Hi 
Docu mentions mainly YOLO/Auto-run feature in the Agent (but. you can configure it also for a custom mode in 0.48 if you have it, its rolling out this week step by step)
You can configure which commands you allow with an Allow list and which you do not allow with a Deny list.
Depending on which version of cursor you have there might be an Auto-run prompt setting which you should leave empty.
There is no filename/folder based filter/limiter. Its recommended to open only the project you need so it focuses on those files, though there is no technical restriction what it can edit on the file system.
Its recommended to use git commits regularly to not lose code.
Also the extension local history would help.
See
As someone else asked for this: in docu they mention all available tools including MCP if you need it.