doc-spec-fixer

Purpose

Automated fix skill that reads the latest review report and applies fixes to SPEC (Specification) documents. This skill bridges the gap between doc-spec-reviewer (which identifies issues) and the corrected SPEC, enabling iterative improvement cycles.

Layer: 9 (SPEC Quality Improvement)

Upstream: REQ documents, CTR documents, SPEC document, Review Report (SPEC-NN.A_audit_report_vNNN.md preferred; SPEC-NN.R_review_report_vNNN.md legacy-compatible)

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

When to Use This Skill

Use doc-spec-fixer when:

• After Review: Run after doc-spec-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 SPECs based on review reports
• YAML Structure Issues: SPEC contains malformed YAML blocks

Do NOT use when:

• No review report exists (run doc-spec-reviewer first)
• Creating new SPEC (use doc-spec or doc-spec-autopilot)
• Only need validation (use doc-spec-validator)

Skill Dependencies

Workflow Overview

flowchart TD
    A[Input: SPEC Path] --> B[Find Latest Audit/Review Report]
    B --> C{Review Found?}
    C -->|No| D[Run doc-spec-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

    subgraph YAMLFix["YAML Structure Fixes"]
        K2 --> Y1[Parse YAML Blocks]
        Y1 --> Y2{YAML Valid?}
        Y2 -->|No| Y3[Repair YAML Structure]
        Y2 -->|Yes| Y4[Validate Schema Compliance]
        Y3 --> Y4
    end

    Y4 --> L[Write Fixed SPEC]
    L --> M[Generate Fix Report]
    M --> N{Re-run Review?}
    N -->|Yes| O[Invoke doc-spec-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 SPEC documents that are not in nested folders. This phase runs FIRST because all subsequent phases depend on correct folder structure.

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

Required Structure:

Fix Actions:

Structure Fix Workflow:

def fix_spec_structure(spec_path: str) -> list[Fix]:
    """Fix SPEC structure violations."""
    fixes = []

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

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

    spec_id = match.group(1)
    slug = match.group(2)
    expected_folder = f"SPEC-{spec_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(spec_path, new_path)
        fixes.append(f"Moved {spec_path} to {new_path}")

        # Update upstream references in YAML file
        content = Path(new_path).read_text()
        updated_content = content.replace('../08_CTR/', '../../08_CTR/')
        updated_content = updated_content.replace('../07_REQ/', '../../07_REQ/')
        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:

SPEC Schema Template:

# SPEC-NN: Schema Definitions
# Auto-generated by doc-spec-fixer - requires completion

schemas:
  version: "1.0.0"
  spec_id: SPEC-NN
  created: "YYYY-MM-DD"
  status: draft

definitions:
  # TODO: Add schema definitions
  ExampleSchema:
    type: object
    properties:
      id:
        type: string
        description: "Unique identifier"
    required:
      - id

validation_rules:
  # TODO: Define validation rules
  - rule_id: VR-001
    description: "Placeholder validation rule"
    severity: error

SPEC Configuration Template:

# SPEC-NN: Configuration Specification
# Auto-generated by doc-spec-fixer - requires completion

configuration:
  spec_id: SPEC-NN
  version: "1.0.0"
  created: "YYYY-MM-DD"

environments:
  development:
    # TODO: Add development settings
    log_level: debug

  staging:
    # TODO: Add staging settings
    log_level: info

  production:
    # TODO: Add production settings
    log_level: warn

feature_flags:
  # TODO: Define feature flags
  - name: placeholder_flag
    description: "Placeholder feature flag"
    default: false

Phase 2: Fix Broken Links

Updates links to point to correct locations.

Fix Actions:

Path Resolution Logic:

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

    # SPEC files: docs/09_SPEC/SPEC-01.md
    # Schema files: docs/09_SPEC/schemas/
    # Config files: docs/09_SPEC/config/

    if is_yaml_include(target_path):
        return fix_yaml_include(spec_location, target_path)
    elif is_schema_reference(target_path):
        return fix_schema_ref(spec_location, target_path)
    else:
        return calculate_relative_path(spec_location, target_path)

YAML Include Fix:

Phase 3: Fix Element IDs

Converts invalid element IDs to correct format.

SPEC Element ID Format:

SPEC documents are primarily YAML-based and use a different ID structure. Element IDs in SPEC follow the pattern: SPEC-NN.field.path for YAML elements.

Conversion Rules:

YAML Path ID Generation:

def generate_yaml_element_id(spec_id: str, yaml_path: list) -> str:
    """Generate element ID from YAML path.

