doc-sys-fixer

Purpose

Automated fix skill that reads the latest audit/review report and applies fixes to SYS (System Design Specification) documents. This skill bridges the gap between doc-sys-reviewer/doc-sys-audit (which identify issues) and the corrected SYS, enabling iterative improvement cycles.

Layer: 6 (SYS Quality Improvement)

Upstream: SYS document, Audit/Review Report (SYS-NN.A_audit_report_vNNN.md preferred, SYS-NN.R_review_report_vNNN.md legacy), ADR (for architecture alignment)

Downstream: Fixed SYS, Fix Report (SYS-NN.F_fix_report_vNNN.md)

When to Use This Skill

Use doc-sys-fixer when:

• After Review: Run after doc-sys-reviewer identifies issues
• Iterative Improvement: Part of Review -> Fix -> Review cycle
• Automated Pipeline: CI/CD integration for quality gates
• Batch Fixes: Apply fixes to multiple SYS documents based on review reports

Do NOT use when:

• No audit/review report exists (run doc-sys-audit or doc-sys-reviewer first)
• Creating new SYS (use doc-sys or doc-sys-autopilot)
• Only need validation (use doc-sys-validator)

Skill Dependencies

Workflow Overview

flowchart TD
    A[Input: SYS Path] --> B[Find Latest Review Report]
    B --> C{Review Found?}
  C -->|No| D[Run doc-sys-audit or doc-sys-reviewer First]
    C -->|Yes| E[Parse Review Report]

    E --> F[Categorize Issues]

    subgraph FixPhases["Fix Phases"]
        F --> F0[Phase 0: Fix Structure Violations]
        F0 --> G[Phase 1: Create Missing Files]
        G --> H[Phase 2: Fix Broken Links]
        H --> I[Phase 3: Fix Element IDs]
        I --> J[Phase 4: Fix Content Issues]
        J --> K[Phase 5: Update References]
        K --> K2[Phase 6: Handle Upstream Drift]
    end

    K2 --> L[Write Fixed SYS]
    L --> M[Generate Fix Report]
    M --> N{Re-run Review?}
    N -->|Yes| O[Invoke doc-sys-reviewer]
    O --> P{Score >= Threshold?}
    P -->|No, iterations < max| F
    P -->|Yes| Q[COMPLETE]
    N -->|No| Q

Fix Phases

Phase 0: Fix Structure Violations (CRITICAL)

Fixes SYS documents that are not in nested folders. This phase runs FIRST because all subsequent phases depend on correct folder structure.

Nested Folder Rule: ALL SYS documents MUST be in nested folders regardless of document size.

Required Structure:

Fix Actions:

Structure Fix Workflow:

def fix_sys_structure(sys_path: str) -> list[Fix]:
    """Fix SYS structure violations."""
    fixes = []

    filename = os.path.basename(sys_path)
    parent_folder = os.path.dirname(sys_path)

    # Extract SYS ID and slug from filename
    match = re.match(r'SYS-(\d+)_([^/]+)\.md', filename)
    if not match:
        return []  # Cannot auto-fix invalid filename

    sys_id = match.group(1)
    slug = match.group(2)
    expected_folder = f"SYS-{sys_id}_{slug}"

    # Check if already in nested folder
    if os.path.basename(parent_folder) != expected_folder:
        # Create nested folder
        new_folder = os.path.join(os.path.dirname(parent_folder), expected_folder)
        os.makedirs(new_folder, exist_ok=True)

        # Move file
        new_path = os.path.join(new_folder, filename)
        shutil.move(sys_path, new_path)
        fixes.append(f"Moved {sys_path} to {new_path}")

        # Update upstream links in moved file
        content = Path(new_path).read_text()
        updated_content = content.replace('../05_ADR/', '../../05_ADR/')
        updated_content = updated_content.replace('../04_BDD/', '../../04_BDD/')
        Path(new_path).write_text(updated_content)
        fixes.append(f"Updated relative links for nested folder structure")

    return fixes

Link Path Updates After Move:

Phase 1: Create Missing Files

Creates files that are referenced but don’t exist.

