Merge vista-stream into main

[braceal]

Brings main up to date with vista-stream, which has served as the de-facto integration branch since PR #25 (Oct 2024). This is 82 commits and merges cleanly into main with no conflicts.

What's included

Seven PRs already reviewed and merged into vista-stream:

• Ips smith #27 Ips smith
• Bugfix/contact map #28 Bugfix/contact map
• Multirectilinearbinner #33 Multirectilinearbinner
• address #35 #36 address Set target_state_inds to None by default #35 (target state indices)
• Binner Update #38 Binner Update
• Feature/basis state init error #39 Feature/basis state init error
• MultiRectilinearBinner bin ID fix #46 MultiRectilinearBinner bin ID fix

Notable changes

• Binners — new MultiRectilinearBinner (deepdrivewe/binners/multirectilinear.py) with bin-ID fixes, plus reworked base.py/rectilinear.py and tests/binner_test.py
• AI — new adversarial autoencoder model (deepdrivewe/ai/aae.py), CVAE updates
• Simulation — substantial simulation/openmm.py work (~420 lines changed), contact-map bugfix, Amber updates
• Workflows — workflows/ddwe.py updates and a new workflows/stream.py
• Parsl/CLI — expanded parsl.py configs, new CLI entry points
• Examples — new openmm_aae_ddwe example; config and script updates across the amber/openmm/synd examples

Merge order note

This should land before the other open PRs. #45 (fix/parsl-proxystore-eviction) touches four files that are also modified here (parsl.py, workflows/ddwe.py, openmm_ntl9_ddwe/inference.py, train.py) and will need a rebase afterward. #40 (test-streaming) and #43 (academy-agents) should follow.

🤖 Generated with Claude Code

[braceal]

LGTM