cli: implement remote submission uploads Issue 1486

[kbuma]

Implements remote archive upload for emmet submit push, resolving #1486.

The CLI now stages submission changes, creates RawArchive HDF5 objects and a complete snapshot manifest, uploads them through presigned URLs, and finalizes the upload before advancing local submission history.

This targets the submission API introduced in #1515

Changes

• Represent added, changed, unchanged, and removed calculations explicitly.
• Generate content-addressed HDF5 archives and a canonical snapshot manifest.
• Implement the prepare → PUT → finalize upload workflow.
• Authenticate control-plane requests using X-API-KEY.
  • Prefer MP_API_KEY.
  • Temporarily support EMMET_API_TOKEN with a deprecation warning.
• Cache upload sessions and checksums so interrupted or expired sessions can resume safely.
• Validate server responses before committing local submission history.
• Add:
  • emmet submit contributor-status
  • emmet submit status TARGET
• Make CLI state updates atomic and protect the state directory and files.
• Add httpx and archival dependencies and update generated requirements and CI coverage.
• Document remote upload configuration and behavior.

Failure and retry behavior

• Local history advances only after the server reports a completed session.
• Failed uploads retain resumable state.
• Expired presigned URLs are refreshed without re-uploading confirmed objects.
• Object sizes and SHA-256 checksums are retained for finalization.
• Credentials and presigned URLs are not persisted or included in errors.
• Changes made to source files after staging abort the push.

Contributor Checklist

• I have broken down my PR scope into the following TODO tasks
  • Model complete submission change sets.
  • Implement archive and manifest uploads.
  • Add resumable, atomic local state handling.
  • Align authentication and responses with [WIP] mock core submission route #1515.
  • Add contributor and submission status commands.
• I have run the tests locally and they passed.
• I have added tests, or extended existing tests, to cover new features and bugs fixed in this PR.

Tests

• python -m pytest -q emmet-cli/tests — 110 passed
• python -m mypy --config-file .mypy.ini emmet-cli/emmet
• Ruff checks passed.
• Black checks passed.
• git diff --check passed.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 93.95248% with 28 lines in your changes missing coverage. Please review.
✅ Project coverage is 73.87%. Comparing base (17a87d0) to head (966ece3).

Files with missing lines	Patch %	Lines
emmet-cli/emmet/cli/upload.py	92.85%	24 Missing ⚠️
emmet-cli/emmet/cli/submit.py	91.83%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1518      +/-   ##
==========================================
+ Coverage   73.14%   73.87%   +0.73%     
==========================================
  Files         152      153       +1     
  Lines       13151    13576     +425     
==========================================
+ Hits         9619    10029     +410     
- Misses       3532     3547      +15     

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