Paper Fetch

If the caller already has the paper — a local .md/.txt/.pdf path, or a direct HTTP(S) PDF URL (path ends in .pdf, ignoring query and fragment) — read it directly before considering any search route. Record source_channel as local_file, local_pdf, or direct_pdf. If the read fails, return not_found and do not fall back to alphaxiv, Semantic Scholar, bioRxiv, or medRxiv.

The pipeline's sole entry point: retrieves a paper and lands it on disk. It checks the cache first, reads already-identified sources (local files, direct PDF URLs) with no search at all, and otherwise uses the fixed fallback (alphaxiv → Semantic Scholar routing → bioRxiv/medRxiv → not_found). Decoupled from literature-engine's literature-research/literature-search/ literature-overview — this SOP holds its own retrieval calls rather than delegating.

Why an already-supplied file still enters through this SOP

Skipping straight to a reading SOP with the caller's own path looks like it saves a step, but 13 downstream SOPs take meta_path and read only section line ranges (star-awarding reads method + results; first-pass-skim's "headings only, never bodies" constraint holds because it is handed shallow ranges). A bare path carries no index, and a bare .pdf carries no extracted text at all.

So the thing to skip is the four-channel search, not the landing and indexing. That is what Step 1 does: no network lookup, same landing step, same output contract. Tactics keep passing paper_ref through unchanged and never learn there was a new input form.

Landed layout

context/papers/<timestamp>-<title-slug>/
  source.md            the paper, as fetched
  source.meta.json     metadata + line-number section index

All landed filenames are lowercase. <title-slug> is lowercased, non-alphanumerics collapsed to hyphens, Windows-illegal characters (: * ? " < > |) stripped, truncated to 60 chars against path-length limits.

Execution

Subagent — spawned via spawn-agent skill.

Why Subagent

Multi-step retrieval with direct-PDF handling and domain-inference judgment calls (is a Semantic-Scholar miss a bio signal or a "just not indexed anywhere" signal?) benefits from a dedicated context that can hold the whole decision tree without the noise of whatever task will consume its output next.

Why it lands files instead of returning text

A paper runs 60-80k tokens. Returning it as full_text means every downstream SOP pays that cost again, and the orchestrating tactic carries it in its own window on top. Landing it once and returning a path means: re-reading the same paper across tactics costs one cache check rather than one fetch; SOPs that need only part of the paper read only that part; the orchestrator holds paths, not text.

Why a section index, not pre-cut slices

source.meta.json records where each section is (line ranges) rather than shipping pre-cut slices. Slicing is a per-consumer concern — unit-segmentation already declares scope: full_text | abstract | intro_only, research-question-appraisal wants intro + abstract, engineering-config-grading wants method + experiments + appendix. Pre-cutting would mean this SOP has to know every downstream SOP's definition of "the part I need", and would need editing every time one is added. An index is neutral: consumers do their own offset reads against source.md.

This also makes first-pass-skim's defining constraint (skim headings and captions, never section bodies) hold by construction rather than by self-restraint — it is handed line ranges for the shallow parts only.

Cache lookup is by identifier, not directory name

Directories are named <timestamp>-<title-slug>, but paper_ref may arrive as an arXiv ID, a DOI, a URL, a local file path, or a title, and matching an arXiv ID against a title-derived directory name fails. So the lookup scans context/papers/*/source.meta.json and matches on identifier or title_slug — both are recorded precisely so any form of paper_ref resolves. For a local file, identifier is its absolute path, so re-running a tactic on the same file is a cache hit rather than a second copy.

Matching tolerates case and punctuation differences in titles but is deliberately not fuzzy: a missed cache hit costs one redundant fetch, while a false hit silently reads the wrong paper for the rest of the pipeline.

Why Not Built on literature-engine

literature-overview/literature-search/literature-research already have an alphaxiv-primary/SS-supplementary pattern, but none has a bioRxiv/medRxiv branch or an explicit "can't retrieve → halt" contract, and this package is deliberately decoupled from that pipeline's scope (see context/2026-08-07-15-15-paper-fetch-sop-design.md and spec §9). Do not refactor this SOP to import those skills later without revisiting that decision explicitly.

Full design reference

context/2026-08-07-15-15-paper-fetch-sop-design.md — the channel decision-flow rationale (why alphaxiv's coverage list is the domain signal, why an SS miss still routes to bio rather than dead-ending). The landing / index / cache design is in context/2026-08-07-23-01-sop-io-contract-simulation.md §4, option C.

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Available SOPs

Optional, no fixed order; the final leaf is always a sop.

| SOP | When to use | | --- | --- | | spawn-agent | Spawn a customized CC subagent with full MCP tool access. |

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