How to stop AI agents from overwriting project configuration files

I found that my automated coding assistants kept resetting my main environment template file every time I asked them to update dependencies. They acted like my config files were scratchpads erasing custom keys I needed for production. That was a headache.

The fix was simple: I set file-level permissions and added a clear exclusion list in the root instruction file. I made sure to tell the AI exactly which files were, off-limits. After that unintended changes stopped completely.

It saved me hours of debugging and made my local test runs consistent again. Now every time I use an agent the prompt includes a reminder to check file boundaries before running any script.

What method do you use to keep your coding tools from making unauthorized edits to sensitive system files?