Integrate clustering track and parser loader reliability updates

[ngamarra]

Summary:

• integrate the Clustering_test branch track into upstream main
• include shared clustering and region analysis workflow additions plus plotting and contrast support
• include parser and loader reliability cleanups, compatibility fixes, and API alias support (counts_from_pileup, vectors_from_pileup)
• include rebased conflict resolution follow up commit restoring parse/load compatibility

Validation:

• pytest -q tests
  • 407 passed, 3 warnings

Notes:

• upstream currently does not have a Clustering_test branch, so this PR targets main from ngamarra:Clustering_test.