research-workspace

Turn a list of papers (Zotero collection, Obsidian cluster, manual list) into a compact comparison matrix written to .research/literature_matrix.md, instead of generic per-paper summaries. Use when the user asks to "make a literature matrix", "compare these papers by method/data/limitations", or "decide which papers are central to my review".

Compare a downloaded NotebookLM brief against the source bundle research-hub uploaded, and report missed sources, unsupported claims, contradictions, and recommended follow-up prompts. Use when the user asks to "verify this NotebookLM brief", "check if the brief missed anything", or "compare downloaded notes to the cluster papers".

Convert a paper draft + figures + Zotero metadata into reusable .paper/claims.yml and .paper/figures.yml files so the academic-writing-skills skill can do writing, revision, and audit passes without re-reading the manuscript every time. Use when the user asks to "build paper memory", "extract claims from this manuscript", or "prepare this paper for AI-assisted writing".

After research-hub ingests a cluster of papers, fill the per-paper Key Findings + Methodology + Relevance sections in BOTH Obsidian markdown and the Zotero child note. Use when the user says "summarize this cluster's papers", "fill the TODO Findings", or "I just ran auto and don't know what these papers are about". Invokes `claude` / `codex` / `gemini` (whichever is on PATH) on each paper's abstract.

Inspect a research repository and write a compact `.research/` workspace manifest (project_manifest.yml, experiment_matrix.yml, data_dictionary.yml) so future AI sessions can orient themselves without rescanning the whole repo. Use when the user asks to "compress this project context", "create a research manifest", or "save the project context for future agents".

Guide a researcher through 5 Socratic segments — research question sharpening, expected mechanism, identifiability check, validation plan, risk register — and produce `.research/design_brief.md`. Use when the user asks to "frame this research question", "design my study", "help me think through what model to build", "sharpen my hypothesis", or "before I start coding, walk me through the design". Does NOT write the model spec; does NOT invent the research question — guides the human to articulate them.

Multi-AI orchestration for research-hub workflows. Use when the user wants Claude, Codex CLI, Gemini CLI, or another shell-capable assistant to share research-hub work such as planning, ingesting, crystal generation, Chinese/English summaries, or long-running literature workflows.

Operate research-hub workflows for literature discovery, source ingest, Zotero/Obsidian/NotebookLM organization, dashboard inspection, and vault maintenance. Use when the user asks to find papers, build a knowledge base, organize references, upload to NotebookLM, generate research briefs, inspect clusters, or maintain a research vault.

Read the .research/ manifest files at a project root and produce a single orientation memo (research question, datasets, current stage, key entrypoints, evidence artifacts, open questions). Use when the user asks to "orient me in this project", "what is this repo about", or "build a context map for this paper" — and the project already has .research/ manifests (or trigger research-context-compressor first).

Audit and curate a Zotero library — find duplicate DOIs, orphan items missing required tags, propose collection rebinds, generate tag hygiene reports, emit preview-only cleanup plans. Use when the user asks to "audit Zotero", "find duplicates", "tag hygiene report", or "propose a Zotero cleanup plan". Defers all CRUD operations to the standalone `zotero-skills` skill or `research-hub zotero` CLI.

Full CRUD operations on Zotero library — search, add, update, delete items with notes, tags, collections, and PDF attachments. Uses dual-API architecture (local API for fast reads, Web API for writes). Use this skill whenever the user mentions Zotero, references, citations, literature management, reading notes, or wants to organize academic papers — even if they don't explicitly say 'Zotero'.