Learn MYOS
Trust and permissions
Your assistant can write files and run commands on your computer. The permission system is how you decide what it may do on its own, without approving every single action for the rest of your life.
The trust prompt
The first time Claude Code starts in a folder, it asks whether you trust the files there. You may see this twice on day one: once for the folder you first launched it from, and once for your vault.
The question is narrower than it sounds. It is asking whether it may use the settings that came inside that folder: the instructions file, the permission list, the status line at the bottom of your screen. Saying yes applies to that folder and nothing else on your computer.
Say yes for your vault. If you say no, the vault's own configuration is ignored and your assistant will ask permission for every file it touches. The fix is to close the window, start again, and say yes.
What the kit allows by default
Writing and editing files is allowed without asking. That is the point of the whole system, and it is confined to your vault.
Running commands asks first. Every time your assistant wants to run something in a terminal, whether that is PowerShell or Bash on your machine, you see the command and approve or deny it.
Why the split is there
A file write inside your vault is low stakes and reversible. You can read exactly what changed, and if you turned on history you can undo it.
A command is different in kind. It could install software, delete something, or reach outside the vault entirely. Seeing them for the first while is how you learn what your assistant actually does, and that is worth a few days of clicking.
Auto mode, as an informed choice
Once you are comfortable, approving routine commands becomes noise rather than safety. At that point you can say so plainly: "you can run commands without asking".
Here is what you are agreeing to. Your assistant will be able to run commands on your machine without pausing for you each time, including ones that reach outside your vault. It is one line in a settings file, you can ask to see it, and you can ask to undo it just as easily.
There is also a middle path built into Claude Code itself. When a permission prompt appears, one of the options is to stop asking for that particular kind of action. That lets you loosen one thing at a time instead of everything at once.
The line that stays
There is a mode that turns off permission checks entirely. MYOS never uses it and never asks you to, and you should be suspicious of anything that tells you to.
Widening permissions is a decision you make knowingly, on your own machine, and reverse the same way.
Next: Rhythms. Or read the full disclosures.