research-adopt

name	research-adopt
description	AnchoredAutoResearch adopt skill for Codex. Anchors the protocol to an in-progress project (existing LaTeX + git + logs). Imports state as read-only Cycle 1; real cycles start at Cycle 2.
version	1.0.0

AnchoredAutoResearch — ADOPT Entrypoint

Use this skill when the user invokes $research-adopt in Codex.

MANDATORY: Read Protocol Before Any Action

1. Read AGENTS.md for project rules
2. Read RSD.md if present — if it exists, REFUSE (ADOPT never overwrites).
3. Follow the ADOPT protocol in ../research/references/adopt-protocol.md
4. Follow the Imported Cycle Format in ../research/references/rsd-schema.md
5. Follow ../research/references/core-principles.md for anti-gaming rules
6. Reuse ../research/references/knowledge-sources.md scan logic for any existing context/ sources

Argument Parsing

From the user's invocation:

• --mode strict|fully-auto — adopt mode. Default: strict.
• --from /path — source project path. Default: CWD.
• Remaining free-form text — extra user context to quote in Research Goal.

Execution

1. Run ADOPT pre-flight:

   • Refuse if RSD.md exists.
   • Resolve --from. Refuse if missing or not a directory.
   • Refuse if --from has no .tex, no .git, no logs/, and no context/ — suggest INIT instead.
   • Validate --mode. Default to strict if omitted.

2. Run the input scan:

   • LaTeX draft (section titles + first paragraphs + abstract)
   • Git history (experiment-looking commits, top 20)
   • Logs (newest 3 files)
   • Context sources (via knowledge-sources protocol)

3. Write RSD.md following the strict or fully-auto protocol in adopt-protocol.md. Use the Imported Cycle Format. Set ## Status: WAITING_HUMAN, ## Phase: ADOPT, ## Cycle: 1.

4. Create missing directories: checkpoints/, logs/, outputs/, context/papers/, context/notes/, context/prior_work/.

5. Run bash scripts/compile_rsd.sh.

6. Copy frozen state to checkpoints/cycle_1_adopt.md and checkpoints/cycle_1_adopt.pdf.

7. Git commit:

   • Strict: "research: adopt existing project (strict)"
   • Fully-auto: "research: adopt existing project (fully-auto)"

8. If a .tex was found, offer the PAPER handoff (ask before copying to outputs/paper/paper.tex; pick venue; invoke PAPER import-from-tex).

9. Stop and tell the human to read RSD.pdf, that Cycle 1 is the imported read-only snapshot, that their first new cycle will be Cycle 2, and to approve or revise in chat or RSD.md before running $research.

Stream all output live. Never run in background.