Extremely lightweight, security-hardened, declarative container runtime for agents and production services

Nucleus is a minimalist container runtime for Linux. It provides isolated execution environments using Linux kernel primitives without the overhead of traditional container runtimes. For production services, it is designed around a fully declarative model: Nix builds the root filesystem, the NixOS module declares the service, and Nucleus mounts a pinned, reproducible closure at runtime.

Nucleus supports three operating modes:

• Agent mode (default) – ephemeral, fast-startup sandboxes for AI agent workloads
• Strict agent mode – fail-closed isolation for ephemeral agent workloads without requiring production rootfs, health checks, sd_notify, or NixOS service semantics
• Production mode – strict isolation for long-running, network-bound NixOS services with declarative configuration, reproducible Nix-built root filesystems, egress policy enforcement, health checks, and systemd integration

Production deployments are built to be:

• Fully declarative – service topology, runtime settings, and mounted rootfs are defined up front instead of assembled imperatively at deploy time
• Nix-native – first-class NixOS module support plus nucleus.lib.mkRootfs for minimal service closures
• Reproducible – flake-based builds, pinned store paths, and rootfs attestation keep runtime inputs stable and auditable

In the native runtime, PostgreSQL stays near bare-metal performance under Nucleus isolation. In this harness, occasional wins over bare metal should be treated as benchmark noise rather than a guaranteed speedup.

SELECT-only (read-heavy)

TPC-B (mixed read/write)

Measured on Linux 6.18 x86_64. This benchmark uses the native runtime with a bind-mounted host pgdata directory and --network host, so it measures the steady-state cost of Nucleus isolation rather than VM or gVisor emulation overhead. Full results: benches/pg18_io/results/

• Declarative by default for services – Production deployments are defined in NixOS and TOML rather than stitched together with ad hoc runtime scripting
• Deep Nix integration – First-class NixOS module, mkRootfs, and Nix store closures for minimal, locked-down service roots
• Reproducible service builds – Flake-based packaging, pinned inputs, and rootfs attestation make runtime state auditable and repeatable
• Zero-overhead isolation – Direct use of cgroups, namespaces, pivot_root, capabilities, seccomp, and Landlock
• Memory-backed filesystems – Container disk mapped to tmpfs, pre-populated with agent context
• gVisor integration – Optional application kernel for enhanced security, including networked service mode
• OCI runtime-spec subset for gVisor – Generates OCI bundle/config data for runsc, including process identity, mounts, namespaces, seccomp, hooks, and cgroup path wiring
• Detached mode – Run containers in the background as systemd transient services with --detach, managed via nucleus stop/logs/attach
• Production service support – Declarative NixOS module, egress policies, health checks, secrets mounting, sd_notify, and journald integration
• Explicit workload identity – Native and gVisor runtimes can drop to a configured uid/gid plus supplementary groups after privileged setup
• Minimal rootfs – Replace host bind mounts with a purpose-built Nix store closure for production services
• External security policies – Per-service seccomp profiles (JSON), capability policies (TOML), and Landlock rules (TOML) with SHA-256 pinning
• Seccomp profile generation – Trace mode records syscalls, then nucleus seccomp generate creates a minimal allowlist profile
• Multi-container topologies – Compose-equivalent TOML format with dependency DAG, reconciliation, and NixOS systemd integration
• Integrity & audit controls – Structured audit log, machine-readable lifecycle event streams, context hashing, rootfs attestation, seccomp deny logging, mount flag verification, and kernel lockdown assertions
• Structured telemetry – Optional OpenTelemetry export for container lifecycle tracing
• Linux-native – Runs on standard Linux and NixOS

Nucleus is not a drop-in Docker replacement, nor a strict subset of Docker. The feature sets overlap, but each tool does things the other does not. Nucleus is a hardened sandbox runtime (closer in spirit to runc/gVisor) that also does lightweight, declarative single-host orchestration. It drops the image-and-distribution half of Docker in exchange for deeper isolation, policy, and reproducibility.

If your mental model is "run my image instead of docker run," it will not fit: there are no images, no registry, and no persistent state. If it is "run untrusted or ephemeral workloads with stronger, auditable isolation," that is the target.

