claude-plugins/fiction-assistance/commands/generate/cleanup-generated.md

---
description: Clean up and standardize generated files
allowed-tools: Edit(40 - Generated/**), MultiEdit(40 - Generated/**), Write(40 - Generated/Analysis/cleanup-log.md), Bash
---
You are performing maintenance and cleanup on the Universalis generated files to ensure consistency, remove orphaned content, and standardize formatting.

## Objectives:

1. **Remove orphaned files** with no valid references
2. **Standardize formatting** across all generated cards
3. **Fix broken internal references** and update links
4. **Consolidate duplicate content** where appropriate
5. **Ensure file organization** follows established conventions

## Cleanup Operations:

### 1. Orphaned File Detection
Identify files to remove:
- **Unreferenced cards**: Files with no incoming links from other cards or chapters
- **Duplicate files**: Multiple files for the same entity (keep most complete)
- **Invalid files**: Malformed or empty card files
- **Outdated files**: Files for entities no longer in the story

### 2. Formatting Standardization
Apply consistent formatting:
- **YAML frontmatter**: Standardize field order, naming, and values
- **Markdown headers**: Ensure consistent heading hierarchy (H1, H2, H3)
- **Section structure**: Match established card templates
- **Link formatting**: Standardize wiki-style link format
- **Date formatting**: Ensure consistent date format in frontmatter

### 3. Reference Cleanup
Fix broken connections:
- **Dead links**: Remove links to non-existent files
- **Incorrect references**: Fix links pointing to wrong files
- **Missing backlinks**: Add missing reciprocal references
- **Outdated aliases**: Update references using old entity names

### 4. Content Consolidation
Merge related content:
- **Duplicate entities**: Combine multiple cards for same character/location
- **Alias resolution**: Merge cards that represent the same entity
- **Related content**: Move misplaced content to correct files

### 5. File Organization
Ensure proper structure:
- **Directory placement**: Move files to correct category directories
- **Filename conventions**: Standardize naming patterns
- **Category consistency**: Ensure files match their directory category

## Cleanup Process:

### Phase 1: Analysis & Detection
1. **Inventory all files** in 40 - Generated/
2. **Map all references** between files and from manuscript chapters
3. **Identify orphaned content** with no incoming references
4. **Detect formatting inconsistencies** against templates
5. **Find duplicate entities** across different files

### Phase 2: Automated Cleanup
1. **Standardize frontmatter** fields and formatting
2. **Fix link syntax** and formatting issues
3. **Update date formats** to consistent pattern
4. **Normalize section headers** to match templates
5. **Apply consistent indentation** and spacing

### Phase 3: Content Consolidation
1. **Merge duplicate files** (keep most complete version)
2. **Resolve alias conflicts** by consolidating references
3. **Move misplaced content** to appropriate files
4. **Update all references** to consolidated files

### Phase 4: File Organization
1. **Move files** to correct directories if needed
2. **Rename files** to follow naming conventions
3. **Update references** to reflect any file moves/renames
4. **Remove empty directories**

### Phase 5: Validation
1. **Verify all links** work correctly
2. **Check frontmatter** completeness and validity
3. **Confirm file organization** follows conventions
4. **Test cross-references** between all files

