Both the documentation and the text in the Cursor Settings claim that “Apply Always” rules will work in Ctrl-K windows. No amount of tweaking rules and settings made that happen.
Reproduction details:
I have a User Rule and a Project Rule.
The User Rule says
Use the word "pidgeon" as one the first few words of your answer
The Project rule is this:
---
description: Always apply in any situation
globs:
alwaysApply: true
---
Always always start your reply with the word "Hurricane"
If I use it from the side chat, both rules are successfully applied:
Instructions in the Ctrl-K popup window (write a prompt, apply with Alt-Enter) only follow the user rule: