Agent Supply Chain Integrity

Generate and verify integrity manifests for AI agent plugins and tools. Detect tampering, enforce version pinning, and establish supply chain provenance.

Overview

Agent plugins and MCP servers have the same supply chain risks as npm packages or container images — except the ecosystem has no equivalent of npm provenance, Sigstore, or SLSA. This skill fills that gap.

Plugin Directory → Hash All Files (SHA-256) → Generate INTEGRITY.json
                                                    ↓
Later: Plugin Directory → Re-Hash Files → Compare Against INTEGRITY.json
                                                    ↓
                                          Match? VERIFIED : TAMPERED

When to Use

• Before promoting a plugin from development to production
• During code review of plugin PRs
• As a CI step to verify no files were modified after review
• When auditing third-party agent tools or MCP servers
• Building a plugin marketplace with integrity requirements

---

Pattern 1: Generate Integrity Manifest

Create a deterministic

INTEGRITY.json

with SHA-256 hashes of all plugin files.

import hashlib
import json
from datetime import datetime, timezone
from pathlib import Path

EXCLUDE_DIRS = {".git", "__pycache__", "node_modules", ".venv", ".pytest_cache"}
EXCLUDE_FILES = {".DS_Store", "Thumbs.db", "INTEGRITY.json"}

def hash_file(path: Path) -> str:
    """Compute SHA-256 hex digest of a file."""
    h = hashlib.sha256()
    with open(path, "rb") as f:
        for chunk in iter(lambda: f.read(8192), b""):
            h.update(chunk)
    return h.hexdigest()

def generate_manifest(plugin_dir: str) -> dict:
    """Generate an integrity manifest for a plugin directory."""
    root = Path(plugin_dir)
    files = {}

    for path in sorted(root.rglob("*")):
        if not path.is_file():
            continue
        if path.name in EXCLUDE_FILES:
            continue
        if any(part in EXCLUDE_DIRS for part in path.relative_to(root).parts):
            continue
        rel = path.relative_to(root).as_posix()
        files[rel] = hash_file(path)

    # Chain hash: SHA-256 of all file hashes concatenated in sorted order
    chain = hashlib.sha256()
    for key in sorted(files.keys()):
        chain.update(files[key].encode("ascii"))

    manifest = {
        "plugin_name": root.name,
        "generated_at": datetime.now(timezone.utc).isoformat(),
        "algorithm": "sha256",
        "file_count": len(files),
        "files": files,
        "manifest_hash": chain.hexdigest(),
    }
    return manifest

# Generate and save
manifest = generate_manifest("my-plugin/")
Path("my-plugin/INTEGRITY.json").write_text(
    json.dumps(manifest, indent=2) + "\n"
)
print(f"Generated manifest: {manifest['file_count']} files, "
      f"hash: {manifest['manifest_hash'][:16]}...")

Output (

INTEGRITY.json

):

{
  "plugin_name": "my-plugin",
  "generated_at": "2026-04-01T03:00:00+00:00",
  "algorithm": "sha256",
  "file_count": 12,
  "files": {
    ".claude-plugin/plugin.json": "a1b2c3d4...",
    "README.md": "e5f6a7b8...",
    "skills/search/SKILL.md": "c9d0e1f2...",
    "agency.json": "3a4b5c6d..."
  },
  "manifest_hash": "7e8f9a0b1c2d3e4f..."
}

---

Pattern 2: Verify Integrity

Check that current files match the manifest.

# Requires: hash_file() and generate_manifest() from Pattern 1 above
import json
from pathlib import Path

def verify_manifest(plugin_dir: str) -> tuple[bool, list[str]]:
    """Verify plugin files against INTEGRITY.json."""
    root = Path(plugin_dir)
    manifest_path = root / "INTEGRITY.json"

    if not manifest_path.exists():
        return False, ["INTEGRITY.json not found"]

    manifest = json.loads(manifest_path.read_text())
    recorded = manifest.get("files", {})
    errors = []

    # Check recorded files
    for rel_path, expected_hash in recorded.items():
        full = root / rel_path
        if not full.exists():
            errors.append(f"MISSING: {rel_path}")
            continue
        actual = hash_file(full)
        if actual != expected_hash:
            errors.append(f"MODIFIED: {rel_path}")

    # Check for new untracked files
    current = generate_manifest(plugin_dir)
    for rel_path in current["files"]:
        if rel_path not in recorded:
            errors.append(f"UNTRACKED: {rel_path}")

    return len(errors) == 0, errors

# Verify
passed, errors = verify_manifest("my-plugin/")
if passed:
    print("VERIFIED: All files match manifest")
else:
    print(f"FAILED: {len(errors)} issue(s)")
    for e in errors:
        print(f"  {e}")

Output on tampered plugin:

FAILED: 3 issue(s)
  MODIFIED: skills/search/SKILL.md
  MISSING: agency.json
  UNTRACKED: backdoor.py

---

Pattern 3: Dependency Version Audit

Check that agent dependencies use pinned versions.

import re

def audit_versions(config_path: str) -> list[dict]:
    """Audit dependency version pinning in a config file."""
    findings = []
    path = Path(config_path)
    content = path.read_text()

    if path.name == "package.json":
        data = json.loads(content)
        for section in ("dependencies", "devDependencies"):
            for pkg, ver in data.get(section, {}).items():
                if ver.startswith("^") or ver.startswith("~") or ver == "*" or ver == "latest":
                    findings.append({
                        "package": pkg,
                        "version": ver,
                        "severity": "HIGH" if ver in ("*", "latest") else "MEDIUM",
                        "fix": f'Pin to exact: "{pkg}": "{ver.lstrip("^~")}"'
                    })

    elif path.name in ("requirements.txt", "pyproject.toml"):
        for line in content.splitlines():
            line = line.strip()
            if ">=" in line and "<" not in line:
                findings.append({
                    "package": line.split(">=")[0].strip(),
                    "version": line,
                    "severity": "MEDIUM",
                    "fix": f"Add upper bound: {line},<next_major"
                })

    return findings

---

Pattern 4: Promotion Gate

Use integrity verification as a gate before promoting plugins.

def promotion_check(plugin_dir: str) -> dict:
    """Check if a plugin is ready for production promotion."""
    checks = {}

    # 1. Integrity manifest exists and verifies
    passed, errors = verify_manifest(plugin_dir)
    checks["integrity"] = {
        "passed": passed,
        "errors": errors
    }

    # 2. Required files exist
    root = Path(plugin_dir)
    required = ["README.md"]
    missing = [f for f in required if not (root / f).exists()]

    # Require at least one plugin manifest (supports both layouts)
    manifest_paths = [
        root / ".github/plugin/plugin.json",
        root / ".claude-plugin/plugin.json",
    ]
    if not any(p.exists() for p in manifest_paths):
        missing.append(".github/plugin/plugin.json (or .claude-plugin/plugin.json)")

    checks["required_files"] = {
        "passed": len(missing) == 0,
        "missing": missing
    }

    # 3. No unpinned dependencies
    mcp_path = root / ".mcp.json"
    if mcp_path.exists():
        config = json.loads(mcp_path.read_text())
        unpinned = []
        for server in config.get("mcpServers", {}).values():
            if isinstance(server, dict):
                for arg in server.get("args", []):
                    if isinstance(arg, str) and "@latest" in arg:
                        unpinned.append(arg)
        checks["pinned_deps"] = {
            "passed": len(unpinned) == 0,
            "unpinned": unpinned
        }

    # Overall
    all_passed = all(c["passed"] for c in checks.values())
    return {"ready": all_passed, "checks": checks}

result = promotion_check("my-plugin/")
if result["ready"]:
    print("Plugin is ready for production promotion")
else:
    print("Plugin NOT ready:")
    for name, check in result["checks"].items():
        if not check["passed"]:
            print(f"  FAILED: {name}")

---

CI Integration

Add to your GitHub Actions workflow:

- name: Verify plugin integrity
  run: |
    PLUGIN_DIR="${{ matrix.plugin || '.' }}"
    cd "$PLUGIN_DIR"
    python -c "
    from pathlib import Path
    import json, hashlib, sys

    def hash_file(p):
        h = hashlib.sha256()
        with open(p, 'rb') as f:
            for c in iter(lambda: f.read(8192), b''):
                h.update(c)
        return h.hexdigest()

    manifest = json.loads(Path('INTEGRITY.json').read_text())
    errors = []
    for rel, expected in manifest['files'].items():
        p = Path(rel)
        if not p.exists():
            errors.append(f'MISSING: {rel}')
        elif hash_file(p) != expected:
            errors.append(f'MODIFIED: {rel}')
    if errors:
        for e in errors:
            print(f'::error::{e}')
        sys.exit(1)
    print(f'Verified {len(manifest[\"files\"])} files')
    "

---

Best Practices

Practice	Rationale
Generate manifest after code review	Ensures reviewed code matches production code
Include manifest in the PR	Reviewers can verify what was hashed
Verify in CI before deploy	Catches post-review modifications
Chain hash for tamper evidence	Single hash represents entire plugin state
Exclude build artifacts	Only hash source files — .git, pycache, node_modules excluded
Pin all dependency versions	Unpinned deps = different code on every install

---

Related Resources

• OpenSSF SLSA — Supply-chain Levels for Software Artifacts
• npm Provenance — Sigstore-based package provenance
• Agent Governance Toolkit — Includes integrity verification and plugin signing
• OWASP ASI-09: Supply Chain Integrity