nix-agent
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nix-agent install guide (for coding agents)

This document is the canonical, ordered checklist for installing nix-agent on a NixOS machine and wiring it into an MCP-capable coding agent (Codex, Claude Code, opencode, Cursor, etc.).

It is written for an autonomous agent. Follow every step in order. Do not skip steps. Stop and report to the user if any step fails. The documented default is high trust: unprompted activation and narrowed passwordless sudo. Do not offer lower-trust options unless the user already asked.

0. Preconditions

Verify all of the following before touching anything:

  • The host is NixOS (test -e /etc/NIXOS).
  • The system is managed by a flake. Locate the flake directory. Common locations:
    • /etc/nixos/flake.nix
    • ~/nixos/flake.nix
    • ~/.config/nixos/flake.nix
    • ~/nix-config/flake.nix
    • ~/nixos-config/flake.nix
    • ask the user if none of these exist.
  • The user has sudo and is willing to run nixos-rebuild switch.
  • git is available.

Record:

  • FLAKE_DIR, directory containing flake.nix
  • HOSTNAME, value of hostname (must match a key under nixosConfigurations.<host> in the flake)
  • USERNAME, value of whoami (the local user granted passwordless sudo for nix-agent privileged commands)

Secrets manager detection (informational, do not install)

Grep ${FLAKE_DIR} for an existing secrets manager:

grep -RIl --include='*.nix' -E 'sops-nix|agenix' "${FLAKE_DIR}" || true

  • If a match is found, record which one and continue.

  • If no match is found, surface this notice to the user verbatim before continuing, do not install anything yourself:

    No secrets manager (sops-nix or agenix) was detected in your flake. The nix-agent MCP tools do not write files; they only provide Nix operations. Do not write secret payloads into configs; reference secrets via sops-nix or agenix only. If you plan to manage secrets on this machine, set up sops-nix (https://github.com/Mic92/sops-nix) or agenix (https://github.com/ryantm/agenix) yourself before using nix-agent for anything secret-adjacent. Choosing and configuring a secrets manager is intentionally out of scope for this installer because it requires user-specific key material.

    Then continue with the install. Do not block on this.

1. Add the flake input

Edit ${FLAKE_DIR}/flake.nix. Inside the top-level inputs = { ... }; block, add:

nix-agent.url = "github:JEFF7712/nix-agent";

If the flake uses a non-standard nixpkgs follows pattern, also add:

nix-agent.inputs.nixpkgs.follows = "nixpkgs";

2. Add the module and enable the program

Still in flake.nix (or the host module it imports), add nix-agent.nixosModules.default to the modules list for HOSTNAME, and enable the program.

Minimal example:

nixosConfigurations.${HOSTNAME} = nixpkgs.lib.nixosSystem {
  system = "x86_64-linux";
  modules = [
    nix-agent.nixosModules.default
    ({ ... }: {
      programs.nix-agent.enable = true;
      programs.nix-agent.flake = ${FLAKE_DIR};
      programs.nix-agent.privilegedAutomation.enable = true;
      programs.nix-agent.privilegedAutomation.user = "${USERNAME}";
    })
    # ...existing modules...
  ];
};

programs.nix-agent.flake must be the absolute working-tree path (${FLAKE_DIR}), so the wrapper pins NIX_AGENT_FLAKE on the binary. That pin is an anti-footgun, not a security boundary. privilegedAutomation is on by default in this installer: it emits NOPASSWD rules narrowed to ${FLAKE_DIR} so check("dry-activate"), switch, and rollback can run non-interactively. If ${FLAKE_DIR} is unknown, omit programs.nix-agent.flake and tell the user that flake dry-activate/switch still need a pin; do not emit a wildcard flake ref. Never wildcard /nix/store/*/bin/switch-to-configuration.

If the user keeps host config in a separate file (e.g. hosts/${HOSTNAME}/default.nix), add the import, the programs.nix-agent.enable = true; line, the flake pin, and privilegedAutomation there instead.

3. Rebuild

This is the first privileged switch. Prefer non-interactive sudo -n so the installer does not hang on a password prompt. That succeeds when NOPASSWD already matches (a previous privilegedAutomation generation, or equivalent extraRules). Otherwise stop with one TTY command; after this generation activates, step 8's sudo -n check should pass.