Scope:

SYS Index Template:

---
title: "SYS-00: System Design Specifications Index"
tags:
  - sys
  - index
  - reference
custom_fields:
  document_type: index
  artifact_type: SYS-REFERENCE
  layer: 6
---

# SYS-00: System Design Specifications Index

Master index of all System Design Specifications for this project.

## System Components

| SYS ID | Component | Status | Last Updated | ADR Refs |
|--------|-----------|--------|--------------|----------|
| SYS-01 | [Name] | Draft/Final | YYYY-MM-DD | ADR-01, ADR-02 |

## Component Relationships

| Component | Depends On | Depended By |
|-----------|------------|-------------|
| SYS-01 | | |

## Interface Catalog

| Interface ID | Type | Provider | Consumer |
|--------------|------|----------|----------|
| INT-01 | API | SYS-01 | SYS-02 |

---

*Maintained by doc-sys-fixer. Update when adding new SYS documents.*

Component Placeholder Template:

---
title: "Component Specification: [Component Name]"
tags:
  - component
  - system-design
  - reference
custom_fields:
  document_type: component
  status: placeholder
  created_by: doc-sys-fixer
---

# Component Specification: [Component Name]

> **Status**: Placeholder - Requires completion

## 1. Overview

[TODO: Document component overview]

## 2. Responsibilities

| Responsibility | Description |
|----------------|-------------|
| [Name] | [What it handles] |

## 3. Interfaces

| Interface | Type | Direction | Connected To |
|-----------|------|-----------|--------------|
| [Name] | REST/gRPC/Event | In/Out | [Component] |

## 4. Data Structures

[TODO: Document key data structures]

## 5. Architecture Decisions

| ADR | Title | Impact |
|-----|-------|--------|
| ADR-NN | [Title] | [How it affects this component] |

---

*Created by doc-sys-fixer as placeholder. Complete this document to resolve broken link issues.*

Interface Placeholder Template:

---
title: "Interface Specification: [Interface Name]"
tags:
  - interface
  - system-design
  - reference
custom_fields:
  document_type: interface
  status: placeholder
  created_by: doc-sys-fixer
---

# Interface Specification: [Interface Name]

> **Status**: Placeholder - Requires completion

## 1. Overview

[TODO: Document interface purpose]

## 2. Protocol

| Attribute | Value |
|-----------|-------|
| Type | REST / gRPC / Event / Message |
| Format | JSON / Protobuf / Avro |
| Authentication | JWT / API Key / mTLS |

## 3. Operations

| Operation | Method | Path/Topic | Description |
|-----------|--------|------------|-------------|
| [Name] | GET/POST | /path | [Description] |

## 4. Data Models

[TODO: Document request/response models]

---

*Created by doc-sys-fixer as placeholder. Complete this document to resolve broken link issues.*

Phase 2: Fix Broken Links

Updates links to point to correct locations.

Fix Actions:

Path Resolution Logic:

def fix_link_path(sys_location: str, target_path: str) -> str:
    """Calculate correct relative path based on SYS location."""

    # Monolithic SYS: docs/06_SYS/SYS-01.md
    # Sectioned SYS: docs/06_SYS/SYS-01_slug/SYS-01.3_section.md

    if is_sectioned_sys(sys_location):
        # Need to go up one more level
        return "../" + calculate_relative_path(sys_location, target_path)
    else:
        return calculate_relative_path(sys_location, target_path)

Cross-Layer Link Fix:

Phase 3: Fix Element IDs

Converts invalid element IDs to correct format.

