

• Code changes (must work)
• Tests exercising your feature/bug fix (check coverage report on Checks -> BuildStockBatch Tests -> Artifacts)
• Coverage has increased or at least not decreased. Update minimum_coverage in .github/workflows/coverage.yml as necessary.
• All other unit and integration tests passing
• Update validation for project config yaml file changes
• Update existing documentation
• Run a small batch run on Kestrel/Eagle to make sure it all works if you made changes that will affect Kestrel/Eagle
• Add to the changelog_dev.rst file and propose migration text in the pull request