Citation Backfill

Rebuild bidirectional citation edges across the entire research corpus. After batch inductions or outgoing citation table updates, incoming citation tables across the corpus become stale. This command computes the inverse citation map and rewrites all incoming tables to match.

Triggers

• "backfill citations"
• "rebuild citation edges"
• "fix incoming citations"
• "propagate citation edges"
• "citation backfill"

• /citation-backfill

Parameters

--dry-run

(optional)

Report what would change without writing any files.

--scope REF-XXX

(optional)

Only propagate edges from a specific paper. Useful after inducting a single new source.

--format

(optional)

Output format:

full

summary

json

Execution Flow

Phase 1: Scan Outgoing Edges

1. Glob all citation sidecar files:

   • .aiwg/research/citations/REF-*.yaml

     (if YAML sidecars exist)

   • .aiwg/research/findings/REF-*.md

     — scan "Outgoing Citations" / "References" / "Cites" sections

   • .aiwg/research/documentation/citations/REF-*.md

     — scan citation tables

2. Extract outgoing edges from each source:

   REF-016 → cites → [REF-018, REF-024, REF-121]
   REF-018 → cites → [REF-016, REF-024]
   REF-024 → cites → [REF-016]
   

3. Build the outgoing map:

   Map<source, Set<target>>

Phase 2: Compute Inverse Map

Invert the outgoing map to produce the incoming map:

REF-016 ← cited-by ← [REF-018, REF-024]
REF-018 ← cited-by ← [REF-016]
REF-024 ← cited-by ← [REF-016, REF-018]
REF-121 ← cited-by ← [REF-016]

Result:

Map<target, Set<source>>

Phase 3: Diff Against Current State

For each target in the incoming map:

1. Read the current "Incoming Citations" / "Cited By" section
2. Parse existing incoming edges
3. Compute the diff: edges to add, edges to remove (if source was deleted)

Phase 4: Write Updates

For each target with changes:

1. Rewrite the "Incoming Citations" section with the computed set
2. Sort entries by REF number for stable output
3. Preserve any manually-added annotations (relationship type, notes)

If

--dry-run

Phase 5: Report

Citation Backfill Complete
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

Sources scanned:        372
Outgoing edges found:   1,247
Incoming edges computed: 1,247
Sidecars updated:       89
New edges propagated:   134
Stale edges removed:    3
Targets not found:      2 (REF-999, REF-888 — referenced but no note exists)

Updated files:
  documentation/citations/REF-016.md  (+3 incoming)
  documentation/citations/REF-018.md  (+1 incoming)
  documentation/citations/REF-024.md  (+2 incoming)
  ...

Edge Detection Patterns

The backfill command recognizes citations in these formats:

| REF-016 | Title | relationship |

REF-016

- REF-016

outgoing:

cites:

[REF-016](../findings/REF-016.md)

related_refs: [REF-016, REF-018]

Integration Points

induct-research

address-issues

research-lint

cross-ref-bidirectional

corpus-health

research-gap-detect

Auto-Integration Hooks

When called from other skills:

# After induct-research batch:
post-induction:
  - /citation-backfill --scope <newly-inducted-refs>

# After address-issues modifies citations:
post-issue-resolution:
  - /citation-backfill --dry-run
  - # If changes detected, prompt user to run full backfill

Examples

# Full corpus backfill
/citation-backfill

# Preview what would change
/citation-backfill --dry-run

# Backfill only edges from a specific paper
/citation-backfill --scope REF-364

# JSON output for programmatic use
/citation-backfill --format json

References

• @$AIWG_ROOT/agentic/code/frameworks/research-complete/skills/induct-research/SKILL.md — Triggers backfill post-induction
• @$AIWG_ROOT/agentic/code/frameworks/research-complete/skills/research-lint/SKILL.md — Validates bidirectional edges
• @$AIWG_ROOT/agentic/code/frameworks/research-complete/lint/cross-ref-bidirectional.yaml — Lint rule for edge validation
• @$AIWG_ROOT/agentic/code/frameworks/research-complete/skills/research-status/SKILL.md — Health scoring includes citation completeness