# Harness Docs Pipeline

> Harness Docs Pipeline

- Skill: `intense-visions/harness-docs-pipeline` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add intense-visions/harness-docs-pipeline`
- Raw SKILL.md: https://api.skillmd.com/api/skills/intense-visions/harness-docs-pipeline/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: DevOps & Infra
- Author: Intense-Visions (https://skillmd.com/u/intense-visions)
- Updated: 2026-09-21
- Page: https://skillmd.com/skills/intense-visions/harness-docs-pipeline

---

# Harness Docs Pipeline

> Orchestrator composing 4 documentation skills into a sequential pipeline with convergence-based remediation, producing a qualitative documentation health report.

## When to Use

- When you want a single-command documentation health check across drift, coverage, links, and freshness
- After major refactoring that may have caused widespread documentation drift
- As a periodic hygiene check (weekly or per-sprint)
- When onboarding a new project that has no AGENTS.md (bootstrap mode)
- When `on_doc_check` triggers fire
- NOT for fixing a single known drift issue (use align-documentation directly)
- NOT for generating AGENTS.md from scratch when you know you have a graph (use harness-knowledge-mapper directly)
- NOT for validating a single file's context (use validate-context-engineering directly)

## Relationship to Sub-Skills

| Skill                        | Pipeline Phase | Role                                        |
| ---------------------------- | -------------- | ------------------------------------------- |
| detect-doc-drift             | DETECT         | Find drift between code and docs            |
| align-documentation          | FIX            | Apply fixes for drift findings              |
| validate-context-engineering | AUDIT          | Find gaps in documentation coverage         |
| harness-knowledge-mapper     | FILL           | Generate/regenerate AGENTS.md and fill gaps |

This orchestrator delegates to sub-skills — it never reimplements their logic. Each sub-skill retains full standalone functionality.

## Iron Law

**The pipeline delegates, never reimplements.** If you find yourself writing drift detection logic, fix application logic, or gap analysis logic inside the pipeline, STOP. Delegate to the dedicated sub-skill.

**Safe fixes are silent, unsafe fixes surface.** Never apply a fix classified as `unsafe` without explicit user approval. Never prompt the user for a fix classified as `safe`.

## Flags

| Flag           | Effect                                                            |
| -------------- | ----------------------------------------------------------------- |
| `--fix`        | Enable convergence-based auto-fix (default: detect + report only) |
| `--no-freshen` | Skip graph staleness check                                        |
| `--bootstrap`  | Force AGENTS.md regeneration even if one exists                   |
| `--ci`         | Non-interactive: apply safe fixes only, report everything else    |

## Shared Context Object

All phases read from and write to a shared `DocPipelineContext`:

```typescript
interface DocPipelineContext {
  // Pipeline state
  graphAvailable: boolean;
  agentsMdExists: boolean;
  bootstrapped: boolean; // true if AGENTS.md was created this run

  // Phase outputs
  driftFindings: DriftFinding[];
  fixesApplied: DocFix[];
  gapFindings: GapFinding[];
  fillsApplied: DocFix[];
  exclusions: Set<string>; // finding IDs already addressed

  // Health verdict
  verdict: 'pass' | 'warn' | 'fail';
  summary: string;
}

interface DriftFinding {
  id: string;
  file: string;
  line?: number;
  driftType: 'renamed' | 'new-code' | 'deleted-code' | 'changed-behavior' | 'moved-code';
  priority: 'critical' | 'high' | 'medium' | 'low';
  staleText: string;
  codeChange: string;
  suggestedFix: string;
  fixSafety: 'safe' | 'probably-safe' | 'unsafe';
}

interface GapFinding {
  id: string;
  file?: string;
  gapType: 'undocumented' | 'broken-link' | 'stale-section' | 'missing-context';
  priority: 'critical' | 'high' | 'medium' | 'low';
  description: string;
  suggestedFix: string;
  fixSafety: 'safe' | 'probably-safe' | 'unsafe';
}

interface DocFix {
  findingId: string;
  file: string;
  oldText: string;
  newText: string;
  safety: 'safe' | 'probably-safe';
  verified: boolean; // harness check-docs passed after applying
}
```

The context is passed to sub-skills via `handoff.json` with a `pipeline` field. Sub-skills check for this field; if absent, they run in standalone mode.