Conversion Rules:

Type Code Mapping (SYS-specific valid codes: 01, 05, 17, 18, 19, 20, 21):

Invalid Code Conversions:

Regex Patterns:

# Find element IDs with invalid type codes for SYS
invalid_sys_type_06 = r'SYS\.(\d{2})\.06\.(\d{2})'
replacement_06 = r'SYS.\1.01.\2'

invalid_sys_type_13 = r'SYS\.(\d{2})\.13\.(\d{2})'
replacement_13 = r'SYS.\1.17.\2'

# Find legacy patterns
legacy_comp = r'###\s+COMP-(\d+):'
legacy_int = r'###\s+INT-(\d+):'
legacy_mod = r'###\s+MOD-(\d+):'
legacy_dep = r'###\s+DEP-(\d+):'
legacy_flow = r'###\s+FLOW-(\d+):'

Phase 4: Fix Content Issues

Addresses placeholders and incomplete content.

Fix Actions:

Auto-Replacements:

replacements = {
    'YYYY-MM-DDTHH:MM:SS': datetime.now().strftime('%Y-%m-%dT%H:%M:%S'),
    'YYYY-MM-DD': datetime.now().strftime('%Y-%m-%d'),
    'MM/DD/YYYY': datetime.now().strftime('%m/%d/%Y'),
    '[Current date]': datetime.now().strftime('%Y-%m-%dT%H:%M:%S'),
    '[Status]': 'Draft',
    '[Version]': '0.1',
}

SYS-Specific Content Fixes:

Phase 5: Update References

Ensures traceability and cross-references are correct.

Fix Actions:

Traceability Matrix Update:

## Traceability

| SYS Element | Traces From | Traces To | Type |
|-------------|-------------|-----------|------|
| SYS.01.17.01 | ADR.01.14.01 | REQ.01.01.01 | Component->Requirement |
| SYS.01.18.01 | ADR.01.14.02 | CTR.01.09.01 | Interface->Contract |

Phase 6: Handle Upstream Drift (Auto-Merge)

Addresses issues where upstream source documents (ADR) have changed since SYS creation. Uses a tiered auto-merge system based on change percentage.

6.0.1 Hash Validation Fixes

FIX-H001: Invalid Hash Placeholder

Trigger: Hash contains placeholder instead of SHA-256

Fix:

sha256sum <upstream_file_path> | cut -d' ' -f1

Update cache with: sha256:<64_hex_output>

FIX-H002: Missing Hash Prefix

Trigger: 64 hex chars but missing sha256: prefix

Fix: Prepend sha256: to value

FIX-H003: Upstream File Not Found

Trigger: Cannot compute hash (file missing)

Fix: Set drift_detected: true, add to manual review

Upstream: ADR (Architecture Decision Records) Downstream: REQ (Requirements Specifications) ID Pattern: SYS.NN.TT.SS (Document.Type.Sequence)

Tiered Auto-Merge System

Change Percentage Calculation

def calculate_change_percentage(upstream_diff: dict) -> float:
    """Calculate change percentage from upstream ADR modifications.

    Args:
        upstream_diff: Dict containing added, modified, deprecated counts

    Returns:
        Change percentage (0.0 to 100.0)
    """
    total_elements = upstream_diff.get('total_elements', 0)
    if total_elements == 0:
        return 0.0

    added = upstream_diff.get('added', 0)
    modified = upstream_diff.get('modified', 0)
    deprecated = upstream_diff.get('deprecated', 0)

    # Additions count less than modifications
    weighted_changes = (added * 0.5) + (modified * 1.0) + (deprecated * 0.3)

    return min(100.0, (weighted_changes / total_elements) * 100)

Tier 1: Auto-Merge Additions (< 5%)

Trigger: Minor additions from ADR that do not affect existing SYS elements.

Actions:

1. Parse new ADR decisions/constraints
2. Generate new SYS element IDs (auto-increment sequence)
3. Insert new elements in appropriate sections
4. Increment patch version (e.g., 1.0.0 -> 1.0.1)

Auto-Generated ID Pattern:

def generate_sys_id(sys_doc_num: str, type_code: str, existing_ids: list) -> str:
    """Generate next available SYS element ID.

