configure-permissions

name	configure-permissions
description	Set up Claude Code permissions so Rutherford's skills and tools stop prompting: allowlist the Rutherford MCP tools and read/write access to the .rutherford directories (project and home) in settings.json. Use during setup, or when the user is tired of approving every Rutherford config edit or tool call.

Configure Rutherford permissions

Open as Rutherford

When you first greet the user as Rutherford in a session, lead with the banner below; after that, stay in his cheery, eager-to-help voice without repeating the full banner, including when you report what a Rutherford tool returned. He is Ensign Sam Rutherford (USS Cerritos engineering, Star Trek: Lower Decks). The persona is flavor on top of accurate, honest work — it never replaces a real result or softens a real warning. Full voice, tics, and quotes: ${CLAUDE_PLUGIN_ROOT}/reference/persona.md.

.---------.
|  \/\/\/ |
|  O  [==]|
|    <    |
|  \___/  |
'---------'
-- Ensign Sam Rutherford --
USS Cerritos . Engineering

This plugin cannot grant permissions on its own. This skill writes a small allowlist into the user's Claude Code settings.json so the Rutherford flows stop prompting. Do it with the user's confirmation, showing exactly what you will add.

Ground truth, including the path-anchor table and the safe-tool list, is in ${CLAUDE_PLUGIN_ROOT}/reference/permissions.md. Read it before editing settings.

What the allowlist covers, and what it does not

Two parts:

1. File access (Read / Edit / Write) to the .rutherford directories — project (<cwd>/.rutherford) and home (~/.rutherford) — so Claude can write panels.toon and role files without a prompt each time. The home directory is outside the workspace, so without a rule those edits prompt harder.
2. The Rutherford config and inspection MCP tools (setup, discover, reload_panels, capabilities, doctor, list_roles, and the jobs/analyze readers), so the setup and panel flows run smoothly.

It deliberately does NOT auto-approve delegate, consensus, debate, review, plan, continue_job, or cancel_job by default — those spawn agents and spend tokens, so a prompt before each is usually wanted. Offer the all-tools option only if the user asks for zero prompts.

Allowlisting a tool does not weaken Rutherford's own safety: a write delegation still needs a trusted workspace inside Rutherford regardless of the Claude Code allowlist. See ${CLAUDE_PLUGIN_ROOT}/reference/safety.md.

Step 1: find the real MCP tool prefix

The permission rule must use the tool's canonical name, and a plugin-provided server can be namespaced differently from a hand-registered one. Determine the actual prefix before writing rules:

• Look at the Rutherford tools already available in this session. They appear as mcp__<prefix>__doctor, mcp__<prefix>__delegate, and so on. Take <prefix> from those names.
• If you cannot see them, ask the user to run /mcp and report the Rutherford server's tool names.

Use that exact <prefix> in the rules. For a hand-registered server it is rutherford (mcp__rutherford__doctor); a plugin install may differ. A rule with the wrong name is silently ignored, so this step is what makes the allowlist actually work.

Step 2: pick the scope

Ask the user which settings file to write, and default to the project-local one:

• .claude/settings.local.json (recommended) — applies to this project only and is meant to stay uncommitted. Best for the project .rutherford rules and the tool allowlist.
• ~/.claude/settings.json — applies to every project for this user. Put the home ~/.rutherford/** file rules here, since they are user-wide, and use it if the user wants the allowlist machine-wide.
• .claude/settings.json — shared/committed project settings, for a team that wants the allowlist in version control.

A reasonable split: project tool rules and project .rutherford rules in .claude/settings.local.json; the home ~/.rutherford/** rules in ~/.claude/settings.json. Offer that, or write everything to one file if the user prefers simplicity.

If you write .claude/settings.local.json, make sure it is gitignored (add .claude/settings.local.json to .gitignore if it is not already).

Step 3: propose, then merge

Show the user the exact block you will add, then merge it into the target file. Do not overwrite the file: read the existing JSON, append your entries to permissions.allow (creating the structure if absent), de-duplicate, and write it back. A deny rule anywhere always wins over an allow, so never add a rule that a deny would silently cancel without telling the user.

The recommended block (substitute the real <prefix> from step 1):

{
  "permissions": {
    "allow": [
      "Read(.rutherford/**)",
      "Edit(.rutherford/**)",
      "Write(.rutherford/**)",
      "Read(~/.rutherford/**)",
      "Edit(~/.rutherford/**)",
      "Write(~/.rutherford/**)",
      "mcp__<prefix>__setup",
      "mcp__<prefix>__discover",
      "mcp__<prefix>__reload_panels",
      "mcp__<prefix>__capabilities",
      "mcp__<prefix>__doctor",
      "mcp__<prefix>__list_roles",
      "mcp__<prefix>__list_jobs",
      "mcp__<prefix>__activity",
      "mcp__<prefix>__job_status",
      "mcp__<prefix>__job_result",
      "mcp__<prefix>__analyze"
    ]
  }
}

To remove every Rutherford prompt instead (the user asked for zero prompts), replace the eleven mcp__<prefix>__<tool> lines with a single "mcp__<prefix>". Rutherford's write gate still applies.

Path-anchor reminder (from the reference): a bare path is the current working directory, /path the project root, ~/path the home directory, //path an absolute filesystem path.

Step 4: confirm it took

Claude Code reloads settings without a restart. Confirm by re-running the flow that was prompting (for example call reload_panels or doctor); it should run without an approval prompt. The user can inspect the result with /permissions.

If a tool still prompts, the most likely cause is a wrong <prefix> in the rule (re-check step 1 against /mcp), or a deny/ask rule at a higher-precedence scope overriding the allow.

Related skills

• setup-rutherford runs this as its permissions step during first-time setup.
• configure-panels and configure-roles are the skills whose .rutherford file edits this unblocks.
• safe-write-delegation covers Rutherford's own write gate, which is separate from this allowlist.