Research SOP

When the user asks a research-shaped question ("investigate X", "does X affect Y", "compare A and B"):

1. Memory lookup: call mcp__memory__match_signatures with the task description. If prior failures exist, read them first.
2. Literature gap: call mcp__memory__query_literature. If fewer than 3 relevant papers exist, spawn the librarian subagent.
3. Hypothesis generation: spawn the researcher subagent with literature context. Ask for 3-5 hypotheses.
4. Hypothesis selection: if you have 3 or more candidates, run $bt-tournament. Use mcp__memory__judge_hypotheses and mcp__memory__record_judgement to rank them. Inspect mcp__memory__get_bt_leaderboard and keep the top 2 only when their 95% intervals separate. Otherwise run more comparisons. Before picking one path among several, optionally call mcp__cockpit__narrate("one-sentence reason for the choice") so the cockpit's activity pane reflects the decision (v5.0; optional, suggestion only).
5. Preregister when the claim becomes confirmatory: for exploratory prototypes, the engineer may run and pin results without a prereg as long as the output is labelled exploratory. Before promoting a result to a main confirmatory claim, run $preregister and lock metric, direction, threshold, alpha, and mc_correction='bonferroni' into ver_preregistrations. The reviewer later refuses confirmatory manuscript claims whose matching prereg is not met.
6. Implementation: spawn the engineer subagent for the top hypothesis. Pass prereg_id when the work is confirmatory; otherwise tell the engineer the run is exploratory. Engineer must consult the budgeter agent before launching expensive work.
7. Verification: spawn the verifier subagent independently. Verifier calls mcp__verify__seed_perturb and resolves preregistrations only for confirmatory claims. Before handing off, optionally call mcp__cockpit__set_phase("verify", focus_nodes=[<hyp_id>]) so the cockpit's phase strip reflects the transition (v5.0; optional).
8. Write-up: only if the verifier passes AND the reviewer agent's verdict is accept for publication-critical claims. The reviewer must trace central result metrics back to a pin_id; confirmatory claims need met prereg and stable seed verdicts, while exploratory claims must be labelled as such. If the manuscript contains theorem-shaped claims (a \begin{theorem} block, a "we prove that" statement, or any quoted proposition node), the reviewer additionally runs the proof checklist from $prove-sop -- empty diagnostic manifest plus either a verified Lean attempt or an explicit unverified flag. Both checklists must pass for verdict='accept'.
9. Realtime pruning (optional): at any point, run mcp__memory__suggest_pause_low_strength(ucb_threshold=...). Default is dry-run; users with RESEARCH_AGENT_AUTO_PRUNE=1 see actual pauses. Use $replay to second-guess a paused branch.

At every step, call mcp__memory__propose_hypothesis and mcp__memory__attach_evidence to keep the graph live. When the BT tournament hands off, cite the current strength and 95% interval for each top candidate.