`GEMINI.md` instructions are ignored

### What happened?

Gemini-3-pro fails to adhere to instructions in `GEMINI.md`. In the linked session the gemini file instructs the model not to create python scripts but to invoke them directly on the command line instead. This is ignored and the model tries to write a file. When reminded of this, the model then tries to use the command line correctly.

This behaviour is reproducible with almost any non-trivial instructions. #11799 uses a trivial instruction which works most of the time, but anything more complex than this seems to be lost.

It is getting really frustrating as we have some important instructions in `AGENTS.md`/`GEMINI.md` which are just being ignored.

### What did you expect to happen?

Instructions in md files should be respected.

### Client information

* **CLI Version:** 0.18.0
* **Git Commit:** 7beccfa03
* **Session ID:** d18f1c3f-486e-45b3-8fc0-318cf70391d9
* **Operating System:** darwin v22.15.1
* **Sandbox Environment:** no sandbox
* **Model Version:** pro
* **Memory Usage:** 187.8 MB
* **IDE Client:** Antigravity

### Login information

Google account

### Anything else we need to know?

_No response_