Computational Research

Plugin computational-research in p135246/CodexPluginComputationalResearch. Commands read from the repo's manifest — 6 days ago.

Skills (34)

• backlog-add

  Create and manage work items in the top-level Work/ folder — each a multi-session effort with a Spec (what to build), a Tasks checklist (one task ≈ one session), and a Progress log. This is the project's execution state, separate from the Wiki knowledge base. Use for: "new work item", "start a work

• backlog-autolab

  Execute approved research backlog tasks autonomously in isolated worktrees, using native subagents when available and reporting a digest for human review.

• backlog-board

  Create a standalone local research backlog board with human edits exported for review and reconciliation.

• backlog-info

  Go through the whole Work/ backlog with the user: read every item in Backlog/, Ready/ and UnderReview/ and every work/a named item branch, and report what waits on the user (a review, a halted run's question, a Waiting-on line, queued board changes), what is stale (no Progress for a month, or a prem

• backlog-refine

  Shape a Work/Backlog item together with the user over a long sitting until it is ready to be worked — the user writes the human parts (Summary, Motivation, Acceptance criteria, any detail they care about) in their editor, while the LLM researches the code and wiki, writes the Technical details, keep

• backlog-review

  Review a finished Work/ item with the user: find it in Work/UnderReview/ or on its unmerged work/a named item branch, show the run digest, walk the Acceptance criteria one by one with the test instructions of the tasks that serve each, run the checks that can be run, and end on the user's verdict —

• backlog-run-scheduled

  Run an approved backlog item unattended through bounded Codex CLI sessions in an isolated worktree.

• backlog-run

  Run one disciplined work session against a Work/ item: pick the next incomplete task, study the Spec, implement exactly ONE task, append a Progress report, mark the task done, sync durable knowledge to the Wiki, commit, and STOP. Built to be run in a FRESH session each time to avoid context accumula

• document-compare

  Review agreement between a current human-owned manuscript or paclet design, its notes companion, and relevant proofs, code, examples or checks. Use when the user asks whether implementation follows the accepted design, which proposals remain unintegrated, or where claims and evidence diverge. Report

• document-propose

  Maintain one concise research companion to a human-owned manuscript or paclet design. Use when the user asks for itemized proposals, mathematical statements, API suggestions, corrections, questions, citations, or updates to a manuscript's or design notebook's _notes companion. Preserve the human bas

• document-revise

  Apply human feedback and direct edits to a document within the requested scope, preserving unrequested content. Use for "revise this", notes left in a notebook, and /document-revise. Keep human manuscripts and _notes companions in place unless a new iteration is explicitly requested. A requested ver

• document-setup

  Locate the current human-owned paper or paclet design and its concise notes companion, or establish that pair during requested setup. Use when the user asks to set up human-led paper/design collaboration, select the current manuscript or design iteration, or identify which design implementation shou

• notebook-create

  Create Wolfram notebooks from Markdown, edit saved .nb files through notebook-aware tools, or export requested Markdown without changing the notebook. Use for "create notebook", "edit notebook", "update notebook", "put this in a notebook", and notebook/Markdown conversion. Preserve direct human edit

• paclet-build

  Build a Wolfram paclet archive and install it locally, consulting the current human-owned design notebook and concise _notes companion when present. Support the design-document workflow during paclet development. Use when the user says "build paclet", "build the paclet", "install paclet locally", "m

• paclet-docs

  Generate real Wolfram documentation for a paclet — one symbol reference page per exported function, written into the paclet's Documentation tree through the official MCP doc tools so it resolves in-product via ?Symbol, F1, and the Documentation Center. Use when the user says "document the paclet", "

• paclet-publish

  Build a Wolfram paclet, install locally, and publish to Wolfram Cloud with a public install URL. Use when the user says "publish paclet", "upload paclet", "deploy paclet", "release paclet", "push paclet to cloud", "share the paclet", or "make paclet available".

• paper-cite

  Produce a BibTeX/biblatex entry from an arXiv ID or DOI. Optionally appends to Research/references.bib if it exists. Use when the user says "cite this", "bibtex for arXiv:...", "DOI 10.xxx/...", "add citation", or when adding a reference during paper writing.