## Process

### Phase 1: FRESHEN — Graph Freshness and AGENTS.md Bootstrap

**Skip this phase if `--no-freshen` flag is set.**

1. **Check graph existence.** Look for `.harness/graph/` directory.
   - If exists: set `context.graphAvailable = true`
   - If not: set `context.graphAvailable = false`, log notice: "No knowledge graph available. Pipeline will use static analysis fallbacks. Run `harness scan` for richer results."

2. **Check graph staleness** (only if graph exists).
   - Count commits since last graph update: `git rev-list --count HEAD ^$(cat .harness/graph/.last-scan-commit 2>/dev/null || echo HEAD)`
   - If >10 commits behind: run `harness scan` to refresh
   - If <=10 commits: proceed with current graph

3. **Check AGENTS.md existence.**
   - If exists and `--bootstrap` not set: set `context.agentsMdExists = true`, proceed to DETECT
   - If exists and `--bootstrap` set: proceed to step 4 (regenerate)
   - If not exists: proceed to step 4

4. **Bootstrap AGENTS.md.**

   **If graph available:**
   - Invoke `harness-knowledge-mapper` to generate AGENTS.md
   - Set `context.bootstrapped = true`
   - Set `context.agentsMdExists = true`

   **If no graph (directory structure fallback):**
   - Glob source directories: `src/*/`, `packages/*/`, `lib/*/`
   - Read `package.json` for project name and description
   - Identify entry points: files matching `src/index.*`, `main` field in package.json
   - List top-level modules: each immediate subdirectory of `src/` (or `packages/`) with its directory name as the module name
   - Generate minimal AGENTS.md:

     ```markdown
     # AGENTS.md

     > Generated from directory structure. Run `harness scan` for richer output.

     ## Project

     <name from package.json> — <description from package.json>

     ## Entry Points

     - <each identified entry point>

     ## Modules

     - **<dir-name>/** — <inferred from directory name>
     ```

   - Set `context.bootstrapped = true`
   - Set `context.agentsMdExists = true`

5. Proceed to DETECT phase.

### Phase 2: DETECT — Find Documentation Drift

1. **Write pipeline context to handoff.json.** Set the `pipeline` field in `.harness/handoff.json` with the current `DocPipelineContext` so detect-doc-drift can read it.

2. **Invoke detect-doc-drift.** Run the skill's full process:
   - Phase 1 (Scan): `harness check-docs` and `harness cleanup --type drift`
   - Phase 2 (Identify): Classify each finding into drift types
   - Phase 3 (Prioritize): Rank by impact (Critical > High > Medium > Low)
   - Phase 4 (Report): Structured output

3. **Populate context with DriftFinding objects.** For each finding from detect-doc-drift, create a `DriftFinding` with:
   - `id`: deterministic hash of `file + line + driftType` (for dedup tracking)
   - `driftType`: map to one of `renamed`, `new-code`, `deleted-code`, `changed-behavior`, `moved-code`
   - `priority`: map to `critical`, `high`, `medium`, `low`
   - `fixSafety`: classify using the safety table below

4. **Store findings.** Set `context.driftFindings = <all DriftFinding objects>`.

5. **If `--fix` flag is not set:** Skip to AUDIT phase (Phase 4).

### Fix Safety Classification

| Category        | Safe (apply silently)                                              | Probably safe (present diff)                                                    | Unsafe (surface to user)                                          |
| --------------- | ------------------------------------------------------------------ | ------------------------------------------------------------------------------- | ----------------------------------------------------------------- |
| **Drift fixes** | Update file path where rename is unambiguous; fix import reference | Rewrite description for simple rename/parameter change; update code examples    | Rewrite behavioral explanations; remove sections for deleted code |
| **Gap fills**   | Add entry for new file with obvious single-purpose name            | Add entry for new file requiring description; update AGENTS.md section ordering | Write documentation for complex modules; create new doc pages     |
| **Link fixes**  | Redirect broken link where target is unambiguous                   | Redirect when multiple candidates exist (present options)                       | Remove link when target no longer exists                          |

