extract-stances

name	extract-stances
description	Extract inter-claim stances and author them through pks source propose-stance.
argument-hint	<papers/Author_Year_Title> [--cluster paper1,paper2,...] or --all
disable-model-invocation	false
compatibility	Claude Code, Codex CLI, and Gemini CLI.

Extract Stances: $ARGUMENTS

Extract argumentative relationships between already-authored claims and write them directly to propstore with pks source propose-stance. Do not create or ingest stance batch files.

Stance Types

• supports — corroborating evidence.
• explains — mechanistic or causal explanation.
• rebuts — direct conflict with the target conclusion.
• undermines — attacks a premise or evidence quality.
• undercuts — attacks the inference or methodology.
• supersedes — replaces the target because it is newer, larger, longer, or corrects an error.

Step 0: Determine Mode

Parse $ARGUMENTS:

if [[ "$ARGUMENTS" == "--all" ]]; then
  ls -d papers/*/ | grep -v "papers/pngs\|papers/tagged" | sort
else
  paper_dir="$ARGUMENTS"
  source_name=$(basename "$paper_dir")
fi

For --all, process each paper source one at a time. Do not run concurrent stance writes against the same source.

Step 1: Load Claim Context

Read:

• The target paper's notes.md, especially discussion, collection cross-references, open questions, and cited-prior-work passages.
• Other papers' notes.md where a proposed target relationship depends on cross-paper evidence.
• Current source-branch claim ids. Local source claims are referenced as claim7; cross-source targets are referenced as OtherPaperDir:claim7.

Do not stance claims in the same paper when the relation is really an intra-paper inference; use extract-justifications for that.

Cross-source boundary

When extracting stances for one source, the current source is the only mutable source.

• Do not run pks source finalize, pks source promote, pks source propose-*, or any other mutation command for another paper source.
• Do not "fix up" another paper so a target claim becomes available.
• If a cross-source target is not already resolvable by pks source propose-stance, skip that stance and report it as unavailable.
• It is acceptable to read another paper's notes and already-promoted claim artifacts to choose a target.
• It is acceptable to finalize the current source only if the local claims must be resolvable before writing stances.

Step 2: Propose Stances Through pks

Before writing only supports links, actively look for disagreement:

• Compare effect direction, endpoint definition, population, follow-up window, and causal interpretation against related papers.
• Use rebuts when two claims answer the same substantive question with incompatible conclusions.
• Use undermines when the source attacks another claim's evidence quality, selection criteria, endpoint, adherence, follow-up, or ascertainment.
• Use undercuts when the source attacks the inference from the target's evidence to its conclusion.
• Use supersedes when the source is a later/larger/corrective synthesis that should replace an older value or conclusion.
• Do not force adversarial stances where the papers merely differ in context. If no adversarial stance is grounded, report the checked targets and the reason they are context differences rather than conflicts.

Use one command per stance:

pks source propose-stance "$source_name" \
  --source-claim claim3 \
  --target OtherPaper_2024_RelatedFinding:claim11 \
  --type supports \
  --strength strong \
  --note "Independent replication of a comparable null result."

Rules:

• --source-claim is a local claim id from the current source.
• --target is either a local claim id or PaperDirName:claimID for another source.
• --type must be one of the stance types above.
• Always include --note with the textual or structural reason for the stance.
• pks source propose-stance resolves local source claims and rejects unresolved local references before writing.

Step 3: Report

Stances extracted for: papers/[dirname]
  Stances proposed: N total
  supports: X
  rebuts: X
  undercuts: X
  undermines: X
  explains: X
  supersedes: X
  Cross-paper links: N
  Validation boundary: pks source propose-stance
  Adversarial checks: checked N targets; authored N; skipped N with reason