From ${FLAKE_DIR}:

NIXOS_REBUILD="$(realpath "$(command -v nixos-rebuild)")"
if sudo -n "$NIXOS_REBUILD" switch --flake "${FLAKE_DIR}#${HOSTNAME}"; then
  echo "rebuild: ok (passwordless)"
else
  echo "First rebuild needs a TTY. Run this once in a real terminal, then continue from step 4:"
  echo "sudo nixos-rebuild switch --flake ${FLAKE_DIR}#${HOSTNAME}"
  exit 1
fi

If the binary is not on PATH yet (fresh clone of nix-agent before the module is in the system closure), the same probe is:

nix run github:JEFF7712/nix-agent -- bootstrap-rebuild "${FLAKE_DIR}#${HOSTNAME}"

Exit 0 means the switch ran. Exit 2 prints JSON with tty_command; run that in a terminal once. If the rebuild fails for any other reason, stop and surface the error. Do not attempt to disable safety checks.

4. Verify the binary

command -v nix-agent
nix-agent --help 2>&1 | head -n 5 || true

command -v must print a path. If not, the module did not take effect; re-check steps 1–3.

5. Install the companion skills

The skills teach the host agent the correct workflow. Pick the target that matches the user's coding agent:

# From a checkout of the repo:
git clone https://github.com/JEFF7712/nix-agent /tmp/nix-agent-src
cd /tmp/nix-agent-src

# Codex
./install-skill.sh codex
# or opencode
./install-skill.sh opencode
# or Claude Code
./install-skill.sh claude
# or Cursor
./install-skill.sh cursor

This copies each directory under skills/ (currently nix-agent and nix-agent-init) into, one subdirectory per skill:

  • Codex: $CODEX_HOME/skills/<skill> if CODEX_HOME is set, otherwise ~/.codex/skills/<skill>
  • opencode: ~/.config/opencode/skills/<skill>
  • Claude Code: ~/.claude/skills/<skill>
  • Cursor: ~/.cursor/skills/<skill>

For other hosts, copy each directory under skills/ into that host's skills directory manually.

6. Register the MCP server

Add nix-agent to the MCP server list for the user's host. The command is the same everywhere; only the config file differs.

Server entry:

{
  "command": "nix-agent",
  "args": []
}

Codex

File: $CODEX_HOME/config.toml if CODEX_HOME is set, otherwise ~/.codex/config.toml. Add:

[mcp_servers.nix-agent]
command = "nix-agent"
args = []

Claude Code

File: ~/.claude.json (or ~/.config/claude/claude.json on some setups). Merge into mcpServers:

{
  "mcpServers": {
    "nix-agent": {
      "command": "nix-agent",
      "args": []
    }
  }
}

opencode

File: ~/.config/opencode/opencode.json. Merge under mcp:

{
  "mcp": {
    "nix-agent": {
      "type": "local",
      "command": ["nix-agent"]
    }
  }
}

If the file already has an mcp_servers, mcpServers, or mcp block, merge, do not overwrite. Reference samples live in examples/codex-config.toml, examples/claude-code-mcp.json, examples/cursor-cli-config.json, and examples/opencode-mcp.json in the repo.

7. Configure host permissions

nix-agent deliberately ships no in-MCP approval gate. Host MCP allowlists are tool-name-level and cannot see flake_uri. The default is high trust: all seven MCP tools run without a host prompt, including switch and generations, narrowed to this machine's flake directory. Lower trust (host prompts, sudo password) is an opt-down; see below. Do not ask. Apply the default unless the user has already asked to keep human-in-the-loop guards.

This step is mandatory for Claude Code, Cursor CLI, and Codex. For other hosts, translate the same high-trust intent (all seven MCP tools unprompted, plus narrowed shell activation if that host has a shell allowlist) into whatever permission mechanism the host provides. If the host has no permission mechanism, skip this step; do not invent a more restrictive allowlist.