### Phase 3: FIX — Convergence-Based Drift Remediation

**This phase runs only when `--fix` flag is set.**

#### Convergence Loop

```
previousCount = context.driftFindings.length
maxIterations = 5

while iteration < maxIterations:
  1. Partition findings by safety
  2. Apply safe fixes → verify → record
  3. Present probably-safe fixes → apply approved → verify → record
  4. Surface unsafe fixes to user (no auto-apply)
  5. Re-run detect-doc-drift
  6. newCount = remaining findings
  7. if newCount >= previousCount: STOP (converged)
  8. previousCount = newCount
  9. iteration++
```

#### Step-by-step

1. **Partition findings by fixSafety.**
   - `safeFixes`: findings where `fixSafety === 'safe'`
   - `probablySafeFixes`: findings where `fixSafety === 'probably-safe'`
   - `unsafeFixes`: findings where `fixSafety === 'unsafe'`

2. **Apply safe fixes silently.**
   - Write pipeline context to handoff.json with `pipeline.fixBatch = safeFixes`
   - Invoke align-documentation to apply the fixes
   - Run `harness check-docs` after the batch
   - If check passes: record each fix as a `DocFix` with `verified: true` in `context.fixesApplied`
   - If check fails: revert the batch (`git checkout -- <files>`), record fixes as `verified: false`
   - Add fixed finding IDs to `context.exclusions`

3. **Present probably-safe fixes** (skip in `--ci` mode).
   - For each fix, show the diff (oldText vs newText) to the user
   - Apply user-approved fixes
   - Run `harness check-docs` after the batch
   - Same verify/revert logic as safe fixes
   - Add fixed finding IDs to `context.exclusions`

4. **Surface unsafe fixes.**
   - List each unsafe finding with its `suggestedFix` text
   - Do not apply — user must handle manually
   - In `--ci` mode: log to report, do not prompt

5. **Re-run detect-doc-drift** to check for cascading issues revealed by fixes.
   - If new finding count < previous count: loop back to step 1
   - If new finding count >= previous count: stop (converged or no progress)
   - If max iterations reached: stop

6. **Record remaining unfixed findings** for the REPORT phase.

### Phase 4: AUDIT — Find Documentation Gaps

1. **Write pipeline context to handoff.json.** Update the `pipeline` field with the current `DocPipelineContext` (including `exclusions` from FIX phase).

2. **Invoke validate-context-engineering.** Run the skill's full process:
   - Phase 1 (Audit): `harness validate` and `harness check-docs`
   - Phase 2 (Detect Gaps): Classify into undocumented, broken-link, stale-section, missing-context
   - Phase 3 (Suggest Updates): Generate specific suggestions
   - Phase 4 (Apply): Deferred to FILL phase

3. **Populate context with GapFinding objects.** For each finding, create a `GapFinding` with:
   - `id`: deterministic hash of `file + gapType + description`
   - `gapType`: map to `undocumented`, `broken-link`, `stale-section`, `missing-context`
   - `priority`: map to `critical`, `high`, `medium`, `low`
   - `fixSafety`: classify using the safety table from DETECT phase

4. **Dedup against FIX phase.** Remove any `GapFinding` whose `id` appears in `context.exclusions`. This prevents double-counting items already fixed in the FIX phase.

5. **Store findings.** Set `context.gapFindings = <deduplicated GapFinding objects>`.

6. **If `--fix` flag is not set:** Skip to REPORT phase (Phase 6).

### Phase 5: FILL — Convergence-Based Gap Remediation

**This phase runs only when `--fix` flag is set.**

1. **Check if AGENTS.md needs regeneration.** If `context.bootstrapped === true` and gap findings include AGENTS.md coverage issues, invoke harness-knowledge-mapper (if graph available) or the directory-structure fallback to improve AGENTS.md quality.

