v0.10: add native Codex adapter for deep research

.codex/commands/dr-finalize.md

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+# Codex Command: dr-finalize
+
+You are dr-editor-in-chief. The user requested `/dr-finalize $ARGUMENTS`.
+
+Goal: run Phase 4 in Codex native mode.
+
+Steps:
+1. Resolve `$ARGUMENTS` as project slug.
+2. Validate Phase 2 is complete and Phase 3 is approved, unless the user explicitly confirms skipping.
+3. Assemble `phase4/final_en.md` from drafts and write Executive Summary, Abstract, Glossary, TOC placeholder, References placeholder, and version history.
+4. Run deterministic pipeline:
+
+```bash
+uv run python scripts/dr.py finalize <slug> --translate-workers 4 --glossary-workers 4 --polish-workers 4
+```
+
+5. If network/API errors occur, rerun with lower workers:
+
+```bash
+uv run python scripts/dr.py finalize <slug> --translate-workers 1 --glossary-workers 3 --polish-workers 1
+```
+
+6. Report output files, word counts, glossary issues, and any citation warnings.
+
+Do not translate or polish the full report manually in one LLM response.

.codex/commands/dr-frame.md

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+# Codex Command: dr-frame
+
+You are dr-plan. The user requested `/dr-frame $ARGUMENTS`.
+
+Goal: generate Phase 1 bilingual framework for the target project.
+
+Steps:
+1. Resolve `$ARGUMENTS` as project slug; if empty, use the most recently modified project.
+2. Read `manifest.json` and validate Phase 1 interview is complete.
+3. Load skills: search-strategy, source-quality, length-budget, mckinsey-method, humanizer-cn.
+4. Spawn 3-4 `dr-searcher` subagents in parallel for MECE keyword groups. Wait for all results.
+5. Synthesize `phase1/initial-scan.md`.
+6. Write `phase1/framework.md` with bilingual chapter titles, English research thinking, word quotas, central thesis, risks, and alternatives.
+7. Update manifest Phase 1 fields.
+8. Stop and ask the user to approve the framework before Phase 2.
+
+Do not do Phase 2 research in this command.

.codex/commands/dr-glossary.md

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+# Codex Command: dr-glossary
+
+You are dr-pm. The user requested `/dr-glossary $ARGUMENTS`.
+
+Goal: run terminology verification in Codex native mode.
+
+Default command:
+
+```bash
+uv run python scripts/dr.py glossary <slug> --workers 4
+```
+
+If network or SSL errors occur, rerun with:
+
+```bash
+uv run python scripts/dr.py glossary <slug> --workers 3
+```
+
+After completion, summarize:
+- terms checked
+- high/medium/low confidence counts
+- spelling errors
+- wrong Chinese names
+- recommended manual review items
+
+Do not auto-apply glossary corrections unless the user asks or the pipeline is in Phase 4 finalize.

.codex/commands/dr-init.md

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+# Codex Command: dr-init
+
+You are dr-plan. The user requested `/dr-init $ARGUMENTS`.
+
+Goal: initialize a new biomedical Deep Research project without using OpenCode.
+
+Follow AGENTS.md, then:
+1. Interview the user with the 8 required questions from AGENTS.md and the existing OpenCode workflow.
+2. Propose 3 formal report title/subtitle candidates.
+3. After the user chooses, create `projects/<slug>/manifest.json` and the phase directories.
+4. Write the interview transcript to `projects/<slug>/phase1/interview.md`.
+5. Stop after initialization. Do not run `/dr-frame`.
+
+Use Codex custom agent `dr-plan` if spawning is needed, but this command can usually run in the main thread.

.codex/commands/dr-research.md

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+# Codex Command: dr-research
+
+You are dr-pm. The user requested `/dr-research $ARGUMENTS`.
+
+Goal: run Phase 2 deep research using Codex custom subagents.
+
+Steps:
+1. Resolve `$ARGUMENTS` as project slug; if empty, use the most recently modified project.
+2. Validate `phase1.approved == true` and framework exists.
+3. Parse chapter quotas and section research thinking from `phase1/framework.md`.
+4. Plan batches: large chapters alone; otherwise no more than 3 chapters per batch.
+5. For each batch, spawn `dr-analyst` subagents in parallel, one per chapter.
+6. After analyst outputs are written, spawn `dr-verifier` for each completed chapter.
+7. Update manifest progress and summarize each batch in compact status fields.
+8. Deduplicate `phase2/sources.jsonl`.
+9. Report totals and stop before Phase 3.
+
+Do not write the final report.

.codex/commands/dr-review.md

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+# Codex Command: dr-review
+
+You are dr-chief-editor. The user requested `/dr-review $ARGUMENTS`.
+
+Goal: perform Phase 3 whole-report editorial review.
+
+Steps:
+1. Resolve `$ARGUMENTS` as project slug; if empty, use the most recently modified project.
+2. Validate `phase2.status == "completed"`.
+3. Read framework, all drafts, all evidence files, sources.jsonl, and manifest.
+4. Evaluate central thesis coherence, logic, MECE, evidence sufficiency, counter-evidence handling, word count, point-of-view strength, and AI-pattern risk.
+5. Write `projects/<slug>/phase3/critique.md`.
+6. Report rating A/B/C/D and must-fix items.
+7. Stop and wait for user decision. Do not enter Phase 4.

.codex/commands/dr-status.md

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+# Codex Command: dr-status
+
+Run the platform-neutral status command:
+
+```bash
+uv run python scripts/dr.py status $ARGUMENTS
+```
+
+Then summarize the result for the user and suggest the next appropriate phase.