## Cleanup Log:

Generate detailed log at `40 - Generated/Analysis/cleanup-log.md`:

```markdown
# Generated Files Cleanup Log

*Cleanup performed: {{current_date}}*

## Cleanup Summary
- **Files Processed**: {{total_files_processed}}
- **Files Removed**: {{files_removed}} (orphaned/duplicate)
- **Files Modified**: {{files_modified}} (formatting/content)
- **Files Moved**: {{files_moved}} (reorganization)
- **Links Fixed**: {{links_fixed}}
- **References Updated**: {{references_updated}}

## Orphaned Files Removed

### No Incoming References
{{list_orphaned_files_removed_with_reason}}

### Duplicate Content
{{list_duplicate_files_consolidated}}

### Invalid Files
{{list_malformed_files_removed}}

## Formatting Standardization

### YAML Frontmatter Fixes
{{list_frontmatter_standardization_changes}}

### Markdown Structure Fixes
{{list_structure_standardization_changes}}

### Link Format Corrections
{{list_link_formatting_fixes}}

## Content Consolidation

### Entity Merges
{{list_entity_consolidations_performed}}

### Alias Resolutions
{{list_alias_consolidations}}

### Content Relocations
{{list_content_moved_between_files}}

## File Organization

### Directory Reorganization
{{list_files_moved_between_directories}}

### Filename Standardization
{{list_filename_changes}}

### Category Corrections
{{list_category_corrections}}

## Reference Updates

### Broken Links Fixed
{{list_broken_links_repaired}}

### Dead References Removed
{{list_dead_references_removed}}

### Missing Backlinks Added
{{list_backlinks_added}}

## Quality Improvements

### Completeness Enhancements
{{list_incomplete_sections_improved}}

### Consistency Fixes
{{list_consistency_improvements}}

### Format Standardization
{{list_format_improvements}}

## Files Requiring Manual Review

### Complex Duplicates
{{list_files_needing_manual_merge_review}}

### Ambiguous References
{{list_references_needing_clarification}}

### Content Questions
{{list_content_requiring_author_decision}}

## Post-Cleanup Statistics

### File Counts by Category
- **Characters**: {{character_file_count}}
- **Locations**: {{location_file_count}}
- **Ships**: {{ship_file_count}}
- **Technology**: {{tech_file_count}}
- **Species**: {{species_file_count}}
- **Plotlines**: {{plotline_file_count}}
- **Events**: {{event_file_count}}
- **Conflicts**: {{conflict_file_count}}
- **Themes**: {{theme_file_count}}

### Link Health
- **Total Links**: {{total_link_count}}
- **Valid Links**: {{valid_link_count}}
- **Broken Links**: {{broken_link_count}}
- **Cross-References**: {{cross_reference_count}}

### Quality Metrics
- **Complete Cards**: {{complete_cards_count}}
- **Standardized Format**: {{standardized_format_count}}
- **Orphaned Files**: {{remaining_orphaned_count}}

## Recommendations

### Immediate Actions
{{list_urgent_cleanup_items_remaining}}

### Future Maintenance
{{list_ongoing_maintenance_recommendations}}

### Prevention Strategies
{{list_strategies_to_prevent_future_issues}}

## Cleanup Methodology

### Detection Criteria
{{criteria_used_for_identifying_cleanup_needs}}

### Automated vs Manual
{{description_of_automated_vs_manual_cleanup_steps}}

### Validation Process
{{process_for_verifying_cleanup_quality}}

---
Generated by Claude Code cleanup system for Universalis writing project.
```

## Cleanup Methodology:

1. **Comprehensive file scanning** for all generated content
2. **Reference mapping** to identify connections and orphans
3. **Pattern matching** for formatting inconsistencies
4. **Automated standardization** where safe to do so
5. **Manual review flagging** for complex cases
6. **Validation testing** after cleanup operations
7. **Documentation** of all changes made

## Safety Measures:

### Backup and Recovery
- Create list of all changes for potential rollback
- Preserve original content when merging duplicates
- Flag complex cases for manual review
- Validate all automated changes

### Content Preservation
- Never delete content without clear justification
- Merge rather than delete when combining duplicates
- Preserve aliases and alternative names
- Maintain all legitimate cross-references

## Cleanup Standards:

### File Naming Conventions
- Consistent capitalization and spacing
- Standard character replacements for special characters
- Category-appropriate prefixes if needed
- Meaningful, searchable filenames

### Content Standards
- Complete frontmatter with all required fields
- Consistent section structure per card type
- Proper wiki-style linking format
- Appropriate content categorization

## Output Requirements:
- Fixed filename: `40 - Generated/Analysis/cleanup-log.md`
- Detailed logging of all changes made
- Statistics on files processed and improvements made
- Recommendations for future maintenance
- Flagged items requiring manual review

**IMPORTANT**: Prioritize content preservation over aggressive cleanup. When in doubt about removing or merging content, flag for manual review rather than auto-delete. Always validate that cleanup operations improve rather than break the generated file system.