dependency-doctor: Security & Code Review for AI Agents | OpenAgentSkill

Overview

Dependency health management. Detects package manager, checks outdated packages and vulnerabilities, and produces a prioritized update plan.

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dependency-doctor

Purpose

Dependency health management covering outdated packages, known vulnerabilities, and update planning. Detects the package manager automatically, runs audit commands, analyzes breaking changes for major version bumps, and outputs a prioritized update plan with risk assessment.

Called By (inbound)

rescue (L1): Phase 0 dependency health assessment
audit (L2): Phase 1 vulnerability scan and outdated dependency check

Calls (outbound)

None — pure L3 utility using Bash for package manager commands.

Executable Instructions

Step 1: Detect Package Manager

Use Glob to find dependency files in the project root:

package.json → Node.js (npm, yarn, or pnpm)
requirements.txt or pyproject.toml → Python (pip or uv)
Cargo.toml → Rust (cargo)
go.mod → Go (go)
Gemfile → Ruby (bundler)

If multiple are found, process all of them. If none found, report NO_DEPENDENCY_FILES and stop.

For Node.js, further detect the package manager:

yarn.lock present → yarn
pnpm-lock.yaml present → pnpm
package-lock.json present → npm
None → default to npm

Step 2: List Dependencies

Use Read to parse the dependency file and extract:

Package name
Current version constraint
Whether it is a dev dependency or production dependency

For package.json, read both dependencies and devDependencies sections.

Step 3: Check Outdated

Run the appropriate command via Bash to find outdated packages:

npm:

npm outdated --json

yarn:

yarn outdated --json

pnpm:

pnpm outdated

pip:

pip list --outdated --format=json

cargo:

cargo outdated

go:

go list -u -m all

Parse the output to extract for each outdated package:

Current version
Latest version
Update type: patch | minor | major

Step 4: Check Vulnerabilities

Run the appropriate audit command via Bash:

npm:

npm audit --json

yarn:

yarn audit --json

pnpm:

pnpm audit --json

pip:

pip-audit --format json

cargo:

cargo audit --json

If the audit tool is not installed, note it as TOOL_MISSING and skip this step (do not fail).

Parse the output to extract:

Package name + vulnerable version
CVE ID (if available)
Severity: critical | high | moderate | low
Fixed version (if available)

Step 5: Analyze Breaking Changes

For each package with a major version bump (e.g. v2 → v3):

Use rune:docs-seeker to look up migration guides if available, or note:

"Breaking change analysis required before updating [package] from v[X] to v[Y]"

Do not blindly recommend major updates without flagging migration risk.

Step 6: Generate Update Plan

Create a prioritized update plan:

Priority order:

CRITICAL — packages with critical/high CVEs → update immediately
SECURITY — packages with moderate/low CVEs → update in current sprint
PATCH — patch version bumps, no breaking changes → safe to batch update
MINOR — minor version bumps, new features added → update with testing
MAJOR — major version bumps, breaking changes → plan migration separately

For each item in the plan, include:

Package name + current → target version
Update type and risk level
Migration notes (for major updates)
Suggested command to run the update

Step 7: Report

Output the following structure:

## Dependency Report: [project name]

- **Package Manager**: [npm|yarn|pnpm|pip|cargo|go]
- **Total Dependencies**: [count]
- **Outdated**: [count]
- **Vulnerable**: [count] ([critical] critical, [high] high, [moderate] moderate)

### Critical — CVEs (Fix Immediately)
- [package]@[current] — [CVE-ID] ([severity]): [description]
  Fix: npm update [package]@[fixed_version]

### Security — CVEs (Fix This Sprint)
- [package]@[current] — [CVE-ID] ([severity]): [description]

### Outdated — Patch (Safe to Update)
- [package]@[current] → [latest] (patch)

### Outdated — Minor (Update with Testing)
- [package]@[current] → [latest] (minor)

### Outdated — Major (Plan Migration)
- [package]@[current] → [latest] (major) — migration guide required

### Unused Dependencies
- [package] — no imports found in src/

### Update Plan (Ordered by Risk)
1. [command] — fixes [CVE-ID]
2. [command] — patch updates (safe batch)
3. [command] — requires migration: [notes]

### Dependency Health Score
- Score: [0-100]
- Grade: A (80-100) | B (60-79) | C (40-59) | D (<40)
- Score basis: -10 per critical CVE, -5 per high CVE, -2 per outdated major, -1 per outdated minor

Upgrade Campaign Mode

When health score < 60 OR CRITICAL/SECURITY items exist, dependency-doctor can orchestrate a full upgrade campaign — not just report, but execute. Triggered by: user says "upgrade all", "fix deps", "run the update plan", or health score triggers.