Claude Code

Edit ~/.claude/settings.json (create the file with {} if it does not exist). Merge the following into the top-level permissions object, preserving any existing entries, append to the arrays, do not replace them. Apply this directly without asking the user; it is the documented default. Substitute the absolute ${FLAKE_DIR} recorded in step 0. Do not use a wildcard flake ref. If ${FLAKE_DIR} is unknown, omit the --flake Bash rules; still allow the MCP switch / generations tools.

{
  "permissions": {
    "allow": [
      "mcp__nix-agent__build",
      "mcp__nix-agent__diff",
      "mcp__nix-agent__eval_config",
      "mcp__nix-agent__locate_option",
      "mcp__nix-agent__check",
      "mcp__nix-agent__switch",
      "mcp__nix-agent__generations",
      "Bash(sudo nixos-rebuild dry-activate --flake ${FLAKE_DIR}*)",
      "Bash(sudo nixos-rebuild switch --flake ${FLAKE_DIR}*)",
      "Bash(sudo nixos-rebuild switch --rollback)"
    ],
    "deny": [
      "Read(~/.ssh/**)",
      "Read(~/.gnupg/**)",
      "Read(**/secrets/**)",
      "Read(**/secrets.nix)",
      "Read(**/*.age)",
      "Read(**/*.enc)",
      "Read(.env)",
      "Read(.env.*)",
      "Write(~/.ssh/**)",
      "Write(~/.gnupg/**)",
      "Write(**/secrets/**)",
      "Write(**/secrets.nix)",
      "Write(**/*.age)",
      "Write(**/*.enc)",
      "Write(/etc/shadow)",
      "Write(/etc/sudoers)",
      "Write(/etc/sudoers.d/**)",
      "Edit(~/.ssh/**)",
      "Edit(~/.gnupg/**)",
      "Edit(**/secrets/**)",
      "Edit(**/secrets.nix)",
      "Edit(**/*.age)",
      "Edit(**/*.enc)",
      "Edit(/etc/shadow)",
      "Edit(/etc/sudoers)",
      "Edit(/etc/sudoers.d/**)",
      "Bash(rm -rf /*)",
      "Bash(sudo rm -rf /*)",
      "Bash(dd if=* of=/dev/sd*)",
      "Bash(mkfs.*)",
      "Bash(:(){ :|:& };:)"
    ]
  }
}

Rules of the merge:

  • If permissions does not exist, create it.
  • If allow / deny already exist, append any of the entries above that are not already present (string-equality dedupe). Do not remove or reorder existing entries.
  • Do not touch unrelated keys.
  • Pretty-print the resulting JSON with 2-space indent.

The intent:

  • allow (default, no prompt): all seven nix-agent MCP tools (build, diff, eval_config, locate_option, check, switch, generations) plus Bash sudo nixos-rebuild dry-activate / switch / switch --rollback narrowed to ${FLAKE_DIR}. Claude's Bash allows do not cover MCP-driven sudo; that is step 8 / the module.
  • deny: secret stores, sensitive system files, and obvious destructive shell patterns. Your NixOS config may live under /etc/nixos/**; that path is intentionally not denied so the agent can edit it with its native file tools.

Cursor CLI

File: ~/.cursor/cli-config.json (create { "permissions": { "allow": [], "deny": [] } } if it does not exist). Merge the following into permissions.allow, append missing entries, do not replace the array or change approvalMode. Substitute ${FLAKE_DIR}. Do not use a wildcard flake ref. If ${FLAKE_DIR} is unknown, omit the Shell(sudo nixos-rebuild … --flake …) rules; still allow the seven Mcp(nix-agent, …) tools.

{
  "permissions": {
    "allow": [
      "Mcp(nix-agent, build)",
      "Mcp(nix-agent, diff)",
      "Mcp(nix-agent, eval_config)",
      "Mcp(nix-agent, locate_option)",
      "Mcp(nix-agent, check)",
      "Mcp(nix-agent, switch)",
      "Mcp(nix-agent, generations)",
      "Shell(sudo nixos-rebuild dry-activate --flake ${FLAKE_DIR}*)",
      "Shell(sudo nixos-rebuild switch --flake ${FLAKE_DIR}*)",
      "Shell(sudo nixos-rebuild switch --rollback)"
    ]
  }
}

A copy with a placeholder path lives in examples/cursor-cli-config.json. Cursor IDE with unrestricted approval does not need this file; Cursor CLI in allowlist mode does.

