extract-justifications

name	extract-justifications
description	Extract intra-paper justification structure and author it through pks source propose-justification.
argument-hint	<papers/Author_Year_Title>
disable-model-invocation	false
compatibility	Claude Code, Codex CLI, and Gemini CLI.

Extract Justifications: $ARGUMENTS

Extract the intra-paper argumentative structure: which already-authored source claims serve together as premises for which conclusions. Author justifications directly through pks source propose-justification; do not create or ingest justification batch files.

What Justifications Are

A justification is a directed hyperedge: a set of premise claims that together support or attack a conclusion claim through a typed inference rule. Stances are inter-claim edges across papers; justifications are intra-paper reasoning structure.

Rule kinds:

• empirical_support
• causal_explanation
• methodological_inference
• statistical_inference
• definition_application
• scope_limitation
• comparison_based_inference
• reported_claim
• supports
• explains

Step 0: Validate

paper_dir="$ARGUMENTS"
source_name=$(basename "$paper_dir")
ls "$paper_dir"/notes.md 2>/dev/null || echo "MISSING: notes.md"
ls knowledge/.git 2>/dev/null || echo "MISSING: knowledge/.git"
pks source finalize "$source_name" 2>&1 || true

• notes.md missing -> STOP. Run paper-reader first.
• Source branch missing -> STOP. Run source-bootstrap, register-concepts, and extract-claims first.

Step 1: Read Source Material

Read:

• <paper_dir>/notes.md for the paper's stated reasoning.
• The already-authored source claims for this source branch. Use local claim ids such as claim1 when referencing conclusions and premises.
• Page images for provenance when exact wording or page numbers matter.

Do not fabricate reasoning links. If the paper states a result without connecting it to another claim, leave it isolated.

Step 2: Propose Justifications Through pks

Use one command per inferential step:

pks source propose-justification "$source_name" \
  --id just1 \
  --conclusion claim12 \
  --premises claim3,claim8 \
  --rule-kind statistical_inference \
  --rule-strength defeasible \
  --page 14 \
  --section "Results" \
  --quote-fragment "Brief supporting quote"

Attack-target structure, when the paper explicitly gives rebuttal/undercut/undermine reasoning:

pks source propose-justification "$source_name" \
  --id just2 \
  --conclusion claim18 \
  --premises claim16,claim17 \
  --rule-kind comparison_based_inference \
  --attack-target-claim claim12 \
  --attack-target-justification-id just1 \
  --attack-target-premise-index 0 \
  --page 21

Rules:

• --conclusion must be a local claim id already authored on this source.
• --premises is a comma-separated list of local claim ids from this source.
• Do not include the conclusion in its own premise list.
• Use one inferential step per justification; chains get multiple justifications.
• Reusing a justification id updates that source-local justification.
• pks source propose-justification resolves local claim ids and rejects unresolved references before writing.
• Use --rule-strength strict only for definitional or mathematical entailment. Use defeasible for empirical or methodological support.
• Attack-target fields are optional. Use them only when the paper identifies the target claim, target justification, or target premise being attacked.

Step 3: Report

Justifications extracted for: papers/[dirname]
  Justifications proposed: N total
  Rule kinds used: [...]
  Validation boundary: pks source propose-justification