citation-backfill

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Rebuild bidirectional citation edges in a research corpus. Scans outgoing citations, computes the inverse map, rewrites incoming tables. Fixes one-directional graphs.

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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 (default), summary, or json.

Execution Flow

Phase 1: Scan Outgoing Edges

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

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]

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:

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

Phase 4: Write Updates

For each target with changes:

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

If --dry-run: report changes without writing.

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:

Pattern	Example	Context
Table row	`\| REF-016 \| Title \| relationship \|`	Citation sidecar tables
Inline reference	`REF-016` in body text	Finding doc body
YAML list	`- REF-016` under `outgoing:` or `cites:`	Citation YAML sidecars
Markdown link	`[REF-016](../findings/REF-016.md)`	Cross-reference links
Frontmatter	`related_refs: [REF-016, REF-018]`	YAML frontmatter

Integration Points

Component	Relationship
`induct-research`	Should auto-run backfill after batch induction (Phase 3.5)
`address-issues`	Should auto-run when citation sidecars are modified
`research-lint`	`cross-ref-bidirectional` rule validates what backfill fixes
`corpus-health`	Reports citation completeness as a health metric
`research-gap-detect`	Uses the completed graph for cluster analysis

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

Deterministic implementation (`aiwg corpus`)

For corpora laid out as documentation/citations/REF-*-citations.md, a TS-native implementation runs the inverse-map backfill deterministically — prefer it over hand-walking the tables:

aiwg corpus citation-backfill            # dry-run: missing incoming edges + dangling targets
aiwg corpus citation-backfill --write    # inject the missing incoming rows

It is paired with extract-crossrefs, which densifies the outgoing side — analysis docs often list peer REFs in a "Cross-References" / "Related Work" / "Referenced By" section that never made it into the formal Outgoing table:

aiwg corpus extract-crossrefs            # dry-run: cross-ref REFs (with sidecars) missing from Outgoing
aiwg corpus extract-crossrefs --write    # inject them as outgoing edges
aiwg corpus extract-crossrefs --refs REF-056,REF-061   # restrict to specific sources

Run extract-crossrefs first (it adds outgoing edges), then citation-backfill (it mirrors them to incoming). Both default to dry-run. This skill orchestrates; the CLI executes. See the sidecar-lint skill for sidecar structural hygiene.

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
@$AIWG_ROOT/agentic/code/frameworks/research-complete/skills/sidecar-lint/SKILL.md — Sidecar structural lint + repair
@$AIWG_ROOT/agentic/code/frameworks/research-complete/lint/cross-ref-bidirectional.yaml — Lint rule for edge validation
@$AIWG_ROOT/agentic/code/frameworks/research-complete/skills/research-status/SKILL.md — Health scoring includes citation completeness
@$AIWG_ROOT/src/artifacts/corpus-tools/citation-densify.ts — extract-crossrefs + citation-backfill (deterministic)