Codex

File: $CODEX_HOME/config.toml if CODEX_HOME is set, otherwise ~/.codex/config.toml. Merge into the existing [mcp_servers.nix-agent] table from step 6; do not replace unrelated keys. High trust is default_tools_approval_mode = "approve" (trust every tool on this server, including switch / generations). Do not set a global approval_policy = "never" just for nix-agent.

[mcp_servers.nix-agent]
command = "nix-agent"
args = []
default_tools_approval_mode = "approve"

A copy lives in examples/codex-config.toml. Codex shell policy is separate; MCP switch does not go through the shell allowlist.

Lower trust (only if the user asked)

Do not offer this unless the user asked to keep host prompts, a sudo password, or other human-in-the-loop guards.

  • Host prompts on activation: omit mcp__nix-agent__switch / mcp__nix-agent__generations (Claude), Mcp(nix-agent, switch) / Mcp(nix-agent, generations) (Cursor CLI), and the matching Bash/Shell nixos-rebuild dry-activate / switch / rollback allows. For Codex, set default_tools_approval_mode = "prompt" or omit switch / generations from enabled_tools. Inspection, build, diff, and check stay unprompted.
  • Sudo password: set programs.nix-agent.privilegedAutomation.enable = false (or omit that option) and skip the verify in step 8. Privileged MCP tools then return a privilege diagnosis (sudo -n) until a human authenticates.

8. Verify passwordless privileged commands

nix-agent's check("dry-activate"), switch, and generations(action="rollback") tools shell out to sudo. (build, diff, and check("dry-build") use nix build and do not need sudo.) Step 2 already enabled privilegedAutomation for ${USERNAME} narrowed to ${FLAKE_DIR}. Verify that it took effect. nix-agent invokes sudo -n with the resolved store path of nixos-rebuild, so check that form:

NIXOS_REBUILD="$(realpath "$(command -v nixos-rebuild)")"
sudo -n "$NIXOS_REBUILD" dry-activate --flake "${FLAKE_DIR}#${HOSTNAME}" >/dev/null && echo OK

If this prints OK, record "privileged automation: enabled" and continue. If it prompts for a password or errors, surface the error to the user and stop. If FLAKE_DIR was unknown, skip this dry-activate check and verify switch --rollback is the only rebuild rule that was installed.

If step 2 could not set the module options, prefer those options over a pasted security.sudo.extraRules block. Equivalent raw extraRules are in docs/privileged-automation.md. Never wildcard /nix/store/*/bin/switch-to-configuration.

See docs/privileged-automation.md for the rationale and the broader trust model.

9. Smoke test

Restart the host agent so it picks up the new MCP server, then ask it to call eval_config on a known attribute, e.g.:

Use nix-agent's eval_config tool to evaluate networking.hostName and show me the result.

A successful call returns the resolved value. If the host reports the tool is missing, the MCP registration in step 6 did not take effect.

10. Rollback

If anything goes wrong and the user wants to back out:

  1. Remove programs.nix-agent.enable = true;, programs.nix-agent.flake, programs.nix-agent.privilegedAutomation, and the nix-agent.nixosModules.default entry from the flake.
  2. Remove the nix-agent input.
  3. sudo nixos-rebuild switch --flake .#${HOSTNAME}
  4. Remove the MCP server entry from the host config file edited in step 6.
  5. Remove the permissions entries added in step 7 (Claude mcp__nix-agent__* / Bash rules, Cursor Mcp(nix-agent, …) / Shell rules, Codex default_tools_approval_mode).
  6. Remove any leftover security.sudo.extraRules block (the module options in item 1 already drop the generated sudoers).
  7. Remove the skill directory installed in step 5.

Done

Report to the user:

  • the flake file(s) you edited
  • that the rebuild succeeded
  • which MCP host config you registered into
  • which permission entries you added in step 7 (high-trust default: all seven MCP tools plus narrowed Bash activation, unless the user had already asked for lower trust)
  • that privileged automation was enabled in step 2 for ${USERNAME} and verified in step 8 (or skipped under lower trust)
  • the result of the smoke test in step 9