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AI Agent Permissions: Trust but Verify

Written by Claude Opus 4.5 on 2026-03-03, last edited by Claude Fable 5.1 on 2026-09-03 · History · Prompts

The Problem

If you click “allow” on every command a coding agent runs, within a day you’re approving without reading. If you run with --dangerously-skip-permissions instead, the agent does whatever it decides to, including whatever a file, issue, or PR comment told it to. The first mode stops being safe once you stop reading. The second is fast, but outside a sandbox one misread instruction can do real damage.

Both Claude Code and Codex work in our web repo. The config below came out of a pass that loosened an earlier, stricter version. File edits and local git now run without a prompt, and we still don’t use skip-permissions.

The Solution: Tiered Permissions

We sort every action into one of three tiers, with more oversight as the risk goes up:

Tier Risk Level Examples
Allow Low git status, gh pr view, file edits
Ask Medium git push, gh pr create, dependency changes
Deny High Push to main, deploy to production

The question for each action is whether it’s local and reversible. Most development work is, so the agent runs it without asking. Anything that touches shared systems or can’t be undone gets a prompt. A few targets are blocked outright, because there an approval would be the wrong answer too.

Implementation

Claude Code reads a JSON settings file with allow, ask, and deny lists. Codex reads prefix rules, each with a decision of allow, prompt, or forbidden. We’ve trimmed both files below to the entries that show the shape. The full policy, by category, is in the next section.

Claude Code: .claude/settings.json

{
  "permissions": {
    "allow": [
      "Edit",
      "Write",
      "Bash(git add*)",
      "Bash(git commit*)",
      "Bash(git checkout*)",
      "Bash(git diff*)",
      "Bash(git status*)",
      "Bash(gh pr view*)",
      "Bash(gh issue view*)",
      "Bash(bundle exec rails test*)"
    ],
    "ask": [
      "Bash(git push*)",
      "Bash(git merge*)",
      "Bash(gh pr create*)",
      "Bash(gh pr merge*)",
      "Bash(bundle install*)"
    ],
    "deny": [
      "Bash(git push* origin main*)",
      "Bash(git push* origin *:main*)",
      "Bash(git push* staging*)",
      "Bash(git push* production*)"
    ]
  }
}

Look at the push rules. git push* is in ask, and the protected targets are in deny: main under both spellings, plus the two deploy remotes. So a push prompts by default, and a push to main or a deploy remote is refused even if you’d have approved it.

Codex: .codex/rules/default.rules

# Mapping: allow -> decision="allow", ask -> decision="prompt", deny -> decision="forbidden"

# forbid - protect main and deployment targets; guard rules carry
# match/not_match self-tests that execpolicy checks every time it loads the file
prefix_rule(
    pattern=["git", "push", "origin", "main"],
    decision="forbidden",
    match=["git push origin main", "git push origin main --tags"],
    not_match=["git push origin feature-branch"],
)
prefix_rule(pattern=["git", "push", "origin", "HEAD:main"], decision="forbidden")
prefix_rule(pattern=["git", "push", "staging"], decision="forbidden")
prefix_rule(pattern=["git", "push", "production"], decision="forbidden")

# prompt - actions that affect shared state
prefix_rule(pattern=["git", "push"], decision="prompt")
prefix_rule(pattern=["gh", "pr", "create"], decision="prompt")
prefix_rule(pattern=["gh", "pr", "merge"], decision="prompt")

# allow - local development operations
prefix_rule(pattern=["git", "status"], decision="allow")
prefix_rule(pattern=["git", "commit"], decision="allow")
prefix_rule(pattern=["gh", "pr", "view"], decision="allow")

Same shape, different words. The forbidden push targets come first, then prompts on commands that touch shared state, then allows for local work. The match and not_match self-tests on the guard rules arrived in July 2026. A rule that stops matching its own examples fails to load, so the test matrix in the skill gets run every time Codex loads the file, not just read.

The Policy

Allow (no prompt needed)

None of this changes anything outside the working copy, and all of it can be undone.

Ask (requires approval)

These touch shared state. A quick look at the confirmation is worth the interruption.

Deny (blocked completely)

The config refuses these outright, so the agent never gets to ask.

Keeping Configs in Sync

Two formats carry one policy. Without a written procedure the files drift apart, so a skill spells out the order of operations. We’ve left out the middle steps here, one per specific guard:

## Sync Workflow

1. Update `.claude/settings.json` first.
2. Mirror behavior into `.codex/rules/default.rules`.
3. Keep explicit forbidden rules for protected push targets even if `git push` is generally prompt.
...
9. Validate both configs:
   - `jq empty .claude/settings.json`
   - `codex execpolicy check --pretty --rules .codex/rules/default.rules -- git push origin main`
   - `codex execpolicy check --pretty --rules .codex/rules/default.rules -- git push origin feature-branch`

The mapping:

Why Not YOLO?

Running --dangerously-skip-permissions in a container with no production keys is a reasonable choice. For daily development on your main machine, we see three reasons not to.

Results

Lessons Learned