Campaign Chain

1. TRIAGE     → Run Steps 1-7 (standard report). Identify upgrade order.
2. CHECKPOINT → Save current lock file state: `cp package-lock.json .rune/dep-backup/`
3. PER-PACKAGE LOOP (CRITICAL → SECURITY → PATCH → MINOR, skip MAJOR):
   a. Upgrade one package at a time: `npm install pkg@latest`
   b. Call `rune:verification` — run tests + build
   c. If PASS → commit: `feat(deps): upgrade {pkg} {old} → {new}`
   d. If FAIL → rollback package: `npm install pkg@{old}`, log as BLOCKED
4. MAJOR BUMPS → present to user: breaking change notes + migration guide link. Never auto-upgrade.
5. REPORT     → final health score delta, packages upgraded/skipped/blocked

One package at a time — bulk upgrades make it impossible to identify which package broke the build.

MAJOR upgrades require:

User confirmation
Breaking change summary (from npm docs or package CHANGELOG)
Migration checklist before upgrading

Calls (outbound — Campaign Mode only)

verification (L3): test + build after each package upgrade
fix (L2): when a minor/patch upgrade breaks tests and fix is straightforward

Output Format

Dependency Report with package manager, counts, CVE findings by severity, outdated packages by risk level, unused dependencies, ordered update plan, and health score (0-100). See Step 7 Report above for full template.

Constraints

MUST check for known vulnerabilities — not just version freshness
MUST NOT auto-upgrade major versions without user confirmation — breaking changes
MUST verify project still builds after any dependency change
MUST show what changed (added, removed, upgraded) in a clear diff format

Sharp Edges

Known failure modes for this skill. Check these before declaring done.

Failure Mode	Severity	Mitigation
Recommending major version update without flagging migration risk	CRITICAL	Constraint 2: breaking changes need explicit migration notes and user confirmation
Silently skipping vulnerability check when tool not installed	HIGH	Report TOOL_MISSING explicitly — never skip without logging it
Missing dependency health score (0-100)	MEDIUM	Score is mandatory in every report — it gives callers a quick health signal
Reporting unused dependencies without verifying (false positive)	MEDIUM	Check actual import patterns in src/ before flagging as unused

Done When

Package manager detected (npm/yarn/pnpm/pip/cargo/go)
Outdated packages listed with current → latest versions and update type
Vulnerability audit run (or TOOL_MISSING noted explicitly)
Breaking changes flagged for all major version bumps
Prioritized update plan generated (CRITICAL → SECURITY → PATCH → MINOR → MAJOR order)
Dependency health score (0-100) calculated
Dependency Report emitted in output format

Cost Profile

~300-600 tokens input, ~200-500 tokens output. Haiku. Most time spent in package manager commands.

View source ↗

File metadata

name: dependency-doctor
description: "Dependency health management. Detects package manager, checks outdated packages and vulnerabilities, and produces a prioritized update plan."
metadata:
  author: runedev
  version: "0.2.0"
  layer: L3
  model: sonnet
  group: deps
  tools: "Read, Bash, Glob, Grep"

View original text

---
name: dependency-doctor
description: "Dependency health management. Detects package manager, checks outdated packages and vulnerabilities, and produces a prioritized update plan."
metadata:
  author: runedev
  version: "0.2.0"
  layer: L3
  model: sonnet
  group: deps
  tools: "Read, Bash, Glob, Grep"
---

# dependency-doctor

## Purpose

Dependency health management covering outdated packages, known vulnerabilities, and update planning. Detects the package manager automatically, runs audit commands, analyzes breaking changes for major version bumps, and outputs a prioritized update plan with risk assessment.

## Called By (inbound)

- `rescue` (L1): Phase 0 dependency health assessment
- `audit` (L2): Phase 1 vulnerability scan and outdated dependency check

## Calls (outbound)

None — pure L3 utility using Bash for package manager commands.

## Executable Instructions

### Step 1: Detect Package Manager

Use `Glob` to find dependency files in the project root:

- `package.json` → Node.js (npm, yarn, or pnpm)
- `requirements.txt` or `pyproject.toml` → Python (pip or uv)
- `Cargo.toml` → Rust (cargo)
- `go.mod` → Go (go)
- `Gemfile` → Ruby (bundler)

If multiple are found, process all of them. If none found, report NO_DEPENDENCY_FILES and stop.

