Pretty much everything in Pi is handled by extensions. There's an extension for customizing the system prompt here: https://pi.dev/packages/pi-custom-system-prompt
My guess is that harnesses don't make core system prompts customizable out of the box because the system prompt is one of the defining features of the agent, and something they constantly iterate on and test between releases.
Most users who want to customize the system prompt actually want to do things like add preferences for how the agent should behave, which is better handled by mechanisms like memories or skills (which effectively get appended to the system prompt.)
Oh no, memories and skills are terrible replacements for system prompts.
Not only they get "lost" and ignored as the context grows, but the baseline behaviour of system prompts is retained in the agent.
Memories are implemented differently agent to agent. They are usually implemented by yet-another-model-call, as a distillation of typed prompts (working memory). Conversational communication is messy with a lower signal to noise ratio than the distillation (semantic memory). Semantic memories are much better than appending raw historical prompts.
Skills are prompts, albeit in a specific format. This is apparent in say, Codex where $MYSKILL is literally injecting the skill-prompt inline into a typed prompt. This all gets passed into the semantic memory system anyways, refining away cruft like redundancy, pleasantries, et al.
And none of this works properly. None.
You have to remind it what's in it's own memory, or the subagent skill is influenced by the main system prompt.
It's sloppy vibe coders productivity porn.