Nucleus leverages Linux kernel isolation primitives:

• Namespaces – PID, mount, network, UTS, IPC, user, cgroup, and optional time isolation
• cgroups v2 – Resource limits (CPU, memory, PIDs, I/O)
• pivot_root – Filesystem isolation (chroot fallback available in agent mode only)
• Capabilities – All capabilities dropped by default, or configured via TOML policy file (irreversible)
• seccomp – Syscall whitelist filtering with per-service JSON profiles and trace-based generation (irreversible)
• Landlock – Path-based filesystem access control via hardcoded defaults or TOML policy file (Linux 5.13+)
• gVisor – Optional application kernel (runsc) with none, bridge handoff, and explicit gvisor-host network modes
• OCI bundle generation – Emits OCI config.json plus bundle layout for gVisor, including process.user, lifecycle hooks, seccomp, resource limits, and namespace mappings
• PID 1 init – Mini-init supervisor in production mode for zombie reaping and signal forwarding
• In-memory secrets – Dedicated tmpfs at /run/secrets with volatile zeroing of source buffers
• Mount audit – Post-setup verification of mount flags in production mode

Container filesystem is backed by tmpfs and either populated with context files (agent mode) or mounted from a pre-built Nix rootfs closure (production mode). That lets production services run from a declaratively built, reproducible root filesystem instead of inheriting mutable host state.

• Linux (kernel 6.x+) on x86_64
• NixOS (first-class NixOS module support)
• Not supported: macOS, Windows, BSDs, 32-bit Linux

cargo install nucleus-container

Or via Nix (recommended for reproducible builds and NixOS integration):

nix run github:wiggum-cc/nucleus

The Cargo package name is nucleus-container; it installs the nucleus binary. The repository itself is packaged as a Nix flake, so nix run, nix build, and the NixOS module all share the same pinned inputs.

• Privilege drop for services – --user, --group, and --additional-group now apply a real post-setup workload identity in both the native runtime and gVisor.
• Ownership-aware secrets and writable paths – Production secret staging and NixOS createHostPath = true defaults now align file ownership with the configured workload user/group.
• OCI bundle identity support – Generated gVisor OCI configs now carry process.user including supplementary groups, alongside namespaces, mounts, resource limits, seccomp, hooks, and cgroupsPath.
• Probe execution under workload identity – Exec-based health and readiness probes now run as the configured service account instead of implicitly as root.
• Systemd/NixOS service integration improvements – The module exposes user, group, and supplementaryGroups, and packaged Nix usage includes gvisor in the flake/dev shell path.

# Run agent in isolated container with pre-populated context
nucleus run --context ./agent-context/ -- /usr/bin/agent

# Specify resource limits
nucleus run --memory 512M --cpus 2 --context ./ctx/ -- ./agent

# Name your container
nucleus run --name my-agent --context ./ctx/ -- ./agent

# Use gVisor for enhanced isolation
nucleus run --runtime gvisor --context ./ctx/ -- ./agent

# Rootless mode
nucleus run --rootless -- /bin/sh

# Optional networking
nucleus run --network host --allow-host-network -- curl https://example.com
nucleus run --network bridge -p 8080:80 -- ./server
nucleus run --network bridge -p 127.0.0.1:8080:80 -- ./server
nucleus run --rootless --network bridge -- ./client
nucleus run --network bridge --nat-backend userspace -- ./client

# Context streaming (bind mount for instant access)
nucleus run --context ./large-dir/ --context-mode bind -- ./agent

# Integrity and audit hardening
nucleus run --context ./ctx/ --verify-context-integrity --seccomp-log-denied -- ./agent

# Environment variables
nucleus run -e DEBUG=1 -- ./agent

# Sensitive environment variables without argv exposure
printf '{"OPENAI_API_KEY":"..."}' | nucleus run --env-fd 3 3<&0 -- ./agent

# Pass sensitive values via --secret (mounted in-memory at /run/secrets)
nucleus run --secret /path/to/api-key:/run/secrets/api_key -- ./agent

# Run a coding agent against a stable /workspace cwd
nucleus run \
  --workspace "$PWD" \
  --workspace-mode bind-rw \
  --workspace-exec \
  -- ./agent

# Mount provider CLI config under the private home directory
nucleus run \
  --provider-config-ro "$HOME/.aws:.aws" \
  --provider-config-rw "$HOME/.config/gh:.config/gh" \
  -- ./agent

# Run an agent with a pinned provider/toolchain rootfs instead of host runtime binds
nucleus run \
  --service-mode mitos-agent \
  --agent-toolchain-rootfs /nix/store/...-nucleus-agent-toolchain-rootfs \
  --workspace "$PWD" \
  --workspace-exec \
  -- codex

nucleus run accepts the same command as nucleus create. Programmatic callers that need a stable launch contract can provide the whole request as JSON or TOML instead of constructing a long argv list:

nucleus run --config ./agent.nucleus.toml
nucleus run --config ./agent.nucleus.json
nucleus run --config-fd 3 3<./agent.nucleus.json

Config mode owns the launch request: put the workload command and all sandbox options in the config document rather than mixing them with per-option CLI flags. The schema uses the long CLI option names converted to snake_case:

name = "mitos-agent"
workspace = "/home/dev/project"
workspace_mode = "bind-rw"
workspace_exec = true
workdir = "/workspace"
runtime = "gvisor"
service_mode = "strict-agent"
agent_toolchain_rootfs = "/nix/store/...-nucleus-agent-toolchain-rootfs"
memory = "1G"
cpus = 2.0
pids = 512
command = ["./agent", "--stdio"]

env_vars = ["RUST_LOG=info"]
seccomp_log_denied = true

--workspace <host-path> mounts the host project tree at /workspace. The process cwd defaults to /workspace via --workdir /workspace.

