fix

What this skill does

# Vulnetix Fix Intelligence Skill

This skill fetches fix intelligence for a vulnerability and proposes concrete, actionable remediation steps for the current repository.

## Output & Analysis Guidelines

**Primary output format:** Markdown. All reports, tables, fix options, version diffs, and verification summaries MUST be presented as formatted markdown text directly — never generate scripts or programs to produce output that can be expressed as markdown.

**Visual data — use Mermaid diagrams** to display data visually when it aids comprehension. Mermaid renders natively in markdown and requires no external tools. Use it for:
- Dependency upgrade paths → `graph LR` showing current → target version with breaking change annotations
- Fix option comparison → `quadrantChart` plotting Safe Harbour confidence vs. version change magnitude
- Dependency tree showing vulnerable path → `graph TD` (root → parent → vulnerable dep)
- Post-fix verification status → `flowchart` (scan → tests → result)

Example — upgrade path:
````markdown
```mermaid
graph LR
    A[log4j-core 2.14.1] -->|patch| B[2.14.2]
    A -->|minor| C[2.17.1 ✓ fix]
    A -->|major| D[3.0.0]
    style A fill:#f66,stroke:#333
    style C fill:#6f6,stroke:#333
```
````

**If `uv` is available**, richer visualizations can be generated with Python (matplotlib, plotly) and saved to `.vulnetix/`:
```bash
command -v uv &>/dev/null && uv run --with matplotlib python3 -c '
import matplotlib.pyplot as plt
# ... generate chart ...
plt.savefig(".vulnetix/chart.png", dpi=150, bbox_inches="tight")
'
```
When Python charts are generated, display them inline and keep the Mermaid version as a text fallback.

**Data processing — tooling cascade (strict order):**

1. **jq / yq + bash builtins** (preferred) — `jq` for JSON (API responses, CycloneDX SBOMs, package manager output), `yq` for YAML (memory file). Pipe to `head`, `tail`, `cut`, `sed`, `grep`, `sort`, `uniq`, `wc` for shaping.
2. **uv** (for complex analysis or charts) — If dependency graph analysis, version comparison logic, or visualization beyond Mermaid are needed, check `uv` first:
   ```bash
   command -v uv &>/dev/null && uv run --with pandas,matplotlib python3 -c '...'
   ```
3. **python3 stdlib** (last resort) — Only if `uv` is unavailable. Use `json`, `csv`, `collections`, `statistics` modules — **no pip dependencies**:
   ```bash
   command -v python3 &>/dev/null && python3 -c 'import json, sys; ...'
   ```

**Never assume any runtime is available** — always check with `command -v` before use. If all programmatic tools are unavailable, analyze manually with the Read tool and present results as markdown with Mermaid diagrams.

**Package manager commands** (`npm install --dry-run`, `pip show`, `go mod tidy`, `cargo check`, etc.) are exempt — they are executed directly as part of the fix workflow, not for data analysis.

## Mandatory Reporting Requirements

**Every output and report from this skill MUST include the following version and provenance information for each affected package:**

### Package Version Reporting

All reports MUST display:

| Field | Description | Required |
|-------|-------------|----------|
| **Current Version** | The version currently installed/resolved | Always |
| **Version Source** | How the version was determined (see below) | Always |
| **Fix Target Version** | The patched version to upgrade to | When available |
| **Fix Source** | Registry, distro patch, or source commit hash | Always |
| **Safe Harbour Confidence** | Confidence score 0.00–1.00 (see below) | Always |

### Version Source Transparency

You MUST be transparent about how the current version was determined. Report one of:

- **User-supplied** — the user provided the version directly
- **Manifest** — read from a package manager manifest file (state which file)
- **Lockfile** — read from a lockfile (state which file)
- **Installed** — derived from the installed package on the filesystem:
  - npm/node: read `node_modules/<pkg>/package.json` (search parent directories too)
  - Python: run `pip show <pkg>` or read `site-packages/<pkg>/METADATA`
  - Go: read `go.sum` or run `go list -m <pkg>`
  - Rust: read `Cargo.lock` or run `cargo metadata`
  - System binaries: run `<binary> --version` or check `PATH` resolution
  - Ruby: run `gem list <pkg>` or read `Gemfile.lock`
  - Maven: read effective POM or local `.m2` cache
- **Context** — the version was already present in conversation context
- **Unknown** — version could not be determined (explain why)

If the user does not supply the version and it is not in conversation context, you MUST attempt to derive it from the filesystem before reporting "Unknown". Search outside the current working directory if needed — check parent directories, global package manager directories, and gitignored directories (e.g., `node_modules/`, `vendor/`, `.venv/`, `target/`, `__pycache__/`).

### Safe Harbour Confidence Score

Express the Safe Harbour score as a decimal between 0.00 and 1.00 where 1.00 = 100% confidence the fix resolves the vulnerability without introducing regressions or breaking changes.

**Confidence tiers:**
- **High confidence (> 0.90):** Patch-level bump in the same minor version, official registry release, well-tested fix, minimal API surface change
- **Reasonable confidence (0.35–0.90):** Minor version bump, distro-repackaged patch, source fix from upstream with commit hash, some API changes but backward-compatible
- **Low confidence (< 0.35):** Major version bump, unofficial patch, cherry-picked commit from development branch, significant API changes, no upstream release yet

**What factors adjust confidence:**
- Registry-published release with changelog: +0.15
- Distro-maintained patch (e.g., Debian, Ubuntu, RHEL): +0.10
- Upstream commit hash verified in release tag: +0.10
- CISA KEV listed (validated exploitation): +0.05 (urgency signal, not fix quality)
- Major version jump: −0.25
- No test suite in project to validate: −0.15
- Transitive dependency (indirect control): −0.10
- Built from source with untagged commit: −0.20

**Report format for each affected package:**

```
Package: <name>
Current Version: <version> (source: <version-source>)
Fix Target: <version> (source: <registry|distro <name> <version>|commit <hash>>)
Safe Harbour: <score> (<High|Reasonable|Low> confidence)
```

## Vulnerability Memory File (.vulnetix/memory.yaml)

This skill maintains a `.vulnetix/memory.yaml` file in the repository root that tracks all vulnerability encounters, decisions, and fix outcomes across sessions. **You MUST read this file at the start of every invocation and update it after every action.**

### Schema

```yaml
# .vulnetix/memory.yaml
# Auto-maintained by Vulnetix Claude Code Plugin
# Do not remove — tracks vulnerability decisions, manifest scans, and fix history

schema_version: 1
manifests:                                # Tracked manifest files and SBOM scan history
  package.json:
    path: "package.json"                  # Relative path from repo root
    ecosystem: npm
    last_scanned: "2024-01-15T10:30:00Z"  # ISO 8601 UTC
    sbom_generated: true
    sbom_path: ".vulnetix/scans/package.json.20240115T103000Z.cdx.json"
    vuln_count: 3                         # Vulnerabilities found in last scan
    scan_source: hook                     # hook | fix | exploits | package-search
  services--api--go.mod:
    path: "services/api/go.mod"           # Supports monorepo paths (key uses -- separator)
    ecosystem: go
    last_scanned: "2024-01-15T10:31:00Z"
    sbom_generated: true
    sbom_path: ".vulnetix/scans/services--api--go.mod.20240115T103100Z.cdx.json"
    vuln_count: 0
    scan_source: hook
vulnerabilities:
  CVE-2021-44228:                       # Primary vuln ID (key)
    aliases:                             # Other IDs for the same vuln
      - GHSA-jfh8-c2jp-5v3q
    package: log4j-core
    ecosystem: maven
    discovery:
      date: "2024-01-15T10:30:00Z"      # ISO 8601 UTC
      source: m