For Node.js, further detect the package manager:
- `yarn.lock` present → yarn
- `pnpm-lock.yaml` present → pnpm
- `package-lock.json` present → npm
- None → default to npm

### Step 2: List Dependencies

Use `Read` to parse the dependency file and extract:
- Package name
- Current version constraint
- Whether it is a dev dependency or production dependency

For `package.json`, read both `dependencies` and `devDependencies` sections.

### Step 3: Check Outdated

Run the appropriate command via `Bash` to find outdated packages:

**npm:**
```bash
npm outdated --json
```

**yarn:**
```bash
yarn outdated --json
```

**pnpm:**
```bash
pnpm outdated
```

**pip:**
```bash
pip list --outdated --format=json
```

**cargo:**
```bash
cargo outdated
```

**go:**
```bash
go list -u -m all
```

Parse the output to extract for each outdated package:
- Current version
- Latest version
- Update type: `patch` | `minor` | `major`

### Step 4: Check Vulnerabilities

Run the appropriate audit command via `Bash`:

**npm:**
```bash
npm audit --json
```

**yarn:**
```bash
yarn audit --json
```

**pnpm:**
```bash
pnpm audit --json
```

**pip:**
```bash
pip-audit --format json
```

**cargo:**
```bash
cargo audit --json
```

If the audit tool is not installed, note it as TOOL_MISSING and skip this step (do not fail).

Parse the output to extract:
- Package name + vulnerable version
- CVE ID (if available)
- Severity: `critical` | `high` | `moderate` | `low`
- Fixed version (if available)

### Step 5: Analyze Breaking Changes

For each package with a **major** version bump (e.g. v2 → v3):

Use `rune:docs-seeker` to look up migration guides if available, or note:
- "Breaking change analysis required before updating [package] from v[X] to v[Y]"

Do not blindly recommend major updates without flagging migration risk.

### Step 6: Generate Update Plan

Create a prioritized update plan:

Priority order:
1. **CRITICAL** — packages with critical/high CVEs → update immediately
2. **SECURITY** — packages with moderate/low CVEs → update in current sprint
3. **PATCH** — patch version bumps, no breaking changes → safe to batch update
4. **MINOR** — minor version bumps, new features added → update with testing
5. **MAJOR** — major version bumps, breaking changes → plan migration separately

For each item in the plan, include:
- Package name + current → target version
- Update type and risk level
- Migration notes (for major updates)
- Suggested command to run the update

### Step 7: Report

Output the following structure:

```
## Dependency Report: [project name]

- **Package Manager**: [npm|yarn|pnpm|pip|cargo|go]
- **Total Dependencies**: [count]
- **Outdated**: [count]
- **Vulnerable**: [count] ([critical] critical, [high] high, [moderate] moderate)

### Critical — CVEs (Fix Immediately)
- [package]@[current] — [CVE-ID] ([severity]): [description]
  Fix: npm update [package]@[fixed_version]

### Security — CVEs (Fix This Sprint)
- [package]@[current] — [CVE-ID] ([severity]): [description]

### Outdated — Patch (Safe to Update)
- [package]@[current] → [latest] (patch)

### Outdated — Minor (Update with Testing)
- [package]@[current] → [latest] (minor)

### Outdated — Major (Plan Migration)
- [package]@[current] → [latest] (major) — migration guide required

### Unused Dependencies
- [package] — no imports found in src/

### Update Plan (Ordered by Risk)
1. [command] — fixes [CVE-ID]
2. [command] — patch updates (safe batch)
3. [command] — requires migration: [notes]

### Dependency Health Score
- Score: [0-100]
- Grade: A (80-100) | B (60-79) | C (40-59) | D (<40)
- Score basis: -10 per critical CVE, -5 per high CVE, -2 per outdated major, -1 per outdated minor
```

## Upgrade Campaign Mode

When health score < 60 OR CRITICAL/SECURITY items exist, dependency-doctor can orchestrate a full upgrade campaign — not just report, but execute. Triggered by: user says "upgrade all", "fix deps", "run the update plan", or health score triggers.

