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A literature review is research work, and it leaves as little behind as a training run does unless somebody records it. probe paper is where it goes. Record during a review and again at its end — not afterwards from memory.
The project and the paper’s title come first. There is no dedupe: two adds of one URL make two rows, so check probe paper list folding first. --discrepancies is the field that earns the entity. “The paper says warmup is linear; the repo’s scheduler is cosine with a floor” is the kind of thing that costs a week when it is rediscovered, and nothing else in a review captures it.

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Provenance: how you got there

Omit --via only when you genuinely cannot say. A review whose paths are recorded can be re-walked; one without them is a bag of citations. Never pass the paper you happened to add last: read order is not derivation.

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How papers relate

--via records how you found a paper. --relates-to records how its content connects to an earlier paper in the project, with --relates-reason saying how in one or two sentences. Choose it by what the papers say, never by which one you added last; pass none for the project’s first paper. --relates-provenance says how the link is known: inferred (your judgment, the default), human, observed_call or provider_citation. Both are readable back:
Read it before adding a paper: the ids --via and --relates-to take are there. Whether one paper’s bibliography cites another is a separate cites link that Probe reads from the bibliographies itself (probe paper citations <paper-id>, probe paper graph --project folding).

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Managing them

update leaves omitted fields untouched. "" clears a field — except --title and --source, which are required and reject an empty value. update --tag replaces the whole tag list; probe paper tag adds or drops one.

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In the dashboard

In a research project, papers are listed in the Overview’s left pane, with filtering, and selecting one opens its details there. A link to /papers/{id} opens the paper selected in its project. The separate Papers tab and the paper’s own page are gone.
The dashboard shows papers; it does not record them. Recording a paper is an act by whoever did the reading — through the CLI or an agent session.

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Finding papers to record

Agents have a find_papers tool over 40M+ abstracts (arXiv, PubMed, bioRxiv, medRxiv), with search, read and similar modes. The same search runs from the shell:
It is read-only: it records nothing, and each call spends one of the team’s weekly web calls.
find_papers wants natural language, not a keyword bag. A question-shaped description retrieves substantially more relevant papers than a bag of terms. Its categories filter is an AND, and its score rises as relevance falls — read the results, do not rank by the number.
See the MCP reference.