--workspace-mode accepts:

Workspace mounts are nosuid,nodev,noexec by default and native Landlock denies execution from /workspace. Use --workspace-exec for agent-mode workflows that build and run test binaries from the workspace. Production mode rejects writable executable workspaces; use an immutable --rootfs and explicit policy files for production services.

Nucleus creates a private tmpfs home at /home/agent by default and sets the workload HOME to that path. The home tmpfs is mounted nosuid,nodev,noexec with mode 0700 and is owned by the configured workload uid/gid. Use --home <container-path> to choose a different private home path; the path must be absolute and must not overlap /workspace.

Provider CLIs that require config under $HOME should use explicit provider config mounts instead of broad host bind mounts:

nucleus run \
  --home /home/agent \
  --provider-config-ro "$HOME/.aws:.aws" \
  --provider-config-ro "$HOME/.config/gcloud:.config/gcloud" \
  --provider-config-rw "$HOME/.config/gh:.config/gh" \
  -- ./agent

--provider-config-ro SOURCE:DEST and --provider-config-rw SOURCE:DEST are repeatable. DEST may be absolute under the configured home, or relative to the home directory. Read-only mounts are preferred for cloud credentials; read-write mounts are intended only for tools that must refresh local tokens.

Mitos-style provider launchers can avoid depending on mutable host /bin, /usr, /lib, or /nix binds by passing a pinned agent toolchain rootfs:

nucleus run \
  --service-mode strict-agent \
  --agent-toolchain-rootfs /nix/store/...-nucleus-agent-toolchain-rootfs \
  --workspace "$PWD" \
  --workspace-exec \
  -- claude

The dedicated flag is for agent, strict-agent, and mitos-agent modes. It uses the same read-only rootfs mount path as --rootfs, but is rejected in production mode so production services keep using --rootfs with attestation.

Build a rootfs with the Nix helper:

nucleus.lib.mkAgentToolchainRootfs {
  inherit pkgs;
  providerPackages = [
    # Derivations that provide claude/codex/gemini executables.
  ];
  extraPackages = [
    pkgs.rustc
    pkgs.cargo
  ];
}

The repository also exposes packages.${system}.agent-toolchain-rootfs as a default shell/Git/compiler/package-manager rootfs. Integrations that need exact provider CLIs should call mkAgentToolchainRootfs with pinned provider package derivations and pass the resulting store path to --agent-toolchain-rootfs.

Use -d/--detach to run a container in the background as a systemd transient service. The CLI prints the container ID and exits immediately; systemd supervises the container process.

# Run a container in the background
nucleus create -d --memory 512M -- /bin/sleep 3600
# prints: a1b2c3d4e5f6...

# All management commands work with detached containers
nucleus state                        # list running containers
nucleus logs <container>             # view stdout/stderr (from journald)
nucleus logs -f <container>          # follow logs
nucleus logs -n 50 <container>       # last 50 lines
nucleus attach <container>           # exec into it
nucleus stop <container>             # graceful SIGTERM → SIGKILL
nucleus kill <container>             # send signal

# Detach works with all create flags
nucleus create -d \
  --name my-service \
  --memory 1G --cpus 2 \
  --network bridge -p 8080:80 \
  -- ./my-server

# systemd unit is named nucleus-<id-prefix>
systemctl status nucleus-a1b2c3d4e5f6
journalctl -u nucleus-a1b2c3d4e5f6

The systemd transient service uses KillMode=mixed and TimeoutStopSec=30, so systemctl stop also works for graceful shutdown. The --collect flag ensures the unit is garbage-collected after the container exits.

Production mode enforces strict security invariants:

• Forbids --allow-degraded-security, --allow-chroot-fallback, and native --network host
• Permits --allow-host-network only with --network gvisor-host --runtime gvisor
• Requires explicit --memory limit
• Requires successful cgroup creation (no fallback to running without limits)
• Egress policy failures are fatal where Nucleus owns the network namespace; gvisor-host cannot use Nucleus egress policy
• Bridge DNS must be configured explicitly (no public resolver defaults)

