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lit-monitor for Zotero

CLI reference

max3925vats/lit-monitor

CLI reference¶

Run lit-monitor --help for the full command surface. Top-level -v / --verbose enables DEBUG console output; a full DEBUG log is always written to logs/{date}_{command}.jsonl.

One-time setup¶

lit-monitor first-run                    # interactive setup, then launch the server
lit-monitor build-vocabulary             # cluster Zotero tags into themes
lit-monitor brain-build --resume         # extract every paper in the collection

Discovery¶

lit-monitor run                          # discover new papers + ingest new Zotero items
lit-monitor run --dry-run                # preview without writes
lit-monitor discovery view --run latest  # rich-table view of the latest results
lit-monitor discovery export-md --to ~/digest.md   # on-demand Markdown export

Ask¶

lit-monitor ask "what methods extend cation exchange?" --rag-mode hybrid

Responses are automatically contextualised to your dominant theme when clusters exist. Requires the knowledge graph (lit-monitor graph backfill --all).

Domain focus extraction¶

lit-monitor domain analyze               # LLM-extract structured concepts from domain_context.yaml
lit-monitor domain view                  # show extracted focus areas
lit-monitor domain clear                 # reset extracted domain focus

Theme clustering¶

Requires ~100 indexed papers.

lit-monitor cluster recompute            # run K-means + LLM naming
lit-monitor cluster view                 # show cluster themes + paper counts
lit-monitor cluster assign               # assign papers to nearest cluster
lit-monitor cluster write-back tags      # tag Zotero items with theme names
lit-monitor cluster write-back collections  # move Zotero items into per-theme collections

lit-monitor trending suggest             # surface rising entity types
lit-monitor trending view                # list pending / accepted / dismissed suggestions
lit-monitor trending accept <id>         # add concept to active topics
lit-monitor trending dismiss <id>        # suppress concept until next cycle

Embeddings¶

lit-monitor embeddings status            # show provider, model, coverage
lit-monitor embeddings switch --provider litellm --model text-embedding-3-small
lit-monitor embeddings rebuild           # re-embed library under new model

Knowledge graph¶

lit-monitor graph status                 # node + edge counts
lit-monitor graph backfill --all         # index existing papers into the graph
lit-monitor graph propose-aliases        # suggest entity normalization rules

Obsidian helpers¶

lit-monitor obsidian relink              # update Related Work sections
lit-monitor obsidian rerender            # regenerate notes from stored extractions
lit-monitor obsidian sync --all          # write deferred per-paper notes
lit-monitor obsidian synthesize --topic "..."   # chunk-level RAG with reranking

Active learning — interest vector + feedback¶

lit-monitor feedback <doi> --saved       # record a feedback event (also --dismissed/--thumbs-up/...)
lit-monitor learning recompute           # recompute the interest vector from feedback
lit-monitor learning view                # show the interest vector (--per-cluster for atrophy weights)

Health¶

lit-monitor check                        # config + Ollama + Zotero reachability
lit-monitor diagnose                     # strict-mode config audit
lit-monitor status                       # extraction + embedding + graph counts
lit-monitor reset state                  # reset pipeline state (also reset vault / reset all)

See also Configuration for strict mode and provider routing.