[codex] Improve CLI validation errors

[iskandr]

Summary

This PR improves the user-facing CLI error path for missing prediction requests.

• Stops printing the full parsed argparse namespace before every run.
• Converts ValueError and OSError failures from the CLI prediction pipeline into normal argparse errors with usage text and exit code 2.
• Adds upfront validation for missing MHC source and missing input source so bare topiary reports both required parts instead of surfacing a traceback.
• Adds regression coverage for bare topiary and missing MHC source errors.
• Bumps the package version to 5.10.1 and updates the changelog.

Root Cause

script.main printed parsed arguments unconditionally and let validation errors raised from predict_epitopes_from_args escape as normal Python exceptions. That made missing-argument mistakes look like internal crashes.

Validation

• ./lint.sh
• ./test.sh (1239 passed, 3 skipped, 11 warnings)

[coveralls]

coverage: 89.171% (+0.3%) from 88.876% — improve-cli-errors into master