Initial Feynman research agent scaffold

prompts/lit-review.md

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+---
+description: Run a literature review on a topic using paper search and primary-source synthesis.
+---
+Investigate the following topic as a literature review: $@
+
+Requirements:
+- Use `alpha_search` first.
+- Use `alpha_get_paper` on the most relevant papers before making strong claims.
+- Use `alpha_ask_paper` for targeted follow-up questions when the report is not enough.
+- Prefer primary sources and note when something appears to be a preprint or secondary summary.
+- Separate consensus, disagreements, and open questions.
+- When useful, propose concrete next experiments or follow-up reading.
+- If the user wants an artifact, write the review to disk as markdown.

prompts/paper-code-audit.md

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+---
+description: Compare a paper's claims against its public codebase and identify mismatches, omissions, and reproducibility risks.
+---
+Audit the paper and codebase for: $@
+
+Requirements:
+- Identify the canonical paper first with `alpha_search` and `alpha_get_paper`.
+- Extract implementation-sensitive claims with `alpha_ask_paper`.
+- If a public repo exists, inspect it with `alpha_read_code`.
+- Compare claimed methods, defaults, metrics, and data handling against the repository.
+- Call out missing code, mismatches, ambiguous defaults, and reproduction risks.
+- Save the audit to `outputs/` as markdown.

prompts/paper-draft.md

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+---
+description: Turn research findings into a polished paper-style draft with equations, sections, and explicit claims.
+---
+Write a paper-style draft for: $@
+
+Requirements:
+- Ground every claim in inspected sources, experiments, or explicit inference.
+- Use clean Markdown structure with LaTeX where equations materially help.
+- Include at minimum:
+  - title
+  - abstract
+  - problem statement
+  - related work
+  - method or synthesis
+  - evidence or experiments
+  - limitations
+  - conclusion
+- If citations are available, include citation placeholders or references clearly enough to convert later.
+- Save the draft to `papers/` as markdown.

prompts/reading-list.md

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+---
+description: Build a prioritized reading list on a research topic with rationale for each paper.
+---
+Create a research reading list for: $@
+
+Requirements:
+- Use `alpha_search` with `all` mode.
+- Inspect the strongest papers with `alpha_get_paper`.
+- Use `alpha_ask_paper` when a paper's fit is unclear.
+- Group papers by role when useful: foundational, strongest recent work, methods, benchmarks, critiques, replication targets.
+- For each paper, explain why it is on the list.
+- Save the final reading list to `outputs/` as markdown.

prompts/replicate.md

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+---
+description: Plan or execute a replication workflow for a paper, claim, or benchmark.
+---
+Design a replication plan for: $@
+
+Requirements:
+- Identify the canonical paper or source material first.
+- Use `alpha_get_paper` for the target paper.
+- Use `alpha_ask_paper` to extract the exact implementation or evaluation details you still need.
+- If the paper links code, inspect it with `alpha_read_code`.
+- Determine what code, datasets, metrics, and environment are needed.
+- If enough information is available locally, implement and run the replication steps.
+- Save notes, scripts, and results to disk in a reproducible layout.
+- Be explicit about what is verified, what is inferred, and what is still missing.