# Run a long-running service with production hardening
nucleus run \
  --service-mode production \
  --trust-level trusted \
  --memory 1G --cpus 2 --pids 256 \
  --rootfs /nix/store/...-my-service-rootfs \
  --verify-rootfs-attestation \
  --require-kernel-lockdown integrity \
  --network bridge --dns 10.0.0.1 \
  --egress-allow 10.0.0.0/8 \
  --egress-domain api.example.com \
  --egress-tcp-port 443 --egress-tcp-port 8443 \
  --health-cmd "curl -sf http://localhost:8080/health" \
  --health-interval 30 --health-retries 3 \
  --secret /run/secrets/tls-cert:/etc/tls/cert.pem \
  --systemd-credential db-url:/run/secrets/db-url \
  --volume /var/lib/myservice:/var/lib/myservice:rw \
  -e CONFIG_PATH=/etc/myservice/config.toml \
  --sd-notify \
  -p 127.0.0.1:8080:8080 \
  -- /bin/my-service --config /etc/myservice/config.toml

# gVisor with network access (sandbox network stack)
nucleus run \
  --service-mode production \
  --runtime gvisor \
  --gvisor-platform kvm \
  --memory 512M \
  --network bridge --dns 10.0.0.1 \
  --rootfs /nix/store/...-proxy-rootfs \
  -- /bin/proxy

Strict agent mode (--service-mode strict-agent, --service-mode mitos-agent, or --strict-agent) keeps agent-style execution while making isolation setup fail closed:

• Forbids --allow-degraded-security, --allow-chroot-fallback, and native --network host
• Permits --allow-host-network only with --network gvisor-host --runtime gvisor
• Requires successful cgroup creation and successful application of configured limits
• Requires pivot_root in native mode; no chroot fallback
• Requires seccomp enforcement; --seccomp-mode trace is rejected
• Requires Landlock enforcement for native runtime
• Requires user namespace UID/GID mapping when running as host root or rootless
• Keeps network mode none by default; bridge mode requires explicit --dns

Strict agent mode does not require a production Nix rootfs, rootfs attestation, health checks, readiness probes, sd_notify, systemd transient services, or NixOS module deployment.

# Run an ephemeral agent with fail-closed native isolation
nucleus run \
  --service-mode strict-agent \
  --runtime native \
  --trust-level trusted \
  --memory 1G --cpus 2 \
  --context ./ctx \
  -- ./agent

Nix defines the service and the root filesystem; separate files define security policy (what the process is allowed to do at the kernel level). This separation keeps deployments declarative, security config auditable, and runtime inputs reproducible without coupling policy changes to application rebuilds.

# Run with external security policies
nucleus run \
  --service-mode production \
  --rootfs /nix/store/...-my-service-rootfs \
  --memory 512M --cpus 1 \
  --seccomp-profile ./config/my-service.seccomp.json \
  --seccomp-profile-sha256 abc123... \
  --caps-policy ./config/my-service.caps.toml \
  --landlock-policy ./config/my-service.landlock.toml \
  -- /bin/my-service

Seccomp profile (JSON – OCI-native format, tooling emits it directly):

{
  "defaultAction": "SCMP_ACT_KILL_PROCESS",
  "architectures": ["SCMP_ARCH_X86_64"],
  "syscalls": [
    {
      "names": ["read", "write", "close", "openat", "fstat",
                "mmap", "munmap", "brk", "futex", "clock_gettime"],
      "action": "SCMP_ACT_ALLOW"
    }
  ]
}

Capability policy (TOML):

# config/my-service.caps.toml
[bounding]
keep = []          # empty = drop all

[ambient]
keep = []

Landlock policy (TOML):

# config/my-service.landlock.toml
min_abi = 3

[[rules]]
path = "/bin"
access = ["read", "execute"]

[[rules]]
path = "/etc/myservice"
access = ["read"]

[[rules]]
path = "/run/secrets"
access = ["read"]

[[rules]]
path = "/tmp"
access = ["read", "write", "create", "remove"]

Profiles shouldn't be hand-written from scratch. Use trace mode to record actual syscall usage, then generate a minimal profile:

# 1. Run in trace mode – all syscalls allowed but logged
nucleus run \
  --seccomp-mode trace \
  --seccomp-log ./trace.ndjson \
  --rootfs /nix/store/...-my-service-rootfs \
  --memory 512M \
  -- /bin/my-service

# 2. Generate minimal profile from trace
nucleus seccomp generate ./trace.ndjson -o config/my-service.seccomp.json

# 3. Review and tighten (remove anything surprising)
# 4. Commit – Nix pins the SHA-256 hash
# 5. Run in enforce mode
nucleus run \
  --seccomp-profile ./config/my-service.seccomp.json \
  --seccomp-profile-sha256 "$(sha256sum config/my-service.seccomp.json | cut -d' ' -f1)" \
  -- /bin/my-service

Trace mode requires root or CAP_SYSLOG (reads /dev/kmsg). It is rejected in production mode – it is a development tool only.