### Campaign Chain

```
1. TRIAGE     → Run Steps 1-7 (standard report). Identify upgrade order.
2. CHECKPOINT → Save current lock file state: `cp package-lock.json .rune/dep-backup/`
3. PER-PACKAGE LOOP (CRITICAL → SECURITY → PATCH → MINOR, skip MAJOR):
   a. Upgrade one package at a time: `npm install pkg@latest`
   b. Call `rune:verification` — run tests + build
   c. If PASS → commit: `feat(deps): upgrade {pkg} {old} → {new}`
   d. If FAIL → rollback package: `npm install pkg@{old}`, log as BLOCKED
4. MAJOR BUMPS → present to user: breaking change notes + migration guide link. Never auto-upgrade.
5. REPORT     → final health score delta, packages upgraded/skipped/blocked
```

**One package at a time** — bulk upgrades make it impossible to identify which package broke the build.

**MAJOR upgrades require:**
- User confirmation
- Breaking change summary (from npm docs or package CHANGELOG)
- Migration checklist before upgrading

### Calls (outbound — Campaign Mode only)

- `verification` (L3): test + build after each package upgrade
- `fix` (L2): when a minor/patch upgrade breaks tests and fix is straightforward

## Output Format

Dependency Report with package manager, counts, CVE findings by severity, outdated packages by risk level, unused dependencies, ordered update plan, and health score (0-100). See Step 7 Report above for full template.

## Constraints

1. MUST check for known vulnerabilities — not just version freshness
2. MUST NOT auto-upgrade major versions without user confirmation — breaking changes
3. MUST verify project still builds after any dependency change
4. MUST show what changed (added, removed, upgraded) in a clear diff format

## Sharp Edges

Known failure modes for this skill. Check these before declaring done.

| Failure Mode | Severity | Mitigation |
|---|---|---|
| Recommending major version update without flagging migration risk | CRITICAL | Constraint 2: breaking changes need explicit migration notes and user confirmation |
| Silently skipping vulnerability check when tool not installed | HIGH | Report TOOL_MISSING explicitly — never skip without logging it |
| Missing dependency health score (0-100) | MEDIUM | Score is mandatory in every report — it gives callers a quick health signal |
| Reporting unused dependencies without verifying (false positive) | MEDIUM | Check actual import patterns in src/ before flagging as unused |

## Done When

- Package manager detected (npm/yarn/pnpm/pip/cargo/go)
- Outdated packages listed with current → latest versions and update type
- Vulnerability audit run (or TOOL_MISSING noted explicitly)
- Breaking changes flagged for all major version bumps
- Prioritized update plan generated (CRITICAL → SECURITY → PATCH → MINOR → MAJOR order)
- Dependency health score (0-100) calculated
- Dependency Report emitted in output format

## Cost Profile

~300-600 tokens input, ~200-500 tokens output. Haiku. Most time spent in package manager commands.

Review the source

Skill source recorded

Skill instructions are recorded. This is not a runtime test, safety guarantee or compatibility certification.

Review before install: Avoid automatic install

License: MIT

Dependency or permission surface needs review
Permission surface may require sandboxing
The skill mentions using `rune:docs-seeker` in Step 5 but declares 'Calls (outbound): None' — this inconsistency may confuse agents.
The report template includes 'Unused Dependencies' but no step explains how to detect unused dependencies.
Missing handling for when outdated-check commands (e.g., `cargo outdated`, `pip-audit`) are not installed — only audit tools are covered.
Quality score needs review
Permission surface needs review: secrets or environment access, shell or command execution
GitHub adoption: 86 GitHub stars
Stars/forks activity: 86 stars, 25 forks; issue activity unavailable in current metadata
Dependency/runtime risk: command execution surface, credential or environment access
Permission surface: secrets or environment access, shell or command execution

Open full audit

Listed tools are metadata hints, not tested compatibility. Agent prompts are suggested handoffs.

Start with one small task

Source & usage notes

Indexed

Repository metadata and review signals are advisory. Popularity, source discovery and successful execution are different facts.

Source repository: Rune-kit/rune
License: MIT
Version: 1.0.0
Last GitHub push: Aug 16, 2026
Registry updated: Sep 7, 2026
Instruction path: skills/dependency-doctor/SKILL.md @ feb5f5d5d9ca

Version reported in registry metadata; check source releases before relying on it.

Quality

63/100

Promising

Trust

52/100

Do not auto-install

Agent access

This page exposes the same decision, trust, audit, use-case, and install signals through the Registry API, so agents can rank this skill without scraping the UI.

