Googles system prompt of the CLI is heavily flawed IMO. That's where most problems arise. I am using a custom one. At least it is highly configurable. The vanilla Gemini Cli is not usable for me. For instance, they have a section they introduce with Proactiveness where they give advice about what is Persistence (in the agent loop). This wrong wording alone causes the agent to be "proactive" in many ways that is not wanted. After I asked the model itself once, why it started to scan my entire codebase when I just asked to create a new branch, it directly said to me there is "Proactiveness" in its system prompt. I was baffled, why would anybody want that? So i digged deeper and did also a thorough analysis with Opus 4.7 of just this system prompt file - that cost me an entire Pro-session btw. - and documented the results in this pr: https://github.com/google-gemini/gemini-cli/pull/26129 - I am using the optimized prompt and had no issues so far I had with the original one.

Another big issue is "model panic" - the Gemini model often overwrites entire files "from memory" with write_file, when the edit tool fails 2 times. That occasionally causes code degradation, and when there are multiple turns and there is no backup, the model starts to get nuts, trying to fix its errors, and destroys even more in the effort to just make it compile / build. I gave it a rotating pre-write backup and a restore_file tool. The model panic vanished. https://github.com/google-gemini/gemini-cli/pull/25947

With these two fixes, Gemini CLI is pretty good - without them I wouldn't use it.