    Example:
        spec_id: "SPEC-01"
        yaml_path: ["schemas", "definitions", "UserSchema"]
        returns: "SPEC-01.schemas.definitions.UserSchema"
    """
    return f"{spec_id}.{'.'.join(yaml_path)}"

ID Normalization:

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'),
    '"1.0.0"': f'"{calculate_version()}"',
}

YAML Structure Repair:

Phase 5: Update References

Ensures traceability and cross-references are correct.

Fix Actions:

REQ/CTR Traceability Fix:

<!-- Before -->
## 3. Schema Definitions

<!-- After -->
## 3. Schema Definitions

@req: [REQ-01.28.01](../07_REQ/REQ-01.md#req-01-28-01)
@ctr: [CTR-01-API](../08_CTR/CTR-01-API.md)

Phase 6: Handle Upstream Drift (Auto-Merge)

Addresses issues where upstream REQ/CTR documents have changed since SPEC creation using a tiered auto-merge system.

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

SPEC ID Pattern: SPEC-NN-COMPONENT-SS

• NN: Sequential spec number (01-99)
• COMPONENT: Component identifier (e.g., AUTH, API, DATA)
• SS: Sub-spec number within component (01-99)

Example: SPEC-01-AUTH-13, SPEC-02-API-05, SPEC-03-DATA-21

Drift Issue Codes (from doc-spec-reviewer):

Tiered Auto-Merge System

Tier 1: Minor Changes (< 5% drift)

Tier 2: Moderate Changes (5-15% drift)

Tier 3: Major Changes (> 15% drift)

Change Percentage Calculation

def calculate_drift_percentage(
    upstream_doc: str,
    spec_references: list,
    upstream_modified: datetime,
    spec_created: datetime
) -> float:
    """Calculate drift percentage between upstream and SPEC.

    Factors:
    - Line diff percentage in referenced sections
    - Number of new/removed requirements
    - Structural changes (new sections, moved content)
    - Time since last sync (decay factor)

    Returns:
        float: Drift percentage (0.0 - 100.0)
    """
    line_changes = count_line_changes(upstream_doc, spec_references)
    total_lines = count_referenced_lines(upstream_doc, spec_references)

    if total_lines == 0:
        return 0.0

    base_percentage = (line_changes / total_lines) * 100

    # Apply time decay factor (older drift = more significant)
    days_stale = (datetime.now() - spec_created).days
    decay_factor = min(1.0 + (days_stale / 30) * 0.1, 1.5)

    return min(base_percentage * decay_factor, 100.0)

Auto-Generated SPEC IDs

def generate_spec_id(
    spec_number: int,
    component: str,
    sub_spec: int
) -> str:
    """Generate SPEC ID following SPEC-NN-COMPONENT-SS pattern.

    Args:
        spec_number: Main spec number (1-99)
        component: Component identifier (e.g., AUTH, API, DATA)
        sub_spec: Sub-spec number (1-99)

    Returns:
        str: Formatted SPEC ID

    Example:
        generate_spec_id(1, "AUTH", 13) -> "SPEC-01-AUTH-13"
    """
    return f"SPEC-{spec_number:02d}-{component.upper()}-{sub_spec:02d}"

No-Deletion Policy

CRITICAL: SPECs are NEVER deleted. Mark as deprecated instead.

<!-- DEPRECATED: 2026-02-10 - Superseded by SPEC-01-AUTH-14 -->
<!-- Reason: Major upstream drift (>15%) triggered regeneration -->
<!-- Archive: archive/SPEC-01-AUTH-13_v1.2.0_20260210.md -->
---
title: "[DEPRECATED] SPEC-01-AUTH-13: Authentication Flow"
status: deprecated
superseded_by: SPEC-01-AUTH-14
---

Deprecation Rules:

Archive Manifest (Tier 3)

When Tier 3 triggers regeneration, create an archive manifest:

