@harness-engineering/cli 1.7.0 → 1.8.1

package/dist/agents/skills/gemini-cli/cleanup-dead-code/SKILL.md

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+# Cleanup Dead Code
+
+> Entropy analysis and safe cleanup. Find unused exports, dead files, and pattern violations — then remove them without breaking anything.
+
+## When to Use
+
+- After a major refactoring or feature removal
+- When the codebase feels "heavy" — too many files, unclear what is used
+- As a periodic hygiene task (monthly or per-quarter)
+- When `on_entropy_check` triggers fire
+- After deleting a feature flag and its associated code paths
+- When `harness cleanup` reports growing entropy in the project health dashboard
+- NOT during active feature development — dead code cleanup is a separate, focused task
+- NOT when tests are failing — fix tests first, then clean up
+- NOT under time pressure — dead code removal requires careful verification
+
+## Process
+
+### Phase 1: Analyze — Run Entropy Report
+
+1. **Run `harness cleanup`** to generate a full entropy report. This analyzes:
+   - **Dead exports** — functions, classes, and constants that are exported but never imported anywhere
+   - **Unused files** — files that are not imported by any other file in the project
+   - **Pattern violations** — code that violates established project patterns (e.g., a service file without a corresponding test file)
+   - **Orphaned dependencies** — npm packages listed in package.json but never imported
+
+2. **Run `harness cleanup --type dead-code --json`** for machine-readable output focused specifically on unused code.
+
+3. **Review the report summary.** Note the total count and distribution. A few dead exports are normal; dozens suggest accumulated entropy from incomplete refactorings.
+
+### Graph-Enhanced Context (when available)
+
+When a knowledge graph exists at `.harness/graph/`, use graph queries for faster, more accurate dead code detection:
+
+- `query_graph` — perform graph reachability analysis from entry point nodes to identify truly unreachable code
+- `get_relationships` — distinguish dynamic imports from genuinely unused code by checking edge types
+
+Graph reachability reduces false positives compared to static analysis alone, since it traces the full transitive import graph including re-exports. Fall back to file-based commands if no graph is available.
+
+### Phase 2: Categorize — Safe vs. Needs Review
+
+**Safe to auto-fix (remove without further analysis):**
+
+- Exports that are not imported anywhere AND not referenced in any config file
+- Files that are not imported anywhere AND have no side effects (no top-level execution)
+- Dead exports (non-public, zero importers) -- remove `export` keyword or delete entirely if zero internal callers
+- Commented-out code blocks -- delete commented block (dead by definition, code is in git history)
+- Orphaned npm dependencies -- remove from package.json (probably safe; needs install+test verification)
+- Unused local variables and imports within a file (linter can catch these)
+
+**Needs human review before removal:**
+
+- Exports that APPEAR unused but might be consumed dynamically (see "What NOT to Delete" below)
+- Files that appear unused but are entry points (CLI scripts, test fixtures, config files)
+- Code that is only used in specific build configurations or environments
+- Exports from a public package — external consumers may depend on them
+
+### Phase 3: Apply Safe Fixes
+
+For each item categorized as safe:
+
+1. **Remove the dead code.** Delete the export, function, file, or import.
+
+2. **Run `harness fix-drift`** to update any documentation references that pointed to the deleted code.
+
+3. **Run the full test suite.** All tests must pass. If any test fails:
+   - **STOP.** The code was not actually dead — something depends on it.
+   - **Undo the deletion immediately.**
+   - **Reclassify** the item as "needs human review" and investigate the hidden dependency.
+
+4. **Run `harness validate` and `harness check-deps`.** Both must pass.
+
+5. **Commit the cleanup.** Group related removals into logical commits (e.g., "remove unused shipping utilities" not "delete dead code").
+
+**New fix types:**
+
+- **Dead exports (non-public):** Use `apply_fixes` with `fixTypes: ['dead-exports']`. The tool removes the `export` keyword. If the function/class has zero internal callers too, delete the entire declaration.
+- **Commented-out code:** Use `apply_fixes` with `fixTypes: ['commented-code']`. The tool deletes commented-out code blocks. This is cosmetic and only needs lint verification.
