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CLI Reference

Generated against research-hub v1.x. 35+ subcommands grouped by workflow stage.

Setup

init

Interactive setup wizard.

research-hub init [--vault PATH] [--zotero-key KEY] [--zotero-library-id ID]
                  [--non-interactive] [--persona researcher|analyst]
Flag Description
--vault PATH Vault root directory (default: ~/knowledge-base)
--zotero-key KEY Zotero API key (researcher persona only)
--zotero-library-id ID Zotero library ID
--non-interactive Skip prompts; require values via flags
--persona researcher (default) or analyst (skip Zotero)

Example:

research-hub init --persona analyst --vault ~/my-vault

doctor

Health check (config, vault, Zotero, dedup, Chrome, NLM session).

research-hub doctor

install

Install portable SKILL.md files for hosts with known default skill directories.

research-hub install --platform claude-code|codex|cursor|gemini
research-hub install --list

OpenClaw, Hermes, and other agents can use research-hub through MCP/REST or manual SKILL.md loading, but they are not built-in installer targets yet.

dashboard

Generate a personal HTML dashboard for the vault.

research-hub dashboard [--open]
Flag Description
--open Open the dashboard in your default browser after generation

Output: <vault>/.research_hub/dashboard.html — single self-contained file with stat cards, cluster table, status badges, and NotebookLM links. Works offline.

Search & verification

search

Query Semantic Scholar.

research-hub search "QUERY" [--limit N] [--verify]

verify

Check paper exists via DOI / arXiv ID / fuzzy title match.

research-hub verify --doi 10.1234/x
research-hub verify --arxiv 2502.10978
research-hub verify --paper "Title" [--paper-year 2025] [--paper-author "Last"]

references

List papers cited by the given paper (its bibliography).

research-hub references <doi-or-arxiv-id> [--limit 20] [--json]

cited-by

List papers that cite the given paper.

research-hub cited-by <doi-or-arxiv-id> [--limit 20] [--json]

Save & organize

add

The one-shot Search → Save command.

research-hub add <doi-or-arxiv-id> [--cluster SLUG]
                                    [--no-zotero] [--no-verify]

ingest / run

Run the full pipeline from papers_input.json.

research-hub ingest [--cluster SLUG] [--no-verify]
research-hub run    [--cluster SLUG]

suggest

Cluster + related-paper suggestions.

research-hub suggest <doi-or-title> [--top 5] [--json]

find

Search within vault notes.

research-hub find "QUERY" [--cluster SLUG] [--status STATUS]
                          [--full] [--json]

mark

Update reading status.

research-hub mark <slug> --status unread|reading|deep-read|cited
research-hub mark --cluster SLUG --status STATUS    # bulk

move

Move a paper between clusters.

research-hub move <slug> --to <cluster>

remove

Remove a paper from the vault.

research-hub remove <doi-or-slug> [--zotero] [--dry-run]

cite

Export citations.

research-hub cite <doi-or-slug> [--format bibtex|biblatex|ris|csljson] [--out FILE]
research-hub cite --cluster <slug> --format bibtex --out cluster.bib

Cluster management

clusters list/show/new

research-hub clusters list
research-hub clusters show <slug>
research-hub clusters new --query "topic" [--name "Display Name"]

clusters bind

Link a cluster to Zotero collection / Obsidian folder / NotebookLM notebook.

research-hub clusters bind <slug> [--zotero KEY] [--obsidian PATH] [--notebooklm "Name"]

clusters rename / delete / merge / split

research-hub clusters rename <slug> --name "New Name"
research-hub clusters delete <slug> [--dry-run]
research-hub clusters merge <source> --into <target>
research-hub clusters split <source> --query "keywords" --new-name "Name"

Maintenance

dedup

research-hub dedup invalidate [--doi DOI] [--path PATH]
research-hub dedup rebuild [--obsidian-only]

index

Rebuild dedup_index.json from Zotero + Obsidian.

research-hub index

status

Per-cluster reading progress.

research-hub status [--cluster SLUG]

sync

research-hub sync status [--cluster SLUG]
research-hub sync reconcile --cluster SLUG [--dry-run] [--execute]

cleanup

Deduplicate hub page wikilinks.

research-hub cleanup [--dry-run]

synthesize

Generate cluster synthesis pages.

research-hub synthesize [--cluster SLUG] [--graph-colors]

migrate-yaml

Patch legacy notes to current YAML spec.

research-hub migrate-yaml [--assign-cluster SLUG] [--folder PATH]
                          [--force] [--dry-run]

NotebookLM

notebooklm login

research-hub notebooklm login --auto-detect [--wait-timeout 300]
research-hub notebooklm login [--wait-file PATH] [--wait-timeout 300]
research-hub notebooklm login --from-browser [chrome|edge|firefox|brave|auto]
research-hub notebooklm login --import-from VAULT_PATH [--overwrite]

notebooklm bundle

research-hub notebooklm bundle --cluster SLUG

notebooklm upload

research-hub notebooklm upload --cluster SLUG [--dry-run] [--headless] [--visible]

notebooklm generate

research-hub notebooklm generate --cluster SLUG --type brief|audio|mind-map|video|all
                                  [--headless] [--visible]

notebooklm download

Pull a generated briefing back to the vault as plain text. v0.9.0 supports --type brief; audio/mind-map/video downloads land in v0.9.1.

research-hub notebooklm download --cluster SLUG [--type brief] [--visible]

Output: <vault>/.research_hub/artifacts/<cluster_slug>/brief-<UTC>.txt with a small header (notebook name, source URL, timestamp, saved briefing titles) followed by the briefing body.

notebooklm read-briefing

Print the most recently downloaded briefing for a cluster.

research-hub notebooklm read-briefing --cluster SLUG

AI integration

serve

Start MCP stdio server for Claude Desktop / Cursor / Claude.ai.

research-hub serve

Add this to your Claude Desktop config:

{
  "mcpServers": {
    "research-hub": {
      "command": "research-hub",
      "args": ["serve"]
    }
  }
}

21 MCP tools exposed. See docs/mcp-tools.md for the full list.