feat: persist formatted agent prompts in run outputs

[claytonlin1110]

Summary

Closes #76

• Adds optional prompt recording to save the formatted prompts used by Optimizer/Retriever/Planner/Stylist/Visualizer/Critic into outputs/<run_id>/prompts/*.txt.
• Wires output.save_prompts from YAML into Settings.save_prompts and adds CLI toggles: --save-prompts/--no-save-prompts for generate and plot.
• Adds offline tests verifying prompts are saved when enabled and absent when disabled.

Key changes

• New helper: paperbanana/core/prompt_recorder.py
• Config plumbing: paperbanana/core/config.py
• Agent integration: paperbanana/agents/base.py + agent prompt labels
• Pipeline wiring: paperbanana/core/pipeline.py
• CLI flags: paperbanana/cli.py
• Tests: tests/test_pipeline/test_save_prompts.py

[claytonlin1110]

Closes #76

[claytonlin1110]

Hi, @dippatel1994 Would you please review my first contribution? Thanks.

[dippatel1994]

Hi @claytonlin1110, thanks for the PR. The overall change looks clean and the prompt recording approach is well scoped. I ran the new prompt-saving tests locally and they passed.

I found one small issue to fix before merge: in paperbanana/agents/critic.py, the prompt gets recorded before user_feedback is appended. That means in continue-run flows, the saved critic prompt is not the exact prompt actually sent to the model, which makes the artifact a bit misleading for debugging. Could you please update that path so the recorded prompt includes the appended user feedback as well?

Also, issue #76 is still open, and this PR does not currently show it as an auto-closing linked issue in GitHub metadata. You may want to add Closes #76 to the PR description so it closes automatically on merge.

Once those are addressed, this looks in good shape. Thanks!

[claytonlin1110]

@dippatel1994 Fixed everything. Please check

[dippatel1994]

changes looks good @claytonlin1110 just check failing ci pipelines.

[claytonlin1110]

@dippatel1994 Just fixed

[dippatel1994]

sorry @claytonlin1110 but one of the ci/lint is still failing.

[dippatel1994]

Hi @claytonlin1110 just one more ci pipeline fix and we can close this ticket!

[claytonlin1110]

@dippatel1994 Fixed.