+- **Orphaned dependencies:** Use `apply_fixes` with `fixTypes: ['orphaned-deps']`. The tool removes the dep from package.json. **Must run `pnpm install && pnpm test` after** to verify nothing breaks.
+
+### Phase 3.5: Convergence Loop (Standalone)
+
+When running standalone (not through the orchestrator), apply a single-concern convergence loop:
+
+1. **Re-run detection.** After applying all safe fixes, run `harness cleanup --type dead-code` again.
+2. **Check if issue count decreased.** Compare the new count to the previous count.
+3. **If decreased: loop.** New dead code may have been exposed by the fixes (e.g., removing a dead export made a file fully unused). Go back to Phase 2 (Categorize) with the new report.
+4. **If unchanged: stop.** No more cascading fixes are possible. Proceed to Phase 4 (Report).
+5. **Maximum iterations: 5.** To prevent infinite loops, stop after 5 convergence cycles regardless.
+
+**Why convergence matters:** Removing dead code can create more dead code. For example:
+
+- Removing a dead export may make all remaining exports in a file dead, making the file itself dead.
+- Removing a dead file removes its imports, which may make other files' exports dead.
+- Removing an orphaned dep may cause lint warnings that reveal unused imports.
+
+### Phase 4: Report Remaining Items
+
+### Graph Refresh
+
+If a knowledge graph exists at `.harness/graph/`, refresh it after code changes to keep graph queries accurate:
+
+```
+harness scan [path]
+```
+
+Dead code removal changes graph topology — skipping this step means subsequent graph queries (impact analysis, dependency health, test advisor) may return stale results.
+
+For items that need human review, report:
+
+1. **What it is** — file path, export name, what it does
+2. **Why it appears dead** — no static imports found
+3. **Why it might not be dead** — dynamic import patterns, external consumers, test utilities
+4. **Recommended action** — delete with confidence, delete with caution, or keep
+
+## What NOT to Delete
+
+These patterns make code APPEAR dead when it is actually in use:
+
+### Dynamically imported modules
+
+```typescript
+// This import won't show up in static analysis
+const module = await import(`./plugins/${pluginName}`);
+```
+
+Files in a `plugins/` directory may appear unused but are loaded dynamically at runtime. Check for `import()` calls, `require()` with variables, and glob-based loading patterns.
+
+### Test utilities and fixtures
+
+```typescript
+// test-helpers.ts — only imported by test files
+export function createMockUser() { ... }
+```
+
+Test utility files may appear unused if the analysis excludes test files. Verify that `harness cleanup` includes test files in its import graph.
+
+### Type-only exports
+
+```typescript
+// Only used as a type, never as a value
+export interface UserConfig { ... }
+```
+
+Some analysis tools miss type-only imports (`import type { UserConfig }`). Verify before deleting any exported interface or type alias.
+
+### Package entry points
+
+```typescript
+// index.ts — re-exports for external consumers
+export { createClient } from './client';
+```
+
+The entry point of a package re-exports things for external consumers. These exports may have zero internal imports but are the public API.
+
+### Side-effect files
+
+```typescript
+// polyfills.ts — imported for side effects, not for exports
+import './polyfills';
+```
+
+Some files are imported for their side effects (polyfills, global registrations, CSS). They have no exports but are not dead.
+
+### Environment-specific code
+
+```typescript
+// Only used when FEATURE_FLAG_X is enabled
+if (process.env.FEATURE_FLAG_X) {
+  const handler = require('./experimental-handler');
+}
+```
+
+Code behind feature flags or environment checks may appear dead in the default configuration.
+
+## Harness Integration
+
+- **`harness cleanup`** — Full entropy analysis. Reports dead exports, unused files, pattern violations, and orphaned dependencies.
+- **`harness cleanup --type dead-code`** — Focused analysis on unused code specifically.
+- **`harness cleanup --type dead-code --json`** — Machine-readable output for automation.
+- **`harness fix-drift`** — Update documentation after removing dead code. Ensures deleted items are not still referenced in docs.
+- **`harness validate`** — Run after cleanup to verify project structure remains valid.
+- **`harness check-deps`** — Run after cleanup to verify no dependency violations were introduced.
