paper-process

name	paper-process
description	Retrieve a paper, read it, and run the full per-paper propstore ingestion flow through nested skills. Give it a URL, DOI, or title.
argument-hint	<url-or-doi-or-title>
disable-model-invocation	false
compatibility	Claude Code, Codex CLI, and Gemini CLI.

Paper Process: $ARGUMENTS

Retrieve one paper, extract the paper artifacts, and run the per-paper propstore ingestion flow.

This is a pure orchestrator. It calls nested skills. It does not inline propstore source-branch mutation commands.

Light Flow (--light / --notes-only)

If $ARGUMENTS includes --light (or --notes-only), run the notes-layer-only flow and stop. This is the supported path for notes-layer lit reviews that do not use the propstore.

Run, in order, skipping every propstore step:

1. /research-papers:paper-retriever <input> — retrieve the PDF.
2. /research-papers:paper-reader <path-from-step-1> — extract the paper artifacts.
3. /research-papers:tag-papers <paper-directory> — tag and update tags.yaml counts.
4. /research-papers:reconcile <paper-directory> — cross-reference into the collection.

Then stop. In --light mode you skip Steps 4 onward of the full flow — i.e. skip source-bootstrap, author-context, register-concepts, extract-claims, extract-justifications, extract-stances, source-promote, and every pks source-branch command. The notes layer (notes/description/abstract/ citations + index + cross-references) is the complete deliverable here; no propstore branch is created or mutated.

If --light is not present, ignore this section and run the full flow below.

Execution Discipline

• Follow the steps in order.
• $ARGUMENTS names exactly one intended paper.
• If nested skill invocation works on this platform, invoke the named skill directly.
• If nested skill invocation does not work, use the fallback helper and follow its stdout literally.
• Do not substitute custom scripts, alternate workflows, or ad hoc shell sequences for the listed steps.
• If any step is blocked, stop at that step and report the exact blocker.

Step 1: Retrieve

Invoke:

/research-papers:paper-retriever $ARGUMENTS

When retrieval finishes, record the resulting paper path.

Step 2: Read The Paper

Invoke:

/research-papers:paper-reader <path-from-step-1>

When reading finishes, record the resulting paper directory.

Step 3: Clean Up Root PDF

If the original argument was a local root-level PDF and the paper directory now contains paper.pdf, remove the original root-level PDF so the papers/ root continues to mean "unprocessed PDFs only".

Step 4: Bootstrap The Source Branch

Invoke:

/research-papers:source-bootstrap <paper-directory-path>

Step 5: Author The Paper's Context

Invoke:

/research-papers:author-context <paper-directory-path>

This creates knowledge/contexts/ctx_<author>_<year>_<slug>.yaml with the trial's structural CEL assumptions, parameters, and perspective. Every claim extracted in later steps references this context by name. Promote fails if claims are contextless.

Step 6: Register Concepts

Invoke:

/research-papers:register-concepts <paper-directory-path>

This is the notes-first concept pass.

Step 7: Extract Claims

Invoke:

/research-papers:extract-claims <paper-directory-path>

Step 8: Iterate Concepts And Claims If Needed

If claim ingestion or auto-finalize feedback reports unknown concepts:

1. rerun register-concepts
2. rerun extract-claims
3. continue until the unknown-concept set is gone

Do not invent a different recovery path. The intended loop is:

• register-concepts
• extract-claims
• inspect feedback
• repeat if necessary

Step 9: Register Predicates

Concepts and claims are stable at this point, so the paper now has a fixed vocabulary for DeLP/Datalog predicate declarations. This step authors one canonical predicate artifact per predicate id via pks predicate add, using paper/source metadata for readability. Those predicates are the symbol table the next step's rules reference; without them, rule heads and bodies have nothing to bind to.

Invoke:

/research-papers:register-predicates <paper-directory-path>

Follow the nested skill literally. Do not invent predicates outside its workflow, do not skip ahead to authoring rules, and if the skill is blocked stop here and report the blocker.

Step 10: Author Rules

With predicates declared, this step encodes the paper's stated argument structure as DeLP strict, defeasible, proper-defeater, and blocking-defeater rule artifacts via pks rule add. These rules are what makes the DeLP layer non-empty for this paper; the later justification and stance passes describe the paper's argumentation in prose-aligned form, but only the rules authored here participate in propstore's defeasible reasoning.

Invoke:

/research-papers:author-rules <paper-directory-path>

Follow the nested skill literally. Do not author rules referencing predicates that were not declared in Step 9, do not substitute an ad hoc rule format, and if the skill is blocked stop here and report the blocker.

Step 11: Extract Justifications

Invoke:

/research-papers:extract-justifications <paper-directory-path>

Step 12: Extract Stances

Invoke:

/research-papers:extract-stances <paper-directory-path>

This is per-paper stance extraction against whatever claims already exist in the current knowledge store.

Step 13: Promote

Invoke:

/research-papers:source-promote <paper-directory-path>

Step 14: Build

If this run is being used as a single-paper ingestion flow rather than a large collection batch, rebuild the sidecar:

pks build

If this run is part of a larger batch orchestrator that will do one final build later, defer the build there instead of rebuilding after every paper.

Step 15: Report

Write a concise report to reports/paper-$SAFE_NAME.md summarizing:

• retrieval result
• reading result
• whether source-bootstrap succeeded
• whether register-concepts needed reruns
• whether extract-claims needed reruns
• whether register-predicates succeeded
• whether author-rules succeeded
• whether extract-justifications succeeded
• whether extract-stances succeeded
• whether source-promote succeeded
• whether pks build was run or deferred

Fallback

If direct nested skill invocation is unavailable, use this skill's helper:

uv run "<skill-dir>/scripts/emit_nested_process_fallback.py"

Read the FULL stdout and follow it exactly instead of opening sibling skills piecemeal.