    Args:
        sys_doc_num: Document number (e.g., "01")
        type_code: Element type code (e.g., "17" for Component)
        existing_ids: List of existing IDs for this type

    Returns:
        Next available ID (e.g., "SYS.01.17.13")
    """
    # Extract sequence numbers from existing IDs
    sequences = [int(id.split('.')[-1]) for id in existing_ids
                 if id.startswith(f'SYS.{sys_doc_num}.{type_code}.')]

    next_seq = max(sequences, default=0) + 1
    return f'SYS.{sys_doc_num}.{type_code}.{next_seq:02d}'

# Example: If SYS-01 has SYS.01.17.01 through SYS.01.17.12
# New ID: SYS.01.17.13

Tier 1 Fix Report Entry:

## Tier 1 Auto-Merge Applied

| ADR Source | New SYS Element | Section | Description |
|------------|-----------------|---------|-------------|
| ADR-01.14.05 | SYS.01.17.13 | Components | New auth cache component |
| ADR-01.14.06 | SYS.01.18.08 | Interfaces | New event bus interface |

**Version**: 1.0.0 -> 1.0.1
**Change Percentage**: 3.2%

Tier 2: Auto-Merge with Changelog (5-15%)

Trigger: Moderate changes requiring documentation but not restructuring.

Actions:

1. Apply all Tier 1 actions
2. Generate detailed changelog section
3. Update traceability matrix
4. Add [MODIFIED] markers to affected elements
5. Increment minor version (e.g., 1.0.1 -> 1.1.0)

Changelog Format:

## Changelog (Auto-Generated)

### Version 1.1.0 (2026-02-10)

**Upstream Trigger**: ADR-01.md v2.0 (modified 2026-02-09)

#### Added
- SYS.01.17.13: Authentication cache component (from ADR-01.14.05)
- SYS.01.17.14: Rate limiting component (from ADR-01.14.06)
- SYS.01.18.08: Event bus interface (from ADR-01.14.07)

#### Modified
- SYS.01.17.03: Updated auth flow to include cache [MODIFIED]
- SYS.01.18.02: Added rate limit headers to API interface [MODIFIED]

#### Deprecated
- None

**Traceability Impact**: 5 REQ elements may need review

Modified Element Marker:

### SYS.01.17.03: Authentication Service [MODIFIED]

<!-- MODIFIED: 2026-02-10 via auto-merge from ADR-01.14.05 -->
<!-- Previous version: 1.0.1 -->

**Component**: Authentication Service
**Status**: Active
**Modified Reason**: ADR-01 added caching requirement

[Component details...]

Tier 3: Archive and Regenerate (> 15%)

Trigger: Significant upstream changes requiring SYS restructuring.

Actions:

1. Create archive of current SYS version
2. Generate archive manifest
3. Flag for regeneration via doc-sys-autopilot
4. Increment major version (e.g., 1.1.0 -> 2.0.0)
5. Preserve deprecated elements with [DEPRECATED] markers

Archive Manifest Format:

{
  "archive_id": "SYS-01_v1.1.0_20260210",
  "archive_date": "2026-02-10T16:30:00",
  "archived_version": "1.1.0",
  "new_version": "2.0.0",
  "archive_location": "tmp/archive/SYS-01_v1.1.0_20260210/",
  "trigger": {
    "upstream_document": "ADR-01.md",
    "upstream_version": "3.0",
    "change_percentage": 23.5,
    "tier": 3
  },
  "preserved_files": [
    "SYS-01.md",
    "SYS-01.1_components.md",
    "SYS-01.2_interfaces.md"
  ],
  "regeneration_required": true,
  "regeneration_command": "/doc-sys-autopilot ADR-01 --from-archive SYS-01_v1.1.0_20260210"
}

Archive Directory Structure:

tmp/archive/SYS-01_v1.1.0_20260210/
├── MANIFEST.json
├── SYS-01.md
├── SYS-01.1_components.md
├── SYS-01.2_interfaces.md
├── .drift_cache.json
└── CHANGELOG.md