+
+## Success Criteria
+
+- `harness cleanup` reports zero dead exports and zero unused files (or all remaining items are documented as intentional)
+- All tests pass after every deletion
+- `harness validate` and `harness check-deps` pass after cleanup
+- Documentation references to deleted code are updated or removed
+- No dynamically-imported, type-only, or side-effect code was accidentally deleted
+- Each cleanup commit is atomic and has a descriptive message explaining what was removed and why
+
+## Examples
+
+### Example: Removing unused utility functions
+
+**Entropy report:**
+
+```
+DEAD EXPORT: src/utils/string-helpers.ts
+  - capitalizeFirst() — 0 imports found
+  - truncateWithEllipsis() — 0 imports found
+  - slugify() — 3 imports found (ACTIVE, not dead)
+```
+
+**Action:** Remove `capitalizeFirst` and `truncateWithEllipsis` from the file. Keep `slugify`. Run tests — all pass. Commit: "remove unused capitalizeFirst and truncateWithEllipsis from string-helpers"
+
+### Example: Detecting a false positive
+
+**Entropy report:**
+
+```
+UNUSED FILE: src/plugins/markdown-renderer.ts
+  - 0 static imports found
+  - File contains: export default class MarkdownRenderer
+```
+
+**Investigation:** Check for dynamic imports:
+
+```typescript
+// src/plugins/index.ts
+const renderer = await import(`./${format}-renderer`);
+```
+
+**Result:** False positive. The file is loaded dynamically based on the `format` variable. Mark as intentional and add a comment in the file explaining the dynamic loading pattern.
+
+### Example: Orphaned npm dependency
+
+**Entropy report:**
+
+```
+ORPHANED DEPENDENCY: moment (package.json)
+  - 0 imports of 'moment' found in src/
+  - Last imported in commit abc123 (removed 3 months ago)
+```
+
+**Action:** Remove `moment` from package.json dependencies. Run `npm install` to update lockfile. Run tests — all pass. Commit: "remove unused moment dependency"
+
+## Escalation
+
+- **When removing code causes unexpected test failures:** The code has a hidden dependency. Undo the deletion, investigate the dependency chain, and document the finding. The code is not dead — it is just hard to trace.
+- **When the entropy report is very large (>50 items):** Do not attempt to clean everything at once. Pick the highest-confidence dead code (files with zero imports, no dynamic patterns) and clean those first. Schedule the rest across multiple sessions.
+- **When you are unsure if an export is used externally:** Check if the code is in a published package. If so, removing an export is a breaking change. Deprecate first, then remove in a major version.
+- **When dead code is tangled with live code in the same file:** Extract the live code first (using harness-refactoring), then delete the remaining dead code. Do not try to surgically remove dead code from a complex file in one step.

package/dist/agents/skills/gemini-cli/cleanup-dead-code/skill.yaml

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+name: cleanup-dead-code
+version: "1.1.0"
+description: Detect and auto-fix dead code including dead exports, commented-out code, and orphaned dependencies
+cognitive_mode: diagnostic-investigator
+triggers:
+  - manual
+platforms:
+  - claude-code
+  - gemini-cli
+tools:
+  - Bash
+  - Read
+  - Glob
+  - Grep
+cli:
+  command: harness skill run cleanup-dead-code
+  args:
+    - name: path
+      description: Project root path
+      required: false
+    - name: fix
+      description: Enable auto-fix with convergence loop
+      required: false
+mcp:
+  tool: run_skill
+  input:
+    skill: cleanup-dead-code
+    path: string
+type: flexible
+state:
+  persistent: false
+  files: []
+depends_on: []

package/dist/agents/skills/gemini-cli/detect-doc-drift/SKILL.md

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+# Detect Doc Drift
+
+> Detect documentation that has drifted from code. Find stale docs before they mislead developers and AI agents.
+
+## When to Use
+
+- After completing a feature, bug fix, or refactoring
+- During code review — check if the changed files have associated docs that need updating
+- As a periodic hygiene check (weekly or per-sprint)
+- When `on_post_feature` or `on_doc_check` triggers fire
+- When onboarding reveals confusion caused by outdated documentation
+- NOT during active development — wait until the code is stable before checking docs
+- NOT for writing new documentation from scratch (use align-documentation instead)
+
+## Process
+
+### Phase 1: Scan — Run Drift Detection
+
+1. **Run `harness check-docs`** to identify all documentation issues. Capture the full output.