• paper-create-note

  Turn a conversation into a concise mathematical note or requested code extract, preserving an existing paper's format and ownership. Use for "research note", "write this up as a note", "make an artifact of this", "code extract", or /paper-create-note. Distinguish proofs, assumptions, computations an

• paper-create-notebook

  Write an explicitly requested mathematics paper or article as a Wolfram notebook, with complete proofs, cited sources, numbered statements and executable examples. Use for an explicit request for a paper as a notebook or /paper-create-notebook; ordinary exploration, conjecture notebooks and demonstr

• paper-create

  Scaffold a human-owned LaTeX or Typst paper and its concise _notes research companion, preserving an existing project's folder and naming conventions. Read the current human manuscript before proposing work; edit it only on an explicit request. Default to itemized proposals, scoped claims, questions

• paper-journal

  Optionally maintain a running scientific journal in LaTeX or Typst — a concise, structured, append-only stream of dated def/thm/rem/claim entries recording the math and physics content and main claims established during research, with every resource cited. Off by default; gated by a per-project togg

• paper-lean

  Drive a Lean 4 / Mathlib formalization session via the lean-lsp MCP. Opens a file, reads the goal state, searches Mathlib for closing lemmas, verifies proofs, and writes a formalization checklist to Work/. Use when the user says "formalize in Lean", "prove this in Lean", "what's the Mathlib name for

• project-check-env

  Check local research tools, connected Wolfram MCP capabilities and license headroom without starting a kernel.

• project-clean

  Archive superseded project materials when cleanup is requested, preserving human work and annotated reading copies.

• project-create

  Scaffold a new research, math-research, paclet-dev, or paclet project and initialize its research infrastructure. Use when the user explicitly asks to create a project, set up a project folder, scaffold a new paclet or dev repo, or invokes /project-create. A request to investigate a topic or run a o

• project-load

  Summarize an existing research project and its next tasks.

• project-provenance

  Optionally record the prompts/intent behind generated artifacts — notebooks, paclet functions/code, wiki articles, and work items. Maintains an append-only ledger at Wiki/Prompts.md and embeds a back-pointer in each artifact so provenance travels with the file. Off by default; gated by a per-project

• project-tour

  Start, resume, or manage a guided tour of the project. Creates an interactive walkthrough with narrative and runnable code for each topic. Use when the user says "start tour", "give me a tour", "continue tour", "where were we", "tour status", or when presenting the project to someone.

• wiki-add-resource

  Add a resource (paper, repo, notebook, dataset, tool, web page) to the wiki. Downloads the file locally (gitignored), creates a wiki article with a Recover section for reproducibility, and updates the index. Use when the user says "add this paper", "save this resource", "note this repo", or when enc

• wiki-check

  Run a health check on the wiki. Finds stale articles, missing coverage, broken backlinks, and opportunities for cross-linking. Use at the start of a new session, or when the user says "check wiki", "wiki health", "audit wiki", "wiki status".

• wiki-init

  Initialize a plain-markdown knowledge base (Wiki/) in the current repo. Use when the user says "init wiki", "set up knowledge base", "add wiki to this repo", or when starting a new project that needs a wiki. Also triggers when wiki-update or wiki-check is invoked but Wiki/ does not exist yet.

• wiki-search-math

  Search external mathematics resources for a topic: MathWorld, nLab, OEIS, DLMF, and Wikipedia math articles. Returns ranked results, optionally hands them to wiki-add-resource. Use when the user says "search math", "find on MathWorld", "look up in nLab", "OEIS sequence", "DLMF formula", "search Wiki

• wiki-search-wolfram

  Search Wolfram ecosystem resources for a topic: documentation, Function Repository, Community forum, Stephen Wolfram's writings, and the Wolfram Physics Technical Introduction. Downloads notebooks, creates wiki articles, and logs findings. Use when the user says "search wolfram", "find wolfram resou

• wiki-update

  Update the wiki after a substantial change. Creates or updates articles, maintains the index, status, and backlinks. Use after any significant step — code changes, new functionality, completed tasks, discoveries. Triggers on: "update wiki", "log this", or automatically after substantial work. Also i

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