Nucleus includes a Compose-equivalent for managing multi-container stacks using TOML configuration with dependency ordering.

# topology.toml
name = "myapp"

[networks.internal]
subnet = "10.42.0.0/24"

[volumes.db-data]
volume_type = "persistent"
path = "/var/lib/nucleus/myapp/db"
owner = "70:70"

[volumes.cache]
volume_type = "ephemeral"
size = "128M"

[services.postgres]
rootfs = "/nix/store/...-postgres"
command = ["postgres", "-D", "/var/lib/postgresql/data"]
memory = "2G"
cpus = 2.0
networks = ["internal"]
volumes = [
  "db-data:/var/lib/postgresql/data",
  "cache:/var/cache/postgresql"
]
health_check = "pg_isready -U myapp"

[services.web]
rootfs = "/nix/store/...-web"
command = ["/bin/web-server"]
memory = "512M"
networks = ["internal"]
nat_backend = "userspace"
port_forwards = ["8443:8443"]
egress_allow = ["10.42.0.0/24"]
egress_domains = ["api.example.com"]

[[services.web.depends_on]]
service = "postgres"
condition = "healthy"

# Validate topology and show dependency order
nucleus compose validate -f topology.toml

# Bring up all services in dependency order
nucleus compose up -f topology.toml

# Show service status
nucleus compose ps -f topology.toml

# Tear down in reverse dependency order
nucleus compose down -f topology.toml

# List running containers
nucleus ps

# List all containers (including stopped)
nucleus ps --all

# Show resource usage statistics
nucleus stats

# View logs for a detached container (from systemd journal)
nucleus logs <container>
nucleus logs -f <container>          # follow output
nucleus logs -n 100 <container>      # last 100 lines

# Stop a container (SIGTERM, then SIGKILL after timeout)
nucleus stop <container>
nucleus stop --timeout 30 <container>

# Kill a container with a specific signal
nucleus kill <container>
nucleus kill --signal TERM <container>

# Remove a stopped container
nucleus rm <container>
nucleus rm --force <container>

# Attach to a running container
nucleus attach <container>
nucleus attach <container> -- /bin/bash

# Checkpoint a running container (requires root, CRIU)
nucleus checkpoint <container> --output /path/to/checkpoint

# Restore from checkpoint
nucleus restore --input /path/to/checkpoint

Nucleus provides a declarative NixOS module for running containers as systemd services. Each container is managed as a nucleus-<name>.service unit with journald logging, sd_notify readiness, and automatic restart.

{
  inputs.nucleus.url = "github:wiggum-cc/nucleus";

  outputs = { self, nixpkgs, nucleus, ... }: {
    nixosConfigurations.myhost = nixpkgs.lib.nixosSystem {
      system = "x86_64-linux";
      modules = [
        nucleus.nixosModules.default
        ./configuration.nix
      ];
    };
  };
}

{ pkgs, nucleus, ... }:

let
  # Build a minimal rootfs containing only the packages your service needs.
  # This replaces host bind mounts with a locked-down Nix closure.
  proxyRootfs = nucleus.lib.mkRootfs {
    inherit pkgs;
    packages = [ my-proxy-pkg pkgs.cacert pkgs.curl ];
  };
in
{
  services.nucleus = {
    enable = true;
    package = nucleus.packages.x86_64-linux.default;

    containers.sigid-proxy = {
      enable = true;
      command = [ "/bin/sigid-proxy" "--config" "/etc/sigid/proxy.toml" ];
      rootfs = proxyRootfs;
      user = "sigid-proxy";
      group = "sigid-proxy";

      # Resource limits (required in production mode)
      memory = "1G";
      cpus = 2.0;
      pids = 256;

      # Security policy files (separate from Nix, auditable by security engineers)
      seccompProfile = {
        path = ./config/sigid-proxy.seccomp.json;
        sha256 = "abc123...";  # Nix verifies at build time
      };
      capsPolicy = ./config/sigid-proxy.caps.toml;
      landlockPolicy = ./config/sigid-proxy.landlock.toml;

      # Optional hardening toggles
      verifyRootfsAttestation = true;
      seccompLogDenied = true;
      requireKernelLockdown = "integrity";

      # Networking
      network = "bridge";
      natBackend = "auto";  # or "userspace" to force slirp4netns
      dns = [ "10.0.0.1" ];  # internal resolver – no public DNS default
      portForwards = [ "127.0.0.1:8080:8080" "127.0.0.1:8443:8443" ];

      # Egress policy – audited outbound access
      egressAllow = [ "10.0.0.0/8" ];
      egressDomains = [ "api.example.com" ];
      egressTcpPorts = [ 443 8443 ];

      # Health checking
      healthCheck = "curl -sf http://localhost:8080/health";
      healthInterval = 30;
      healthRetries = 3;
      healthStartPeriod = 10;