+
+2. **Run `harness cleanup --type drift`** for a deeper analysis that cross-references code changes against documentation references.
+
+3. **Optionally, run `git diff` against a baseline** (last release, last sprint, etc.) to identify which code files changed. This helps prioritize — docs for recently changed files are most likely to be drifted.
+
+### Graph-Enhanced Context (when available)
+
+When a knowledge graph exists at `.harness/graph/`, use graph queries for faster, more accurate drift detection:
+
+- `query_graph` — find `documents` edges where the target code node has changed since the doc node was last updated
+
+When a graph is available, drift is simply stale edges: doc-to-code edges where the code side has been modified more recently than the doc side. This replaces regex pattern matching and catches semantic drift that text search misses. Fall back to file-based commands if no graph is available.
+
+### Pipeline Context (when orchestrated)
+
+When invoked by `harness-docs-pipeline`, check for a `pipeline` field in `.harness/handoff.json`:
+
+- If `pipeline` field exists: read `DocPipelineContext` from it
+  - Use `pipeline.exclusions` to skip findings that were already addressed in a previous phase
+  - Write `DriftFinding[]` results back to `pipeline.driftFindings` in handoff.json
+  - This enables the orchestrator to track findings across phases and avoid double-counting
+- If `pipeline` field does not exist: behave exactly as today (standalone mode)
+
+No changes to the skill's interface or output format — the pipeline field is purely additive.
+
+### Phase 2: Identify — Classify Drift Types
+
+Categorize each finding into one of these drift types:
+
+**Renamed but not updated:**
+A function, class, variable, or file was renamed in code, but documentation still references the old name. This is the most common type of drift.
+
+- Example: `calculateShipping()` was renamed to `computeShippingCost()`, but AGENTS.md and three inline comments still say `calculateShipping`.
+
+**New code with no docs:**
+A new module, function, or API was added but no documentation entry exists. This is not "drift" in the strict sense but a gap that grows into drift over time.
+
+- Example: `src/services/notification-service.ts` was added two sprints ago. It has 5 public exports. No AGENTS.md section, no doc page, no inline doc comments beyond basic JSDoc.
+
+**Deleted code still referenced:**
+A file, function, or feature was removed, but documentation still describes it as if it exists. This actively misleads readers.
+
+- Example: `src/utils/legacy-parser.ts` was deleted. The architecture doc still includes it in the data flow diagram. AGENTS.md still warns about its quirks.
+
+**Changed behavior not reflected:**
+A function's signature, return type, error handling, or side effects changed, but the documentation describes the old behavior.
+
+- Example: `createUser()` now throws `ValidationError` instead of returning `null` on invalid input. The API docs still say "returns null if validation fails."
+
+**Moved code with stale paths:**
+A file or module was moved to a different directory, but documentation references the old path.
+
+- Example: `src/helpers/format.ts` was moved to `src/utils/format.ts`. Three doc files and AGENTS.md reference the old path.
+
+### Phase 3: Prioritize — Rank by Impact
+
+Not all drift is equally harmful. Prioritize fixes:
+
+**Critical (fix immediately):**
+
+- Public API documentation that describes wrong behavior — external consumers will write broken code
+- AGENTS.md sections that reference deleted files — AI agents will hallucinate about non-existent code
+- README getting-started guides with wrong commands — new developers cannot onboard
+
+**High (fix before next release):**
+
+- Internal API docs with wrong signatures — developers waste time debugging
+- Architecture docs with stale diagrams — wrong mental models lead to wrong decisions
+- Frequently accessed docs with broken links — high-traffic pages with dead ends
+
+**Medium (fix in next sprint):**
+
+- Internal docs for stable code — low change rate means low confusion rate
+- Comments in rarely modified files — few people read them
+- Edge case documentation — affects few users
+
+**Low (fix when convenient):**
+
+- Stylistic inconsistencies in docs (capitalization, formatting)
+- Redundant documentation that says the same thing in multiple places
+- Historical notes that are outdated but clearly marked as historical
+
+### Phase 4: Report — Generate Actionable Output
+
+For each drift finding, provide:
+
+1. **File and line number** of the drifted documentation
+2. **The specific stale content** (quote the exact text that is wrong)
+3. **What changed in code** (the commit, file, and nature of the change)
+4. **Suggested fix** (the replacement text or action needed)
+5. **Priority tier** (Critical / High / Medium / Low)
+
+Group findings by documentation file so that fixes can be applied file-by-file.
