Agent instructions and permissions

assist sync sets Claude Code up to work with assist: every session gets instructions written for its repo, read-only commands run without asking you, and commands you don’t want agents to run are blocked with a message saying what to do instead.

Repo instructions

Each Claude Code session starts with instructions composed for its repo, such as how to verify a change and how to commit. Sections are included when they apply: the verify section only appears when the repo has verify checks, and the TypeScript refactoring section only in TypeScript repos.

Tune them per repo:

• Add your own notes, shown as a Repo notes section:

  assist config set advice.extra "Deploy from main only"

• Force a section on or off, whatever its condition says. assist advise --explain lists every section’s name:

  assist config set advice.sections.verify false

• Replace the verify section’s text, which also forces it on:

  assist config set advice.verify "Run make check"

• List your own rules under advice.rules, each with a title and text, shown as a Your rules section:

  advice:
    rules:
      - title: Link, don't navigate
        text: Give the direct URL whenever you send me to a web page or setting.

Fewer permission prompts

Read-only commands of common CLIs, such as git log or gh pr view, run without a permission prompt. Commands that change things still ask.

When the same prompts keep coming up, run /prompts. The agent lists the commands you’ve been asked about most, suggests which are safe to allow, and makes only the changes you agree to.

Blocking commands

A deny rule stops agents running a command and tells them what to do instead. Add one with assist deny add:

assist deny add "rm -rf" "Delete files one at a time with rm"

Rules are kept in the deny config key, so they can also be edited on the Config page.

assist also blocks some commands for agents, such as git commit, gh pr create and npm run, so they use the assist command that does the job. To let agents use npm run in a repo:

assist config set cliHook.blockNpmRun false

Desktop notifications

assist shows a desktop notification when Claude Code needs your permission or is waiting for input. To turn them off:

assist config set notify.enabled false