      # Secrets (mounted read-only)
      secrets = [
        { source = config.age.secrets.proxy-tls.path; dest = "/etc/tls/cert.pem"; }
      ];

      # systemd-creds integration
      credentials = [
        {
          name = "proxy-key";
          source = config.age.secrets.proxy-key.path;
          dest = "/run/secrets/proxy-key";
          encrypted = false;
        }
      ];

      # Volumes (bind-mounted host paths)
      volumes = [
        {
          source = "/var/lib/sigid-proxy";
          dest = "/var/lib/sigid-proxy";
          createHostPath = true;
        }
      ];

      # Environment
      environment = {
        RUST_LOG = "info";
        CONFIG_PATH = "/etc/sigid/proxy.toml";
      };

      # systemd integration
      sdNotify = true;  # Type=notify, passes NOTIFY_SOCKET into container
    };
  };
}

Writable bind volumes are automatically added to the generated systemd unit's ReadWritePaths. When createHostPath = true, the NixOS module creates the host directory with systemd-tmpfiles before the container starts. If the container declares a workload user/group, those become the default tmpfiles owner for new writable paths unless the volume overrides them.

Credentials declared via credentials = [ ... ] use systemd's credential pipeline (LoadCredential or LoadCredentialEncrypted) and are mounted into the container through Nucleus's secret path. The CLI flag --systemd-credential NAME:DEST resolves NAME from CREDENTIALS_DIRECTORY at runtime.

Set user, group, and optional supplementaryGroups on a NixOS container definition when the workload should run as a dedicated service account instead of root.

Topologies can also be managed as systemd services:

{
  services.nucleus = {
    enable = true;
    package = nucleus.packages.x86_64-linux.default;

    topologies.myapp = {
      enable = true;
      configFile = ./topology.toml;
    };
  };
}

This creates a nucleus-topology-myapp.service (Type=oneshot, RemainAfterExit) that runs nucleus compose up on start and nucleus compose down on stop.

For each enabled container, the module creates a systemd service:

• Unit: nucleus-<name>.service, ordered after network-online.target
• Type: notify (when sdNotify = true) or simple
• Restart: on-failure with 5s backoff
• Logging: stdout/stderr captured to journald with SyslogIdentifier=nucleus-<name>
• Command: nucleus run --service-mode production ... with all configured options
• Workload identity: Nucleus itself starts as root for setup, then drops the container workload to the configured user / group before exec
• Hardening: ProtectSystem=strict, ProtectHome=true at the systemd level (defense-in-depth)

Use nucleus.lib.mkRootfs to build a minimal, reproducible root filesystem:

nucleus.lib.mkRootfs {
  inherit pkgs;
  name = "my-service-rootfs";  # optional, defaults to "nucleus-rootfs"
  packages = [
    my-service-package
    pkgs.cacert       # TLS certificates
    pkgs.curl         # for health checks
    pkgs.busybox      # minimal coreutils
  ];
}

This produces a Nix store path containing /bin, /lib, /etc, etc. from the specified packages. It is mounted read-only inside the container, replacing the host bind mounts used in agent mode.

mkRootfs also emits a .nucleus-rootfs-sha256 manifest at the root of the closure. Use --verify-rootfs-attestation or verifyRootfsAttestation = true; to require that manifest to match the mounted rootfs at startup.

For ephemeral provider agents, use nucleus.lib.mkAgentToolchainRootfs instead. It layers a broad agent development toolchain on top of mkRootfs, keeps /bin/sh and /usr/bin/env compatibility paths available, and accepts provider CLI packages through providerPackages.

Do not pass secrets via -e / --env. Environment variables are visible in /proc/<pid>/environ to any process that can read it (mitigated by hidepid=2 in production mode, but not in agent mode). Use --secret instead when a file works. If a provider CLI requires sensitive environment variables, use --env-fd FD; the fd carries a JSON object such as {"OPENAI_API_KEY":"..."} or a JSON array of KEY=VALUE strings so the values are not exposed through Nucleus argv.

Privilege dropping is explicit. Nucleus must start with elevated privileges to create namespaces, mount filesystems, and configure cgroups/networking. Use --user / --group (or the NixOS module's user / group options) so the workload itself does not continue running as root after setup. In production mode, staged secrets under /run/secrets are re-owned to that workload identity.

Agent mode is not hardened. By design, agent mode applies several security mechanisms on a best-effort basis: seccomp and Landlock failures are warn-and-continue (with --allow-degraded-security), chroot fallback is available (with --allow-chroot-fallback), bridge DNS defaults to public resolvers (8.8.8.8), and cgroup creation failures are non-fatal. Operators requiring strict isolation for ephemeral workloads should use --service-mode strict-agent; operators deploying long-running NixOS services should use production mode.