2. **Run convergence loop** (same pattern as FIX phase):

   ```
   previousCount = context.gapFindings.length
   maxIterations = 5

   while iteration < maxIterations:
     1. Partition findings by safety
     2. Apply safe fills → verify → record
     3. Present probably-safe fills → apply approved → verify → record
     4. Surface unsafe fills to user
     5. Re-run validate-context-engineering
     6. newCount = remaining gaps (after dedup against exclusions)
     7. if newCount >= previousCount: STOP (converged)
     8. previousCount = newCount
     9. iteration++
   ```

3. **Apply safe fills silently.**
   - For `broken-link` with unambiguous target: redirect the link
   - For `undocumented` with obvious single-purpose name: add minimal entry
   - Run `harness check-docs` after each batch
   - Record in `context.fillsApplied`
   - Add filled finding IDs to `context.exclusions`

4. **Present probably-safe fills** (skip in `--ci` mode).
   - Show diff for: new file entries requiring description, AGENTS.md section reordering
   - Apply approved fills, verify, record

5. **Surface unsafe fills.**
   - Documentation for complex modules, new doc pages
   - Log for report, do not apply

6. **Record remaining unfilled gaps** for the REPORT phase.

### Phase 6: REPORT — Synthesize Health Verdict

1. **Run final `harness check-docs`** to establish the post-pipeline state.

2. **Compute verdict.**

   **FAIL if any of:**
   - Any critical drift findings remain unfixed
   - `harness check-docs` fails after all fix attempts
   - AGENTS.md does not exist and bootstrap failed

   **WARN if any of:**
   - High-priority drift or gap findings remain (user-deferred)
   - > 30% of source modules are undocumented
   - Graph not available (reduced accuracy notice)

   **PASS if:**
   - No critical or high findings remaining
   - `harness check-docs` passes
   - AGENTS.md exists and covers >70% of modules

3. **Generate per-category breakdown:**

   | Category  | Metric                                 |
   | --------- | -------------------------------------- |
   | Accuracy  | Drift findings remaining (by priority) |
   | Coverage  | Undocumented modules remaining         |
   | Links     | Broken references remaining            |
   | Freshness | Graph staleness status                 |

4. **List actions taken:**
   - Auto-fixes applied (safe): count and file list
   - User-approved fixes (probably-safe): count and file list
   - Findings deferred to user (unsafe): count and details
   - AGENTS.md bootstrapped: yes/no and method (graph or directory structure)

5. **Set context verdict and summary.** Write `context.verdict` and `context.summary`.

6. **Output report** to console. Format:

   ```
   === Documentation Health Report ===

   Verdict: PASS | WARN | FAIL

   Accuracy:  N drift findings remaining (0 critical, 0 high, N medium, N low)
   Coverage:  N/M modules documented (N%)
   Links:     N broken references remaining
   Freshness: Graph current | Graph stale (N commits behind) | No graph

   Actions:
     - N safe fixes applied silently
     - N probably-safe fixes applied (user-approved)
     - N unsafe findings deferred to user
     - AGENTS.md bootstrapped from <graph|directory structure>

   Remaining findings:
     [list of unfixed findings with priority and suggested action]
   ```

## Harness Integration

- **`harness check-docs`** — Run in DETECT, after each fix batch in FIX/FILL, and in REPORT for final state
- **`harness cleanup --type drift`** — Used by detect-doc-drift during DETECT phase
- **`harness scan`** — Used in FRESHEN to refresh stale graph
- **`harness validate`** — Run as final step in each task to verify project health

## Success Criteria

- `harness-docs-pipeline` runs all 4 sub-skills in the right order with shared context
- FIX and FILL phases iterate until converged; cascading fixes are caught
- Safe fixes are applied silently; unsafe changes surface to user
- `harness check-docs` runs after every fix batch; failed fixes are reverted
- Bootstrap handles cold start (no AGENTS.md) with graph path and directory structure fallback
- Standalone skills work independently exactly as today when invoked without pipeline context
- Entire pipeline runs without graph using static analysis fallbacks
- PASS/WARN/FAIL report includes per-category breakdown and specific remaining findings
- Drift fixes in FIX phase are excluded from AUDIT findings (no double-counting)

## Rationalizations to Reject

These are common rationalizations that sound reasonable but lead to incorrect results. When you catch yourself thinking any of these, stop and follow the documented process instead.

| Rationalization                                                                                               | Why It Is Wrong                                                                                                                                   |
| ------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- |
| "The drift finding is marked unsafe but the fix is obvious, so I will apply it silently"                      | Never apply a fix classified as unsafe without explicit user approval. The Iron Law: safe fixes are silent, unsafe fixes surface.                 |
| "The convergence loop reduced findings from 8 to 6, but the remaining ones are hard -- I will keep iterating" | If a convergence iteration does not reduce the finding count, stop immediately. Continuing without progress wastes iterations.                    |
| "I can write the drift detection logic directly instead of delegating to detect-doc-drift"                    | The pipeline delegates, never reimplements. Each sub-skill retains full standalone functionality.                                                 |
| "The graph is not available so the pipeline results will be unreliable"                                       | The entire pipeline runs without a graph using static analysis fallbacks. Reduced accuracy is noted in the report, not used as an excuse to skip. |