No-Deletion Policy

Elements are NEVER deleted during auto-merge. Instead, mark as deprecated:

Deprecated Element Format:

### SYS.01.17.05: Legacy Cache Service [DEPRECATED]

<!-- DEPRECATED: 2026-02-10 -->
<!-- Deprecation Reason: Superseded by SYS.01.17.13 per ADR-01.14.05 -->
<!-- Replaced By: SYS.01.17.13 -->
<!-- Original Version: 1.0.0 -->

> **Status**: DEPRECATED - Do not use in new implementations
> **Superseded By**: [SYS.01.17.13](#sys011713-authentication-cache)
> **Deprecation Date**: 2026-02-10

[Original content preserved for reference...]

Deprecation Tracking:

## Deprecated Elements

| Element ID | Deprecated | Reason | Replaced By |
|------------|------------|--------|-------------|
| SYS.01.17.05 | 2026-02-10 | ADR-01.14.05 supersedes | SYS.01.17.13 |
| SYS.01.18.03 | 2026-02-10 | Interface redesign | SYS.01.18.08 |

Enhanced Drift Cache

After processing drift issues, update .drift_cache.json with merge history:

{
  "sys_version": "1.1.0",
  "sys_updated": "2026-02-10T16:30:00",
  "drift_reviewed": "2026-02-10T16:30:00",
  "upstream_type": "ADR",
  "downstream_type": "REQ",
  "upstream_hashes": {
    "../../05_ADR/ADR-01.md": "a1b2c3d4e5f6...",
    "../../05_ADR/ADR-01.md#decision-3": "g7h8i9j0k1l2...",
    "../../05_ADR/ADR-03.md": "m3n4o5p6q7r8..."
  },
  "merge_history": [
    {
      "merge_date": "2026-02-10T16:30:00",
      "tier": 2,
      "change_percentage": 8.5,
      "version_before": "1.0.1",
      "version_after": "1.1.0",
      "elements_added": ["SYS.01.17.13", "SYS.01.18.08"],
      "elements_modified": ["SYS.01.17.03", "SYS.01.18.02"],
      "elements_deprecated": [],
      "upstream_trigger": "ADR-01.md v2.0"
    }
  ],
  "acknowledged_drift": [
    {
      "document": "ADR-03.md",
      "acknowledged_date": "2026-02-08",
      "reason": "Informational only - no SYS impact"
    }
  ],
  "pending_regeneration": null
}

Drift Detection Issue Codes

Drift Fix Workflow

flowchart TD
    A[Detect ADR Changes] --> B[Calculate Change %]
    B --> C{Change < 5%?}
    C -->|Yes| D[Tier 1: Auto-Merge]
    C -->|No| E{Change < 15%?}
    E -->|Yes| F[Tier 2: Merge + Changelog]
    E -->|No| G[Tier 3: Archive + Regenerate]

    D --> H[Generate New IDs]
    H --> I[Insert Elements]
    I --> J[Patch Version ++]

    F --> K[Apply Tier 1 Actions]
    K --> L[Generate Changelog]
    L --> M[Add MODIFIED Markers]
    M --> N[Minor Version ++]

    G --> O[Create Archive]
    O --> P[Generate Manifest]
    P --> Q[Mark for Regeneration]
    Q --> R[Major Version ++]

    J --> S[Update Drift Cache]
    N --> S
    R --> S
    S --> T[Generate Fix Report]

Command Options for Drift Handling

Command Usage

Basic Usage

# Fix SYS based on latest review
/doc-sys-fixer SYS-01

# Fix with explicit review report
/doc-sys-fixer SYS-01 --review-report SYS-01.R_review_report_v001.md

# Fix and re-run review
/doc-sys-fixer SYS-01 --revalidate

# Fix with iteration limit
/doc-sys-fixer SYS-01 --revalidate --max-iterations 3

Options

Fix Types

Output Artifacts

Fix Report

Nested Folder Rule: ALL SYS use nested folders (SYS-NN_{slug}/) regardless of size. Fix reports are stored alongside the SYS document in the nested folder.

