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CLI Reference

Commands

Scanning

Command Description
agents Discover MCP clients, extract dependencies, scan packages, and compute blast radius
quickstart Print local scan, sample-data, and API/UI first-run next steps
manifest Emit the canonical Agent BOM manifest for local agent, MCP server, tool, and credential-reference posture
skills Scan, verify, and rescan AI instruction files and skills
image Scan a container image
fs Scan a filesystem directory or mounted VM disk snapshot
iac Scan Dockerfile, Kubernetes, Terraform, CloudFormation, and live Kubernetes posture
sbom Ingest an existing CycloneDX or SPDX SBOM and scan it
cloud Scan AWS, Azure, or GCP infrastructure posture
check Check one package before install or approval
verify Verify package integrity / provenance or self-verify agent-bom
secrets Scan a directory for hardcoded secrets and PII
code Analyze source code for AI components, prompts, guardrails, and tools
scanners List scanner driver capabilities, inputs, outputs, and failure semantics

Runtime

Command Description
proxy Run an MCP server through the agent-bom security proxy
watch Watch MCP client configuration files for drift and alert on new risks
audit View and analyze a proxy audit JSONL log
audit-drain-dlq Replay or inspect proxy audit dead-letter queue entries

MCP

Command Description
mcp Discover, scan, and manage MCP agents and servers
mcp inventory Discover MCP agents and servers without CVE scanning
mcp scan Check a single MCP server package or npx/uvx spec
mcp introspect Connect to live servers and list tools
mcp registry Browse and manage the MCP server security registry
mcp server Start agent-bom as an MCP server over stdio
mcp where Show MCP discovery paths checked on this machine
mcp validate Validate an MCP/client inventory file
where Top-level shortcut for MCP discovery paths

Reporting

Command Description
graph Export the transitive dependency graph from a scan report
mesh Show lightweight agent/MCP topology without CVE scanning
report History, diff, pipeline-event artifacts, local queries, analytics, dashboard, and compliance narrative workflows

Governance And Operations

Command Description
policy Policy templates, application, and install-guard checks
firewall Inter-agent firewall policy validate / list / check
trust Show data access, network, auth, and storage boundaries
fleet Manage AI agent fleet discovery, lifecycle, and posture
serve Start the API server and dashboard
api Start the REST API server
schedule Manage recurring scan schedules
remediate Generate a prioritized remediation plan; with explicit --apply, patch supported dependency manifests
teardown Tear down the AWS/EKS reference install owned by agent-bom

Database And Utilities

Command Description
db Manage the local vulnerability database
doctor Check environment readiness for scanning
gateway Multi-MCP gateway commands
interactive Start an interactive command shell for repeated CLI workflows
plugins Inspect extension plugin registry status without loading third-party plugin code
profiles Manage named CLI profiles for repeatable scan contexts
proxy-bootstrap Generate managed endpoint onboarding material
samples Create bundled sample inputs for demos and first runs
sidecar-injector Run the TLS admission webhook for sidecar injection
upgrade Check for and install the latest version of agent-bom
completions Print a shell completion script

Command contracts

  • check supports terminal output by default plus --format json for machine-readable pre-install verdicts.
  • report history and report diff support --format json for CI and automation.
  • report pipeline-events <scan-job.json> exports structured scan progress as JSONL for DAG/dashboard consumers.
  • report query "SELECT ..." runs read-only SQL against the local scan analytics store.
  • remediate is read-only by default and supports --format json as the machine-readable remediation contract.
  • remediate --apply patches supported package dependency manifests only after confirmation; --apply --open-pr creates a draft PR instead of pushing to the default branch.
  • agents --agent-mode emits a stable JSON envelope for assistant and automation callers. It defaults to JSON stdout, reports ok, exit_code, summary counts, confidence signals, truncation metadata, and the full scan payload under data.
  • Use agent-bom agents -f <format> -o <path> for SARIF, HTML, SBOM, and richer environment exports.
  • Use agent-bom agents -f sarif -o - when you need SARIF on stdout for piping.
  • where is available both as agent-bom where and agent-bom mcp where.
  • agent-bom verify and agent-bom verify agent-bom both self-verify the installed package.

Common flags

# Output format
agent-bom agents -f json|html|sarif|csv|cyclonedx|spdx

# Output file
agent-bom agents -o report.json
agent-bom check requests@2.33.0 -e pypi -f json -o check.json
agent-bom report diff before.json after.json -f json -o diff.json
agent-bom report pipeline-events scan-job.json -o pipeline-events.jsonl
agent-bom report query "SELECT severity, COUNT(*) AS count FROM scan_findings GROUP BY severity" --format json

# Assistant / automation envelope
agent-bom agents --agent-mode
agent-bom agents --agent-mode --agent-token-budget 4000

# Compliance
agent-bom agents --compliance owasp-llm,eu-ai-act,all

# SBOM
agent-bom agents -f cyclonedx -o bom.json
agent-bom agents -f spdx -o bom.spdx.json

# Image scanning
agent-bom agents --image python:3.12-slim

# Policy
agent-bom agents --policy policy.json

# Enrichment
agent-bom agents --enrich    # NVD CVSS v4 + EPSS

# Prometheus
agent-bom agents --push-gateway http://pushgateway:9091

# VEX
agent-bom agents --vex vex.json
agent-bom agents --generate-vex --vex-output vex.json

# Config directory
agent-bom agents --config-dir /path/to/configs

# Self-scan (scan agent-bom's own installed dependencies)
agent-bom agents --self-scan

The --self-scan flag is on the agents subcommand (not top-level). It walks the active Python environment via importlib.metadata.distributions() and emits a CVE report against agent-bom's own runtime so you can audit the tool with the tool.

Troubleshooting

See CLI Debug Guide for quiet/logging behavior, stdout vs file output, discovery triage, and package verification workflows.

Use the Inaccurate Finding template for false positives, false negatives, wrong severity/advisory mapping, or misleading remediation. Include sanitized JSON/SARIF output and public evidence; do not post secrets, private source code, private package names, or customer data. The repository includes a sanitized inaccurate-finding report example with a copy-paste-safe issue body.

For the JSON contract behind agent-bom remediate, see remediate Output Contract.

Environment variables

Variable Purpose Required
NVD_API_KEY Increase NVD rate limit No
SNYK_TOKEN Optional commercial vuln-API enrichment No
AGENT_BOM_CLICKHOUSE_URL Analytics storage No
AWS_PROFILE AWS CIS benchmark Only for cis-benchmark --provider aws
SNOWFLAKE_ACCOUNT Snowflake CIS benchmark Only for cis-benchmark --provider snowflake