## Examples

### Example: Full pipeline run with fixes

```
Input: --fix flag set, graph available, AGENTS.md exists

1. FRESHEN  — Graph exists, 3 commits behind (< 10, skip refresh)
               AGENTS.md exists, no bootstrap needed
2. DETECT   — detect-doc-drift found 8 findings:
               2 critical (deleted file still referenced)
               3 high (renamed functions)
               2 medium (stale descriptions)
               1 low (formatting)
3. FIX      — Iteration 1:
                 3 safe fixes applied (renamed file paths)
                 2 probably-safe presented, 2 approved
                 2 unsafe surfaced to user
                 harness check-docs: pass
               Re-detect: 1 new finding (cascading rename)
               Iteration 2:
                 1 safe fix applied
                 Re-detect: 0 new findings — converged
4. AUDIT    — validate-context-engineering found 5 gaps
               2 already in exclusions (fixed in FIX) → 3 remaining
5. FILL     — 1 safe fill (broken link redirect)
               1 probably-safe (new module entry) → approved
               1 unsafe (complex module docs) → deferred
               Re-audit: converged
6. REPORT   — Verdict: WARN
               Accuracy: 2 drift findings remaining (0 critical, 0 high, 1 medium, 1 low)
               Coverage: 12/14 modules documented (86%)
               Links: 0 broken references
               Freshness: Graph current
```

### Example: CI mode (non-interactive)

```
Input: --fix --ci flags set, no graph

1. FRESHEN  — No graph (notice logged), AGENTS.md exists
2. DETECT   — 4 findings (1 critical, 2 high, 1 medium)
3. FIX      — 2 safe fixes applied silently
               probably-safe and unsafe: logged to report (no prompts)
4. AUDIT    — 2 gaps (1 deduped) → 1 remaining
5. FILL     — 0 safe fills, 1 probably-safe logged to report
6. REPORT   — Verdict: FAIL (1 critical finding remains)
```

### Example: Bootstrap from directory structure

```
Input: --bootstrap flag set, no graph, no AGENTS.md

1. FRESHEN  — No graph, no AGENTS.md
               Fallback bootstrap: glob src/*, read package.json
               Generated minimal AGENTS.md (32 lines)
               context.bootstrapped = true
2. DETECT   — 0 drift findings (fresh AGENTS.md, no stale refs)
3. AUDIT    — 6 gaps (4 undocumented modules, 2 missing context)
4. REPORT   — Verdict: WARN (>30% modules undocumented, no graph)
```

## Gates

- **No fix without verification.** Every fix batch must be followed by `harness check-docs`. If check fails, revert the batch.
- **No unsafe auto-apply.** Fixes classified as `unsafe` are never applied without explicit user approval. In `--ci` mode, they are logged but never applied.
- **No reimplementation of sub-skill logic.** The pipeline delegates to sub-skills. If the DETECT phase is writing drift detection code, the plan is wrong.
- **No convergence without progress.** If a convergence loop iteration does not reduce the finding count, stop immediately. Do not retry.
- **Max 5 iterations per convergence loop.** Hard cap to prevent runaway loops.

## Escalation

- **When findings exceed 50:** Focus on critical and high priority only. Defer medium and low to a follow-up run.
- **When bootstrap produces low-quality AGENTS.md:** This is expected without a graph. Log a notice recommending `harness scan` and accept the reduced quality for the current run.
- **When convergence loop does not converge within 5 iterations:** Stop the loop, log remaining findings, and proceed to the next phase. The report will reflect the unconverged state.
- **When a sub-skill fails:** Log the failure, skip the phase, and continue the pipeline. The report will note the skipped phase with a WARN or FAIL verdict.
- **When `harness check-docs` is unavailable:** Fall back to file existence checks and link validation via grep. Log a notice about reduced verification accuracy.