# archive/SPEC-01-AUTH-13_archive_manifest.yaml
archive_manifest:
  spec_id: SPEC-01-AUTH-13
  archived_version: "1.2.0"
  archive_date: "2026-02-10T16:00:00"
  archive_reason: "Major upstream drift (>15%)"

  drift_details:
    upstream_documents:
      - doc: REQ-01.md
        drift_percentage: 23.5
        lines_changed: 47
        sections_affected: [3, 5, 7]
      - doc: CTR-01-API.yaml
        drift_percentage: 18.2
        endpoints_changed: 5
        schemas_modified: 3

    total_drift: 20.85
    trigger_tier: 3

  archived_files:
    - source: docs/09_SPEC/SPEC-01-AUTH-13.md
      archive: archive/SPEC-01-AUTH-13_v1.2.0_20260210.md
    - source: docs/09_SPEC/schemas/SPEC-01-AUTH-13_schemas.yaml
      archive: archive/SPEC-01-AUTH-13_schemas_v1.2.0_20260210.yaml

  regeneration:
    triggered: true
    new_spec_id: SPEC-01-AUTH-14
    new_version: "2.0.0"

  downstream_impact:
    tspec_documents:
      - TSPEC-01-AUTH-13 (requires update)
    tasks_documents:
      - TASKS-01-AUTH-13 (requires review)

Enhanced Drift Cache

The .drift_cache.json file tracks drift state and merge history:

{
  "cache_version": "2.0",
  "last_updated": "2026-02-10T16:00:00",
  "specs": {
    "SPEC-01-AUTH-13": {
      "current_version": "1.2.0",
      "created": "2026-02-05T10:00:00",
      "last_sync": "2026-02-08T14:30:00",
      "upstream_refs": {
        "REQ-01.md": {
          "last_known_hash": "a1b2c3d4",
          "last_modified": "2026-02-08T09:00:00",
          "sections_tracked": ["3.1", "3.2", "5.4"]
        },
        "CTR-01-API.yaml": {
          "last_known_hash": "e5f6g7h8",
          "last_modified": "2026-02-07T16:00:00",
          "endpoints_tracked": ["/auth/login", "/auth/refresh"]
        }
      },
      "merge_history": [
        {
          "date": "2026-02-06T11:00:00",
          "tier": 1,
          "drift_percentage": 3.2,
          "version_before": "1.0.0",
          "version_after": "1.0.1",
          "changes_merged": ["REQ-01.md: Updated validation rules"]
        },
        {
          "date": "2026-02-08T14:30:00",
          "tier": 2,
          "drift_percentage": 8.5,
          "version_before": "1.0.1",
          "version_after": "1.1.0",
          "changes_merged": [
            "REQ-01.md: Added new requirement REQ-01.28.05",
            "CTR-01-API.yaml: Modified /auth/refresh response"
          ],
          "changelog_file": "changelogs/SPEC-01-AUTH-13_v1.1.0_changelog.md"
        }
      ],
      "downstream_documents": {
        "tspec": ["TSPEC-01-AUTH-13"],
        "tasks": ["TASKS-01-AUTH-13"]
      }
    }
  }
}

YAML Spec Format Handling

SPEC documents use embedded YAML blocks. Drift handling preserves YAML structure:

# Merged YAML section with drift metadata
schemas:
  _drift_metadata:
    last_merge: "2026-02-08T14:30:00"
    merge_tier: 2
    upstream_version: "REQ-01.md@v1.3.0"

  AuthRequest:
    type: object
    properties:
      username:
        type: string
        # @merged: 2026-02-08 from REQ-01.28.01
        minLength: 3
        maxLength: 64
      password:
        type: string
        format: password
        # @merged: 2026-02-08 from REQ-01.28.02 (new validation)
        minLength: 12

Fix Actions by Tier

Drift Marker Format (Updated for v2.0):

<!-- DRIFT-MERGED: Tier 1 | REQ-01.md | 3.2% | 2026-02-08 | v1.0.0 -> v1.0.1 -->
@req: [REQ-01.28.01](../07_REQ/REQ-01.md#req-01-28-01) @version:1.3.0

<!-- DRIFT-MERGED: Tier 2 | CTR-01-API.yaml | 8.5% | 2026-02-08 | v1.0.1 -> v1.1.0 -->
<!-- See: changelogs/SPEC-01-AUTH-13_v1.1.0_changelog.md -->
@ctr: [CTR-01-API](../08_CTR/CTR-01-API.md) @version:2.1.0

<!-- DRIFT-ARCHIVED: Tier 3 | 20.85% | 2026-02-10 | Regeneration triggered -->
<!-- Archive: archive/SPEC-01-AUTH-13_v1.2.0_20260210.md -->
<!-- New SPEC: SPEC-01-AUTH-14 -->

YAML Structure Fixes

SPEC documents heavily rely on embedded YAML. This section details specific YAML repair strategies.

