How to stop a Claude Code agent writing outside a directory

When you're sitting in front of an agent, "don't touch anything outside src/ " is enforced by you noticing. Unattended, it has to be enforced by something that runs whether or not anyone is watching. Claude Code gives you two mechanisms for that, and they are not interchangeable. One is declarative and can't express what you probably want. The other can, but is structurally blind to a whole category of writes. Here's what each one actually does, and the code for the second. Why permissions.deny isn't enough Permission rules live in settings.json and take the form Tool(specifier) : { "permissions" : { "deny" : [ "Read(./.env)" , "Read(./.env.*)" , "Write(./.github/**)" , "Write(//etc/**)" ] } } Paths are gitignore-style. A leading // means absolute, ~ means home, and anything else is relative to the settings file. deny beats ask , which beats allow , and rules merge across scopes rather than override — so a deny in project settings still applies even when your personal ~/.claude/settings.json allows the same thing. That precedence is the useful part: a deny rule is hard to undo by accident. The problem is shape. What you want for an unattended agent is an allow-list — only these directories, nothing else. What deny gives you is a block-list, and you cannot build the first out of the second. The obvious trick of denying everything and allowing back the exceptions fails on exactly the precedence rule that makes deny valuable: Write(**) in deny outranks every allow you pair it with, so the agent can write nothing at all. Claude Code does have one allow-list-shaped boundary — the project root, plus whatever you list in additionalDirectories . That stops an agent wandering into /etc . It says nothing about which directories inside your project it may write, which is usually the interesting question. Nobody's real worry is that a scheduled agent edits /etc/hosts . It's that the agent tasked with writing articles decides to fix its own scheduling config. So for anything fin