claude-for-researchers

The write-side inverse of /check-pipeline and the pipeline-auditor — read a Pipeline/ doc (and/or an audit report) and EDIT the code accordingly: apply an optimization the pipeline describes, correct code the pipeline (backed by your authoritative notes) shows is wrong, or bring the code in line with the documented behavior. Use when the user wants the code changed based on the pipeline. High-stakes: bakes in live-editor editing, mirror sync, ground-truth protection, and control-gating. Proposes a diff and gets approval before any risky edit.

Check that a code and its Pipeline/ .md are still compatible — that every symbol, cell number, data file, and data-flow claim in the pipeline doc still matches the current code (drift detection). Use after editing a documented notebook/engine/script, before trusting a pipeline doc, or on request ("does the pipeline still match the code?"). Reports mismatches (missing symbols, wrong cell numbers, renamed functions, changed I/O) and can update the doc. Companion to /write-pipeline.

Write (or refresh) a Pipeline/ .md that documents the calculation-and-code pipeline of ANY large code in the project — a notebook (.wb/.nb/.ipynb), an engine, or a script. Use when a load-bearing code has no pipeline doc yet, when a new main code is added, or when the user asks to "write the pipeline" for a file. Produces the standard Purpose / data-flow diagram / key-symbols table / gotchas / inputs-outputs format used across Pipeline/, cross-referenced to the project's authoritative notes (workbook.tex).

Playbook for the Wolfbook MCP tools — driving the LIVE Wolfram kernel and a .wb/.nb notebook in VS Code from Claude Code (read/search/edit/run cells, evaluate expressions, checkpoint/restore kernel state, step-debug, look up symbols, find paclets, search INSPIRE/arXiv papers). Use whenever working through the Wolfbook MCP (mcp__wolfbook__*) instead of headless wolframscript: pick the right tool, avoid the multi-statement reparse and runCell bridge bugs, and use kernel checkpoints for safe rollbacks. Complements the wolfram-headless skill (which covers headless .wls runs).

Run heavy Wolfram Language (wolframscript) computations from Claude Code reliably, and diagnose the misleading "The product exited because of a license error". Use whenever invoking wolframscript on a non-trivial computation, when a wolframscript job dies with a "license error" despite a valid license, or when Wolfram numerics give silently wrong results in headless runs.

Convert Mathematica .nb or .m files to Wolfbook .wb format so they open and run in VS Code. Use when bringing existing .nb/.m files into Wolfbook, or to make an existing .wb bridge-safe.

Format a result, derivation, or numerical value for independent verification by a second model. Use when you want a cross-check on an important or contested result.

Re-derive a contested or pushed-back claim in isolation from the definitions, to catch sycophantic capitulation. Use when a result is disputed or you suspect you changed an answer only because the user pushed back.

Confirm a paper actually exists (arXiv / Semantic Scholar / OpenAlex) before citing it. Use before writing any new citation.

Compile a LaTeX document and fix every error plus aesthetic issue (overfull/underfull boxes, widows, alignment, fonts) for a clean PDF and log. Use this instead of running pdflatex/latexmk manually — it avoids the latexmk stale-log trap and silent grep failures on binary log output, and it reformats rather than rewording.

Propagate a change made in a Wolfbook .wb notebook into the paired .nb notebook so the two stay identical. Use immediately after every .wb edit.