YAML Block Detection

def find_yaml_blocks(content: str) -> list:
    """Find all YAML code blocks in markdown content."""
    pattern = r'```ya?ml\n(.*?)```'
    return re.findall(pattern, content, re.DOTALL)

Schema Validation

Common YAML Fixes

Command Usage

Basic Usage

# Fix SPEC based on latest review
/doc-spec-fixer SPEC-01

# Fix with explicit review report
/doc-spec-fixer SPEC-01 --review-report SPEC-01.R_review_report_v001.md

# Fix and re-run review
/doc-spec-fixer SPEC-01 --revalidate

# Fix with iteration limit
/doc-spec-fixer SPEC-01 --revalidate --max-iterations 3

# Fix YAML only
/doc-spec-fixer SPEC-01 --fix-types yaml

Options

Fix Types

Output Artifacts

Fix Report

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

File Naming: SPEC-NN.F_fix_report_vNNN.md

Upstream Selection Precedence:

1. Select newest report timestamp.
2. If timestamps are equal, prefer .A_audit_report over .R_review_report.

Location: Inside the SPEC nested folder: docs/09_SPEC/SPEC-NN_{slug}/

Structure:

---
title: "SPEC-NN.F: Fix Report v001"
tags:
  - spec
  - fix-report
  - quality-assurance
custom_fields:
  document_type: fix-report
  artifact_type: SPEC-FIX
  layer: 9
  parent_doc: SPEC-NN
  source_review: SPEC-NN.A_audit_report_v001.md
  fix_date: "YYYY-MM-DDTHH:MM:SS"
  fix_tool: doc-spec-fixer
  fix_version: "1.0"
---

# SPEC-NN Fix Report v001

## Summary

| Metric | Value |
|--------|-------|
| Source Review | SPEC-NN.R_review_report_v001.md |
| Issues in Review | 18 |
| Issues Fixed | 15 |
| Issues Remaining | 3 (manual review required) |
| Files Created | 2 |
| Files Modified | 1 |
| YAML Blocks Repaired | 4 |

## Files Created

| File | Type | Location |
|------|------|----------|
| SPEC-01_schemas.yaml | Schema Definitions | docs/09_SPEC/schemas/ |
| SPEC-01_config.yaml | Configuration Spec | docs/09_SPEC/config/ |

## YAML Repairs

| Block Location | Issue | Repair Applied |
|----------------|-------|----------------|
| Line 45-62 | Invalid indentation | Fixed to 2-space |
| Line 98-105 | Missing quotes | Added quotes to values |
| Line 142-150 | Duplicate key | Removed duplicate |
| Line 201-215 | Invalid boolean | Converted to true/false |

## Fixes Applied

| # | Issue Code | Issue | Fix Applied | File |
|---|------------|-------|-------------|------|
| 1 | REV-L006 | Broken YAML include | Updated include path | SPEC-01.md |
| 2 | REV-Y001 | Invalid YAML syntax | Repaired 4 blocks | SPEC-01.md |
| 3 | REV-L003 | Absolute path used | Converted to relative | SPEC-01.md |

## Issues Requiring Manual Review

| # | Issue Code | Issue | Location | Reason |
|---|------------|-------|----------|--------|
| 1 | REV-P001 | [TODO] placeholder | SPEC-01.md:L78 | Domain knowledge needed |
| 2 | REV-D002 | REQ content changed | REQ-01.28.01 | Review requirement update |

## Upstream Drift Summary

| Upstream Document | Reference | Modified | SPEC Updated | Days Stale | Action Required |
|-------------------|-----------|----------|--------------|------------|-----------------|
| REQ-01.md | SPEC-01:L57 | 2026-02-08 | 2026-02-05 | 3 | Review for changes |
| CTR-01-API.yaml | SPEC-01:L92 | 2026-02-09 | 2026-02-05 | 4 | Review for changes |

## Validation After Fix

| Metric | Before | After | Delta |
|--------|--------|-------|-------|
| Review Score | 85 | 95 | +10 |
| Errors | 5 | 0 | -5 |
| Warnings | 6 | 2 | -4 |
| YAML Valid | No | Yes | Fixed |

## Next Steps

1. Complete [TODO] placeholders in SPEC-01.md
2. Review upstream REQ/CTR drift
3. Populate schema definitions in SPEC-01_schemas.yaml
4. Run `/doc-spec-reviewer SPEC-01` to verify fixes

Integration with Autopilot

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

flowchart LR
    subgraph Phase5["Phase 5: Review & Fix Cycle"]
        A[doc-spec-reviewer] --> B{Score >= 90?}
        B -->|No| C[doc-spec-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/SPEC-NN_YYYYMMDD_HHMMSS/
2. Copy all SPEC files to backup location
3. Apply fixes to original files
4. If error during fix, restore from backup

Related Skills

Version History