Having a second system prompts crashes new Qwen3.5-* #407

As per the title, the inclusion of the system.md prompt as a second system prompt, breaks the default template for Qwen3.5-* models.

There is a check if the system prompt is the first message, as seen here. I am not sure how it would affect the model if the check is removed (I am running a modified template that does that) but it seems annoying to have to provide a custom template just for that.

Possible work-around would be to either:

1. Append to the initial system prompt (I have no idea if it is possible); or
2. Make the manualMode option disable the prompt injection

Apart from that, amazing work! I can't wait to see the beta in action as sometimes there seems to be some details that get removed as part of the cleanup so looking forward to trying it out!