Open install API LLM text format Open manifest Auto-resolve Plan

More details

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    "signals": [],
    "penalties": [
      "No real agent outcome evidence yet"
    ]
  },
  "audit": {
    "score": 70,
    "risk_level": "needs_review",
    "risk_label": "Needs review",
    "warnings": [
      "Dependency or permission surface needs review",
      "Permission surface may require sandboxing",
      "The skill mentions using `rune:docs-seeker` in Step 5 but declares 'Calls (outbound): None' — this inconsistency may confuse agents.",
      "The report template includes 'Unused Dependencies' but no step explains how to detect unused dependencies.",
      "Missing handling for when outdated-check commands (e.g., `cargo outdated`, `pip-audit`) are not installed — only audit tools are covered.",
      "Quality score needs review",
      "Permission surface needs review: secrets or environment access, shell or command execution",
      "GitHub adoption: 86 GitHub stars"
    ]
  },
  "safety_gate": {
    "tier": "blocked",
    "label": "Blocked for auto-install",
    "auto_install_policy": "block",
    "auto_install_allowed": false,
    "human_review_required": true,
    "blocked": true,
    "recommended_action": "Do not auto-install. Inspect the source, dependencies, and permission surface first."
  },
  "quality": {
    "score": 63,
    "label": "Promising"
  },
  "supply": {
    "track": "Data, BI, and analytics",
    "scenario": "Security and compliance",
    "maintenance": "1mo since push",
    "risk": "Needs review"
  },
  "alternative_skills": [],
  "do_not_use_when": [
    "teams that need a vendor-supported SLA",
    "production agents without a repository review",
    "The skill mentions using `rune:docs-seeker` in Step 5 but declares 'Calls (outbound): None' — this inconsistency may confuse agents.",
    "No OpenAgentSkill engagement data yet",
    "High-risk permission hints: Shell or command execution, Secrets or environment access",
    "Dependency or permission surface needs review",
    "Permission surface may require sandboxing",
    "The report template includes 'Unused Dependencies' but no step explains how to detect unused dependencies."
  ],
  "agent_contract": {
    "task_input": "Use dependency-doctor in an agent workflow",
    "recommended_action": "Do not auto-install. Inspect the source, dependencies, and permission surface first.",
    "install_policy": "block",
    "minimum_review_before_use": [
      "Trust: 60/100 Manual review",
      "Audit: 70/100 Needs review",
      "Safety: 26/100 Avoid automatic install",
      "Review repository, license, install command, and permission surface before production use."
    ],
    "expected_agent_output": {
      "selected_skill": "rune-kit-dependency-doctor (dependency-doctor)",
      "install_command": "npx skills add Rune-kit/rune --skill dependency-doctor",
      "risk_summary": "Needs review; Blocked for auto-install; Review before production",
      "verification_result": "Report the smallest successful task, files touched, warnings, and any missing setup."
    }
  },
  "outcome_feedback": {
    "endpoint": "https://www.openagentskill.com/api/agent/outcome",
    "method": "POST",
    "requires_resolve_event_id": true,
    "event_id_source": "Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.",
    "expected_outcomes": [
      "success",
      "failed",
      "not_relevant",
      "blocked_by_risk",
      "setup_required"
    ],
    "payload_template": {
      "event_id": "<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>",
      "skill_slug": "rune-kit-dependency-doctor",
      "task": "Use dependency-doctor in an agent workflow",
      "agent": "codex",
      "outcome": "success",
      "install_used": true,
      "risk_blocked": false,
      "setup_required": false,
      "task_success": true,
      "output_quality": 4,
      "error_type": null,
      "human_review_required": false,
      "workspace": "sandbox",
      "time_to_useful_ms": 120000,
      "notes": "Report the smallest successful task, setup friction, files touched, and risk notes."
    }
  },
  "endpoints": {
    "web": "https://www.openagentskill.com/skills/rune-kit-dependency-doctor",
    "api": "https://www.openagentskill.com/api/agent/skills/rune-kit-dependency-doctor",
    "audit": "https://www.openagentskill.com/skills/rune-kit-dependency-doctor/audit",
    "eval": "https://www.openagentskill.com/api/agent/evals?slug=rune-kit-dependency-doctor&task=Use%20dependency-doctor%20in%20an%20agent%20workflow&max_risk=medium",
    "resolve": "https://www.openagentskill.com/api/agent/resolve?task=Use%20dependency-doctor%20in%20an%20agent%20workflow&agent=codex&max_risk=medium",
    "receipt": "https://www.openagentskill.com/api/agent/receipt?task=Use%20dependency-doctor%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text",
    "install": "https://www.openagentskill.com/api/skills/rune-kit-dependency-doctor/install",
    "manifest": "https://www.openagentskill.com/api/registry/manifest/rune-kit-dependency-doctor"
  }
}

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Creator: Rune-kit
Source: Rune-kit/rune
Indexed by: OpenAgentSkill community index

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