+
+## Harness Integration
+
+- **`harness check-docs`** — Primary tool. Scans all documentation files for broken references, stale paths, and missing entries.
+- **`harness cleanup --type drift`** — Deeper analysis that cross-references git history with documentation references to detect semantic drift.
+- **`harness cleanup --type drift --json`** — Machine-readable output for automated pipelines.
+- **`harness fix-drift`** — Auto-fix simple drift issues after review (use align-documentation skill for applying fixes).
+
+## Success Criteria
+
+- `harness check-docs` reports zero errors
+- All file paths referenced in documentation resolve to existing files
+- All function/class names referenced in documentation match current code
+- All API documentation matches current function signatures and behavior
+- No documentation references deleted files, functions, or features
+- Drift findings are prioritized and assigned to the appropriate fix cycle
+
+## Examples
+
+### Example: Renamed function detected
+
+**Drift finding:**
+
+```
+DRIFT: Renamed reference detected
+  Doc: AGENTS.md:47
+  Stale text: "Use `calculateShipping()` to compute shipping costs"
+  Code change: calculateShipping renamed to computeShippingCost (commit a1b2c3d)
+  File: src/services/shipping.ts:24
+  Priority: High
+  Suggested fix: Replace `calculateShipping()` with `computeShippingCost()`
+```
+
+### Example: Deleted file still documented
+
+**Drift finding:**
+
+```
+DRIFT: Reference to deleted file
+  Doc: docs/architecture.md:112
+  Stale text: "The legacy parser (src/utils/legacy-parser.ts) handles XML input"
+  Code change: File deleted in commit d4e5f6g, functionality merged into unified-parser.ts
+  Priority: Critical
+  Suggested fix: Update section to reference unified-parser.ts, remove legacy parser description
+```
+
+### Example: New module with no documentation
+
+**Drift finding:**
+
+```
+GAP: Undocumented module
+  File: src/services/notification-service.ts
+  Created: commit h7i8j9k (3 weeks ago)
+  Public exports: NotificationService, NotificationType, sendNotification
+  Imported by: 4 modules
+  Documentation references: 0
+  Priority: High
+  Suggested fix: Add AGENTS.md section describing purpose, constraints, and public API
+```
+
+## Escalation
+
+- **When drift is extensive (>30 findings):** Do not try to fix everything. Focus on Critical and High priority items. Create a tracking issue for the remaining items and schedule them across sprints.
+- **When you cannot determine the correct replacement text:** The code change may have been complex. Check the commit message and PR description for context. If still unclear, flag the finding for the original author to resolve.
+- **When documentation is in a format you cannot parse:** Some docs may be in wiki pages, Confluence, or other external systems. Report the finding with a link and flag it for manual review.
+- **When drift reveals a deeper problem (code changed but nobody knew):** This suggests a process gap. Recommend adding `harness check-docs` to the CI pipeline or pre-merge hooks to catch drift at the source.

package/dist/agents/skills/gemini-cli/detect-doc-drift/skill.yaml

@@ -0,0 +1,30 @@
+name: detect-doc-drift
+version: "1.0.0"
+description: Detect documentation that has drifted from code
+cognitive_mode: diagnostic-investigator
+triggers:
+  - manual
+  - on_pr
+platforms:
+  - claude-code
+  - gemini-cli
+tools:
+  - Bash
+  - Read
+  - Glob
+cli:
+  command: harness skill run detect-doc-drift
+  args:
+    - name: path
+      description: Project root path
+      required: false
+mcp:
+  tool: run_skill
+  input:
+    skill: detect-doc-drift
+    path: string
+type: flexible
+state:
+  persistent: false
+  files: []
+depends_on: []