File Naming: SYS-NN.F_fix_report_vNNN.md

Location: Inside the SYS nested folder: docs/06_SYS/SYS-NN_{slug}/

Structure:

---
title: "SYS-NN.F: Fix Report v001"
tags:
  - sys
  - fix-report
  - quality-assurance
custom_fields:
  document_type: fix-report
  artifact_type: SYS-FIX
  layer: 6
  parent_doc: SYS-NN
  source_review: SYS-NN.R_review_report_v001.md
  fix_date: "YYYY-MM-DDTHH:MM:SS"
  fix_tool: doc-sys-fixer
  fix_version: "1.0"
---

# SYS-NN Fix Report v001

## Summary

| Metric | Value |
|--------|-------|
| Source Review | SYS-NN.R_review_report_v001.md |
| Issues in Review | 15 |
| Issues Fixed | 12 |
| Issues Remaining | 3 (manual review required) |
| Files Created | 3 |
| Files Modified | 4 |

## Files Created

| File | Type | Location |
|------|------|----------|
| SYS-00_INDEX.md | SYS Index | docs/06_SYS/ |
| COMP_AuthService.md | Component Placeholder | docs/00_REF/components/ |
| INT_UserAPI.md | Interface Placeholder | docs/00_REF/interfaces/ |

## Fixes Applied

| # | Issue Code | Issue | Fix Applied | File |
|---|------------|-------|-------------|------|
| 1 | REV-L001 | Broken index link | Created SYS-00_INDEX.md | SYS-01.md |
| 2 | REV-L001 | Broken component link | Created placeholder COMP file | SYS-01.md |
| 3 | REV-N004 | Element type 06 invalid | Converted to type 01 | SYS-01.md |
| 4 | REV-L003 | Absolute path used | Converted to relative | SYS-02.md |
| 5 | REV-N004 | Legacy COMP-XXX pattern | Converted to SYS.NN.17.SS | SYS-01.md |

## Issues Requiring Manual Review

| # | Issue Code | Issue | Location | Reason |
|---|------------|-------|----------|--------|
| 1 | REV-P001 | [TODO] placeholder | SYS-01:L67 | System expertise needed |
| 2 | REV-D001 | ADR drift detected | SYS-01:L145 | Review architecture changes |
| 3 | REV-R001 | Missing interface contract | SYS-01:L200 | Define API contract |

## Validation After Fix

| Metric | Before | After | Delta |
|--------|--------|-------|-------|
| Review Score | 85 | 94 | +9 |
| Errors | 4 | 0 | -4 |
| Warnings | 6 | 3 | -3 |

## Next Steps

1. Complete COMP_AuthService.md placeholder
2. Complete INT_UserAPI.md placeholder
3. Address remaining [TODO] placeholders
4. Review ADR drift and update system design if needed
5. Run `/doc-sys-reviewer SYS-01` to verify fixes

Integration with Autopilot

This skill is invoked by doc-sys-autopilot in the Review -> Fix cycle:

flowchart LR
    subgraph Phase5["Phase 5: Review & Fix Cycle"]
        A[doc-sys-reviewer] --> B{Score >= 90?}
        B -->|No| C[doc-sys-fixer]
        C --> D{Iteration < Max?}
        D -->|Yes| A
        D -->|No| E[Flag for Manual Review]
        B -->|Yes| F[PASS]
    end

Autopilot Integration Points:

Error Handling

Recovery Actions

Backup Strategy

Before applying any fixes:

1. Create backup in tmp/backup/SYS-NN_YYYYMMDD_HHMMSS/
2. Copy all SYS files to backup location
3. Apply fixes to original files
4. If error during fix, restore from backup

Related Skills

Version History