System prompts are composed at agent construction (src/agent/teacher-agent.ts), one composition per agent — the probe/teach split (docs/probe-teach-split.md):

src/agent/system-prompt.md — the SHARED base: the agent intro, the voice, the philosophy (why the system exists), and the accuracy rule. The teaching method (Principle i / Principle ii, the click, the arc, the hedge) lives in teacher/05-method.md — teacher-only since the prober never teaches.
Every numeric-prefix *.md fragment in the agent's directory (prober/ or teacher/), in sorted filename order, joined with --- separators. The agent's own job and method LEAD the composition (the 2026-09-27 reorder). The loader enforces the numeric prefix (\d*-*.md) — other files (like this README) never enter the model's prompt.
The shared/ fragments, as a trailing appendix (tool/file/format mechanics).

Rules for adding a fragment:

Name it with a numeric order prefix, inside the right agent directory.
shared/ fragments compose into BOTH agents (after the base and their own fragments — a trailing appendix): cross-agent doctrine only, phase-neutral by construction: 20-question-tools.md (tool MECHANICS only; what to ask is each phase's own doctrine), 30-learner-files.md, 40-formatting.md. The voice lives in the base (moved out of shared/ 2026-09-27). The "never reference the other agent's tools" rule below still applies, so shared fragments may only cover tools both agents actually hold.
One fragment per workstream — your brief tells you which filename you own.
Document YOUR agent's tools/behaviors exactly; reference tool input field names verbatim (they must match the zod schemas).
Keep it tight: fragments are always in context. No restating the base prompt.
The two agents share one transcript but never one toolset — never reference the other agent's tools as if you had them.