Integrate ChARGe RSA algorithm

[shashankk42]

Summary

Integrate ChARGe RSA into FLASK-Copilot retrosynthesis, with consolidated flag handling, extracted RSA driver, and shared root-node creation. Addresses all PR review comments.

Changes

Backend

• New file charge_backend/retrosynthesis/ai_rsa.py — chemistry-specific RSA driver wrapping ChARGe's RSATask via a
  RetroRSATask subclass (overrides format_candidates, validate_proposal)
• ai_based_retrosynthesis gains root_smiles: Optional[str] = None — creates the root Node itself when called from compute;
  db_then_ai_retrosynthesis path unchanged
• New helper build_root_node(smiles, run_settings) -> Node in backend_helper_funcs.py, reused by
  template_based_retrosynthesis (dedupe)
• Drop FlaskRunSettings.use_ai_based; everything reads data.get("aiOnly", True) at the top level of the WS payload
• Drop redundant os.path.exists(config_file) checks in ai.py and backend_manager.py; the consolidated check now lives only
  in template.py:run_retro_planner
• Surface a clogger.warning(...) when the model returns no reactants (refusal indicator)
• Unhighlight reactant node when template expansion is skipped (avoid stuck-yellow UI)

Frontend (flask-app)

• State rename useAiBased → aiOnly; sent at top level of compute / custom-query / compute-reaction-from payloads (always
  passed)
• Updated combined_customization_modal.tsx, retrosynthesis_customization_content.tsx, types.ts accordingly
• retrosynthesis_customization_content.tsx imports RsaSettingsPanel from lc-conductor (single source of truth)
• Revert package-lock.json and .gitignore to upstream main (per review)

Prompts (charge_backend/retrosynthesis/prompts/)

• 3-part chemistry prompts for both RAG and standalone modes: rsa_{mode}_system.txt, rsa_{mode}_proposal.txt,
  rsa_{mode}_aggregation.txt

Modes

• Standalone: pure chemistry reasoning, query_reaction_database removed from tools
• RAG: queries the reaction DB once, injects results into all proposal prompts; tool removed afterward

Testing

• Server boots; HTTP 200; all import sanity passes
• AI-only, RSA-standalone, and RSA-RAG verified end-to-end on caffeine
• Template mode verified against local test_reactions.db
• pytest charge_backend/tests/test_websocket_callbacks.py 2/2

Dependencies

• Add generic RSA (Recursive Self-Aggregation) algorithm framework ChARGe#124 must merge first (this PR imports RSATask from charge.algorithms)
• Add RSA settings LC-Conductor#15 must merge before this PR's submodule pointer can be cleanly bumped on FLASK-LLNL/main

Related

• Closes Add Recursive Self Aggregation (RSA) algorithm #190 (superseded)

[tbennun]

Overall this looks great! Prompts are well-written etc. The code itself should be refactored to a separate top-level function or file that is called from within ai_based_retrosynthesis since it is quite lengthy. Additionally, some code duplication exists in this PR, as well as a potential merge conflict.

[tbennun]

mostly minor comments

[tbennun]

it's a bit strange that we extend Task but then end up not using the built in API to run a task with a created Agent. If we only extend Task by name, there is no reason to extend it. I think we should use it and run RSA somehow with the Task. Maybe Task can define a generic run function that in the superclass is just agent.run(instructions=self.system_prompt, task=self.user_prompt) etc. and then RSATask's run will execute run_rsa with the agents?

[shashankk42]

Addressed in 835e21e (here) + FLASK-LLNL/ChARGe#124 (deacaa0). Task now has a generic run(agent, ...); RSATask.run overrides to delegate to run_rsa. RSA is now invoked via the Task API in ai_rsa.py. The N-K-T loop and run_rsa are unchanged for backward compatibility. ChARGe#124 to be approved first.

[tbennun]

why were these kwargs removed?

[shashankk42]

Re-added: Previous commit by BVE.