Claude Research Pack

A portable bundle that turns any Windows laptop into a literature-aware research workstation: multi-mode deep research, automatic paper download, structured paper capture into an Obsidian vault, and project-aware citation reuse.

Built on top of the academic-research-skills project by Cheng-I Wu (CC-BY-NC 4.0) -- see ATTRIBUTION.md. Reimplemented in Claude-native primitives (skills + hooks + slash commands + MCP servers).

v2 -- three install paths

Pick one based on which Claude product you want to drive:

| | Path A -- Code on WSL | Path B -- Code on Windows native | Path C -- Claude Desktop | |---|---|---|---| | Audience | Linux-comfortable; existing rig | CLI users without WSL | Non-developer / GUI users | | Slash commands | ✅ | ✅ | ❌ (free-text invocation) | | Sub-agent integrity gates | ✅ | ✅ | ❌ -- single-pass + self-critique | | Hooks (handoff, todo persistence, statusline) | ✅ | ✅ | ❌ | | Iron Rules + citation discipline | ✅ | ✅ | ✅ | | Paper capture into vault | ✅ | ✅ | ✅ | | Cross-device research continuity (snapshot/resume via synced vault) | ❌ | ❌ | ✅ -- v3 | | Local-PDF ingestion | ❌ | ✅ -- v5 | ✅ -- v4 | | Interactive research co-pilot loop | ❌ | ✅ -- v5 | ✅ -- v4 | | Mandatory scope confirmation + citation pre-flight | ❌ | ✅ -- v5 | ✅ -- v4 | | One-command install (winget + auto-detect + self-test) | ❌ | ✅ -- v5 | ❌ | | Setup time | 30-45 min | ~5 min (after Claude Code) | 20-30 min |

Decision tree and capability matrix in INSTALL_WINDOWS.md.

Path C honest disclosure: Claude Desktop has no Agent tool, so deep-research runs single-pass with explicit in-context self-critique instead of independent parallel sub-agents. Iron Rules still apply (no fabricated citations) but the integrity gate is mechanically weaker. Read desktop-skills/academic-deep-research/references/desktop_limitations.md before relying on Path C output for publication-grade work.

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What's in the box

Skills (full versions -- used by Path A and Path B)

• deep-research -- 7-mode research pipeline (full / quick / lit-review / fact-check / socratic / systematic-review / review). Citation-disciplined: every claim must resolve through a real source. Multi-agent: spawns parallel investigators, synthesizer, devil's-advocate. See skills/deep-research/SKILL.md.
• paper-capture -- Resolve DOI/arXiv/URL/title -> metadata + PDF + structured Obsidian note. Idempotent and de-duped.
• lit-status -- Read-only library inspector: counts, tags, gaps, citation links to active projects.
• handoff -- Capture a session snapshot for the next chat.

Skills (lite versions -- used by Path C)

• desktop-skills/academic-deep-research -- Same 7 modes, same Iron Rules, same templates, but workflow is serial in one context with explicit === DEVIL'S ADVOCATE CHECKPOINT N === self-critique banners. The skill is named academic-deep-research (not deep-research) to avoid colliding with Claude Desktop's built-in deep-research feature. See desktop-skills/academic-deep-research/SKILL.md.
• desktop-skills/paper-capture and desktop-skills/lit-status -- Identical to the Code variants (no Agent tool dependency).
• desktop-skills/capture-research-state, resume-research-state, sync-check, paper-map -- v3 cross-device continuity. Snapshot a Desktop session into a synced Obsidian folder; resume it on another device. See INSTALL_WINDOWS.md for setup. Backed by a stdlib Python helper at tools/research_sync_agent.py bundled into each skill's bin/ at zip time.
• desktop-skills/ingest-pdf -- v4. Drop a local PDF (or a folder of PDFs); the skill extracts the DOI / arXiv id / title from the file, hands off to paper-capture for resolution, and moves the original into 80_Attachments/papers/{citekey}.pdf. Closes the gap where users had a paper on disk but no DOI handy.
• desktop-skills/research-copilot -- v4. The interactive loop layer: Orient -> Question -> Suggest -> Synthesize -> Escalate. One conversational move per turn, never invents citations, defers heavy lifting to the other skills. Turns the pack from a one-shot lit-review tool into an ongoing research conversation.