When production bridge mode runs without --egress-allow or --egress-domain, Nucleus installs a strict deny-all OUTPUT policy, including DNS. When --egress-allow or --egress-domain is specified, Nucleus applies iptables OUTPUT chain rules inside the container's network namespace:

1. Allow loopback traffic
2. Allow established/related connections
3. Allow DNS to configured resolvers
4. Resolve permitted domains to IPv4 /32 rules at startup
5. Allow traffic to permitted CIDRs and resolved domain addresses (optionally restricted to specific ports)
6. Log denied packets (rate-limited, nucleus-egress-denied: prefix)
7. Drop everything else

# Allow outbound to internal network on HTTPS only
nucleus run --network bridge --dns 10.0.0.1 \
  --egress-allow 10.0.0.0/8 --egress-tcp-port 443 \
  -- ./my-service

# Allow outbound to a provider API domain on HTTPS only
nucleus run --network bridge --dns 10.0.0.1 \
  --egress-domain api.example.com --egress-tcp-port 443 \
  -- ./provider-client

# Production deny-all egress, including DNS
nucleus run --service-mode production --network bridge --dns 10.0.0.1 \
  -- ./isolated-service

Domain egress entries are exact DNS names, not wildcard or suffix rules. Nucleus resolves each domain with the supervisor host resolver before installing the namespace-local iptables policy, keeps only IPv4 answers, and fails startup if a domain has no IPv4 address. Long-running services that depend on provider IP rotation should restart after DNS changes, use provider-published CIDR ranges, or route traffic through a stable internal proxy and allow that proxy CIDR instead.

For the native runtime, --network bridge now has two backends:

This changes the native rootless behavior from "degrade to none" to a real userspace NAT path.

When using gVisor (--runtime gvisor), the network mode is selected explicitly:

The gvisor-host mode is intentionally separate from native host networking. Native host remains a direct host namespace mode. gvisor-host keeps the gVisor runtime boundary, but weakens network isolation by letting runsc hostinet use the host network stack. Because there is no Nucleus-owned network namespace in this mode, Nucleus egress policy is unavailable with gvisor-host.

--terminal runs the workload behind a pseudoterminal. Supplying --console-socket <path> implies terminal mode and follows the OCI console socket convention: the runtime connects to the AF_UNIX socket and sends the PTY master file descriptor with SCM_RIGHTS.

Native containers allocate the PTY directly. The workload process becomes a session leader, the PTY slave becomes its controlling TTY, and stdin/stdout/stderr all point at that slave. gVisor containers set process.terminal = true and process.consoleSize in the generated OCI config, then pass --console-socket through to runsc.

Console bytes are not decoded or rewritten by Nucleus. Clients such as mitos/libghostty are expected to parse and render the raw stream. Window resizing uses PTY window-size ioctls; foreground SIGWINCH is also forwarded to the container process.

Nucleus is not a generic external OCI runtime. For gVisor execution it generates an OCI bundle layout and config.json that follow the OCI runtime-spec fields Nucleus uses in practice.

• process: args, env, cwd, noNewPrivileges, terminal settings, rlimits, and process.user (uid, gid, additionalGids)
• root and mounts: read-only rootfs plus bind, tmpfs, and secret mounts
• linux: namespaces, cgroup path, resource limits, uid/gid mappings, masked paths, readonly paths, devices, seccomp, and sysctls
• hooks: OCI lifecycle hooks with OCI state JSON on stdin
• annotations: runtime metadata passed through to the bundle

That OCI path is the contract used with runsc. The native runtime uses Nucleus's direct Linux setup path rather than exposing a separate OCI CLI surface.

Lifecycle hooks execute host-side commands with supervisor privileges. They are not accepted in topology service definitions; use only explicit administrative nucleus create --hooks configuration for hooks.

Use --events-jsonl <path> to write control-plane lifecycle events as JSON Lines, or --events-fd <fd> to write them to an inherited file descriptor. The stream is separate from workload stdout/stderr and PTY bytes; operators can consume it without parsing user process output. --events-fd rejects stdio descriptors and is not available with --detach; use --events-jsonl for detached containers.

Events include a container start record and a final summary record. The records carry the container ID, PID, cgroup path, workspace/context mount, network mode, seccomp mode, Landlock status, capability status, resource limits, exit status, resource stats, and whether cleanup succeeded.

