DOCX Footnote Repair & Cross-References

Fix footnote formatting damage caused by Google Docs and Word Online, and convert hardcoded supra note references to NOTEREF field codes.

Quick Start

Scripts are in this skill's scripts/ directory. Use $SKILL_DIR below as a placeholder for the absolute path to this skill (the directory containing this SKILL.md).

# Fix all cloud editor damage + convert cross-references
pixi exec --spec python=3.13 --spec lxml -- python3 \
  "$SKILL_DIR/scripts/fix_gdocs_footnotes.py" path/to/file.docx --crossrefs

# Dry run (show what would change)
pixi exec --spec python=3.13 --spec lxml -- python3 \
  "$SKILL_DIR/scripts/fix_gdocs_footnotes.py" path/to/file.docx --dry-run

# Cross-references only
pixi exec --spec python=3.13 --spec lxml -- python3 \
  "$SKILL_DIR/scripts/create_crossrefs.py" --docx path/to/file.docx

Scripts

fix_gdocs_footnotes.py

Detects and repairs OOXML damage from Google Docs / Word Online round-trips. Idempotent.

What it fixes:

• Missing separator/continuation footnotes (id=-1, 0)
• Custom mark restoration for author bio footnotes (*, dagger, double-dagger)
• Footnote ID renumbering (shifted by missing system footnotes)
• Missing paragraph styles (adds configurable pStyle to all footnotes)
• TOC separator paragraph inflation (shrinks to near-zero height)

Flags:

• --output / -o: Output path (default: overwrite input)
• --dry-run: Show what would change without modifying
• --bio-footnotes N: Number of author bio footnotes (default: 3)
• --crossrefs: Chain to create_crossrefs.py after fixing
• --fix-numbering: Fix numbering offset from customMarkFollows bio footnotes (adds numRestart, updates NOTEREFs and supra references)

create_crossrefs.py

Converts hardcoded "supra note N" references to NOTEREF field codes that auto-update.

What it does:

• Finds all supra note <number> patterns in document body and footnotes
• Creates bookmark targets on referenced footnotes
• Replaces hardcoded numbers with NOTEREF _RefFN<id> \h field codes
• Preserves italic formatting on "supra"

Reference

See footnotes-reference.md for detailed technical reference covering:

1. Run-level editing gotchas (NBSP, cross-run matching, xml:space)
2. Cloud editor damage patterns (what gets destroyed and why)
3. Direct ZIP surgery patterns (bypassing Document libraries)

Footnote Numbering Offset Fix

When author bio footnotes use customMarkFollows (*, †, ‡), they consume auto-numbers 1–3, causing body footnotes to start at 4. Fix by adding numRestart=eachSect to settings.xml and updating NOTEREF cached values.

Requires: A section break between title page and body. Must use Word (not LibreOffice) for PDF — LibreOffice renders numRestart as zeros.

See footnotes-reference.md § 4 for details, code patterns, and the critical rule: numRestart goes in settings.xml ONLY (not in sectPr — causes all-zeros).