Slash commands (Path A / B only)

• /research [--mode <name>] <topic>
• /capture-paper <doi|arxiv|url|title> [--citekey <key>] [--project <slug>]
• /lit-map [summary|unread|tags|gaps|orphans|citation-map <citekey>]
• /status, /port-to-vault

MCP servers (installed by the bundled installer)

• arxiv, semantic-scholar, paper-search, paper-mcp -- paper search & metadata
• university-paper-access -- institutional full-text via Unpaywall
• scihub -- last-resort PDF
• obsidian -- read/search/write the Obsidian vault

Two installers ship in this pack:

• mcp-servers/install-mcp-servers.sh -- bash, for WSL (Path A)
• mcp-servers/install-mcp-servers.ps1 -- PowerShell, for Windows native and Desktop (Path B and C; pick target with -Target Native|Desktop)

Hooks (Path A / B only -- Desktop has no hooks API)

• precompact-handoff.py -- write handoff_latest.md before context compaction
• session-start-context.py -- inject latest handoff + review summary on resume
• stop-persist-todos.py -- keep TodoWrite items alive across sessions
• statusline.sh (WSL) / statusline.ps1 (Windows native) -- bottom-bar status
• paper-mention-detect.py -- off by default -- suggest /capture-paper when a DOI is mentioned

Vault templates (all three paths)

PARA-style scaffolding for Obsidian. Drop into a fresh vault to get 30_Literature/, 70_Templates/literature.md, lit-review and research-question templates.

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Install + use

• INSTALL_WINDOWS.md -- full decision tree and walkthroughs.
• USAGE.md -- how to actually use the pack after install: trigger prompts for deep research, auto-download papers, fine-tune search, ingest local PDFs, force quote-backed answers.

The router is:

PS> .\scripts\setup.ps1 -Mode WSL       # Path A (default)
PS> .\scripts\setup.ps1 -Mode Native    # Path B
PS> .\scripts\setup.ps1 -Mode Desktop   # Path C

Quickstart (after install)

Path A / B -- slash commands in Claude Code

/research --mode lit-review "ion-gated transistors for reservoir computing"
/capture-paper 10.1038/s41586-021-03819-2
/lit-map gaps

Path C -- free-text in Claude Desktop

> Do a lit review on ion-gated transistors for reservoir computing.
> Save this paper: 10.1038/s41586-021-03819-2
> What are the gaps in my reading on transistors?

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Design principles

• Citation discipline first. A "fact" without a citation that resolves through Semantic Scholar / arXiv / OpenAlex is a hallucination, not a fact. Deep-research is structured to make hallucination expensive -- the Devil's Advocate has block authority on Path A/B and uses an explicit mechanical checklist on Path C.
• Vault is the canonical brain. Drafts land in 00_Inbox/ for user curation; only paper-capture writes directly to 30_Literature/. Project notes accumulate citekeys; the same papers come back as context on the next project.
• One pack, three runtimes. WSL, Windows native, and Desktop ship in the same pack. Recipients pick by path; nothing is renamed across versions, so v1 users can git pull to v2 with zero migration.
• Bring your own institutional access. university-paper-access uses Unpaywall + your campus IP. If you don't have institutional access, the pack still works via arXiv + (optionally) Sci-Hub.

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Versions and provenance

• v5.0 -- Path B (Windows-native Code) overhaul: one-command install with winget pre-flight, auto-detect vault path + REST API key, automatic vault bootstrap + Obsidian config, post-install self-test. Plus full feature parity with Path C: ingest-pdf, research-copilot, mandatory scoping, citation pre-flight, lit-status next-action. New slash commands /ingest-pdf and /copilot.
• v4.0 -- adds local-PDF ingestion (ingest-pdf), interactive co-pilot (research-copilot), mandatory scope confirmation + post-composition citation pre-flight in academic-deep-research, and a next-action mode in lit-status. (Path C only at v4; ported to Path B in v5.)
• v3.0 -- cross-device research continuity for Path C (capture-research-state, resume-research-state, sync-check, paper-map + tools/research_sync_agent.py).
• v2.0 -- adds Path B (Windows native) and Path C (Claude Desktop) on top of the original Path A WSL build.
• v1.0 -- Path A only (Claude Code on WSL).

Built against the upstream Imbad0202/academic-research-skills v3.6.5 (April 2026).

License

CC-BY-NC 4.0. See LICENSE and ATTRIBUTION.md.