• --seccomp-profile <path> loads a custom per-service seccomp profile (OCI JSON format).
• --seccomp-profile-sha256 <hex> verifies the profile's SHA-256 hash before loading.
• --seccomp-mode trace|enforce switches between trace (record all syscalls) and enforce (default).
• --seccomp-log <path> writes NDJSON syscall trace when in trace mode.
• --caps-policy <path> loads a TOML capability policy (replaces default drop-all).
• --caps-policy-sha256 <hex> verifies the capability policy hash.
• --landlock-policy <path> loads a TOML Landlock filesystem policy (replaces default rules).
• --landlock-policy-sha256 <hex> verifies the Landlock policy hash.
• --verify-context-integrity hashes the source context tree before launch and verifies the populated /context tree matches.
• --verify-rootfs-attestation requires a .nucleus-rootfs-sha256 manifest and verifies the mounted rootfs against it.
• --seccomp-log-denied requests kernel logging for denied seccomp decisions when the host supports SECCOMP_FILTER_FLAG_LOG.
• --require-kernel-lockdown integrity|confidentiality refuses startup unless /sys/kernel/security/lockdown satisfies the requested mode.
• --gvisor-platform systrap|kvm|ptrace selects the runsc backend explicitly.
• --time-namespace enables Linux time namespaces for native containers.
• --disable-cgroup-namespace turns off cgroup namespace isolation when a workload needs the host cgroup view.

If NUCLEUS_OTLP_ENDPOINT or OTEL_EXPORTER_OTLP_ENDPOINT is set, Nucleus exports lifecycle spans over OTLP in addition to normal local logging.

This project uses Nix flakes for reproducible builds:

# Enter development shell
nix develop

# Build
cargo build

# Run tests
cargo test

# Run with Apalache installed (for TLA+ trace replay)
cargo test -- --include-ignored

# Build release binary
cargo build --release

# Clippy
cargo clippy --all-targets -- --deny warnings

# Host vs container runtime benchmarks (requires root)
sudo -E cargo bench --bench container_runtime

nucleus/
├── src/
│   ├── container/      # Container orchestration, lifecycle, state, config
│   ├── isolation/      # Namespace management, user mapping, attach
│   ├── resources/      # cgroup v2 resource control, stats
│   ├── filesystem/     # tmpfs, rootfs mounting, context population, secrets, attestation
│   ├── security/       # Capabilities, seccomp, Landlock, gVisor, OCI, policy files
│   │   ├── caps_policy.rs       # TOML capability policy loader
│   │   ├── landlock_policy.rs   # TOML Landlock policy loader
│   │   ├── seccomp_trace.rs     # Seccomp trace mode (syscall recording)
│   │   ├── seccomp_generate.rs  # Profile generator from traces
│   │   └── policy.rs            # Shared policy infrastructure (SHA-256, TOML/JSON loaders)
│   ├── network/        # Networking (none/host/bridge), egress policy
│   ├── topology/       # Multi-container topology (Compose equivalent)
│   │   ├── config.rs   # TOML topology config (services, networks, volumes)
│   │   ├── dag.rs      # Dependency DAG with topological sort
│   │   ├── reconcile.rs # Diff running vs desired state, apply changes
│   │   └── dns.rs      # Per-topology /etc/hosts DNS
│   ├── checkpoint/     # CRIU checkpoint/restore
│   ├── audit.rs        # Structured audit log (JSON events)
│   └── error.rs        # Error types
├── nix/
│   └── module.nix      # NixOS module (containers + topologies)
├── config/             # Security policy files (per-service)
│   ├── *.seccomp.json  # Seccomp syscall allowlists (OCI format)
│   ├── *.caps.toml     # Capability bounding set policies
│   └── *.landlock.toml # Landlock filesystem access rules
├── tests/
│   ├── model_based_*   # Property-based tests from TLA+ specs
│   └── tla_*           # tla-connect driver tests
├── formal/tla/         # TLA+ formal specifications
├── intent/             # Intent high-level specs
└── flake.nix           # Nix flake (packages, modules, lib.mkRootfs)

Nucleus uses spec-driven development with comprehensive testing:

• Unit tests: Individual component functionality
• Model-based tests: Property-based tests verifying TLA+ specifications
• tla-connect tests: TLA+ to Rust state machine mapping
• Integration tests: Complete container lifecycle

All state machines are formally verified using TLA+ and the Apalache model checker.

benches/container_runtime.rs compares the same workloads when run directly on the host vs inside a native Nucleus container. The matrix covers:

• cold startup (/bin/sh -lc ':')
• a CPU-bound shell arithmetic loop
• context-heavy file scans with both bind-mounted and copied context
• a constrained profile that applies the same cgroup limits to the direct host process and the containerized process

Because the benchmark creates namespaces and cgroups, it must run as root:

sudo -E cargo bench --bench container_runtime

Criterion writes the comparison reports to target/criterion/container_runtime/.

A composed system model verifies cross-subsystem ordering, authorization, and end-to-end progress:

apalache-mc check --config=formal/tla/Nucleus_System.cfg formal/tla/Nucleus_System.tla

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at your option.