Start Research

Start-Research

Interview-style flow that takes a freshly-installed OMXR project (post-$omxr-setup) and walks the user through filling in what their research is about — working title, hypothesis, target venue, datasets, narrative spine, preset choice — then scaffolds the LaTeX manuscript directory.

When this skill is invoked, immediately execute the workflow below. Do not only restate or summarize these instructions back to the user.

This is the "deep interview" complement to $omxr-setup's "install" role.

Argument parsing

Inspect $ARGUMENTS (passed through by commands/start-research.md). Treat the first token as the preset hint:

• minimal — skip the preset-overlay prompt entirely (no examples/<field>/ overlay)
• neuro-fmri — pre-select the neuro-fMRI preset overlay (still confirms before applying in phase 2)
• no-overlay — alias of minimal
• (empty) — ask the user during the interview (phase 2)

Additional standalone flags (may appear in any position; not mutually exclusive with the preset hint):

• --no-venue-seed — skip phase 5 (venue scope seed). @reviewer stays generic. Record this so phase 7 surfaces it.

Record the preset hint as preset_arg and any flags as flags so downstream phases can consume them.

Phase execution

Execute phases sequentially. For each phase, read the linked file and follow its instructions exactly. If an earlier phase reports an early stop (e.g. user cancelled, $omxr-setup not run and user declined to run it), do not skip phase 7 (the report) — surface the stop reason there.

1. Phase 1 — Precheck. Read phases/01-precheck.md.
2. Phase 2 — Interview. Read phases/02-interview.md.
3. Phase 3 — Fill AGENTS.md. Read phases/03-fill-agents-md.md.
4. Phase 4 — Preset overlay (agent memory). Read phases/04-preset-overlay.md.
5. Phase 5 — Venue scope seed (reviewer specialization). Read phases/05-venue-scope-seed.md. Runs after phase 4 on purpose: if phase 4 installed a preset reviewer MEMORY.md, phase 5 appends the venue block to it without disturbing the preset content. If phase 4 didn't run (no preset), the canonical template is still byte-identical to the schema, so phase 5 performs a full structured replacement instead.
6. Phase 6 — Manuscript scaffold (delegated). Read phases/06-manuscript-scaffold.md. This phase delegates to the manuscript-scaffold skill.
7. Phase 7 — Report. Read phases/07-report.md.

Re-running policy

Safe to re-run on an initialized project. The re-run contract:

• Phase 2 surfaces existing AGENTS.md values as defaults. The user can confirm-all to apply only newly-added fields.
• Phase 3 writes only fields that changed.
• Phase 4 only replaces agent MEMORY.md files that are still byte-identical to the canonical template (untouched). Modified memory is never overwritten.
• Phase 5 leaves an existing ## Venue-specific bar section in reviewer/MEMORY.md alone. To refresh, delete just that section and re-run.
• Phase 6 delegates to manuscript-scaffold, which has its own existing-content guard.

If the user wants to reset an agent's memory, instruct them to delete that specific .omx/omxr/agent-memory/<agent>/MEMORY.md and re-run $start-research. There is intentionally no --reset flag — deletion is an explicit, reviewable action.

Final recommendation

After phase 7's report, end by recommending the user run @supervisor where are we? for the first real conversation.