feat: design the Clone Agent (Mitosis) — assistant reproduction conductor

[Jammy2211]

Overview

Design (not implement) the Clone Agent — organism-facing name Mitosis Agent — the future PyAutoBrain conductor that reproduces a mature domain assistant (initially autolens_assistant, freshly hardened by #33/#35 there) into a new specialised assistant cell (autofit_assistant, autogalaxy_assistant, …). Deliverable: a design document in PyAutoBrain following the conductor house pattern; implementation is a follow-up task.

Autonomy: launched --auto, effective level supervised (feature cap). Plan recorded here; run proceeds through mechanical stretches and parks at ship sign-off. No Heart reasons acknowledged at launch. Merge stays human.

Plan

1. Write PyAutoBrain/agents/conductors/clone/DESIGN.md in the house conductor-doc shape (tier, fundamental principle, boundary table, decision record, modes, must-never-do), explicitly marked design-not-yet-implemented.
2. Cover the prompt's requirements: inputs (library + workspace + optional HowTo + reference assistant); CloneDecision before any write (dry-run default, --apply gated, mirroring IntakeDecision); the exact-clone / differentiated-sibling / lightweight-seed question; the organ boundary (Mind stores intent, Brain plans, Build/Hands executes repo+file generation, Heart validates, Memory supplies architectural knowledge); CLI pyauto-brain clone with Mitosis as the docs-facing name.
3. Anchor the generic-vs-domain seam on the reference assistant's modes/maintainer.md "Assistant-as-template" section (added in Autonomy contract: make the Autonomy: header load-bearing (AUTONOMY.md) #34's audit exactly for this).
4. Phased implementation plan inside the design (v0 decision-only → v1 seed → v2 differentiated sibling), each phase a future Mind prompt — not bulk-issued now.
5. Validate (Brain skill line-count guard, link check), open draft PR, park at ship sign-off.

Details

Affected Repositories

• PyAutoBrain (primary, only) — new agents/conductors/clone/DESIGN.md; no CLI wiring, no behaviour change.

Branch Survey

Repository	Current Branch	Dirty?
./PyAutoBrain	main	clean

Suggested branch: feature/clone-mitosis-agent (in-place; design-doc only)

Original Prompt

PyAutoMind/feature/pyautobrain/clone_mitosis_agent.md (filed 2026-07-08; moves to issued/ with this issue).

[Jammy2211]

Checkpoint — design complete; parked at ship sign-off per the supervised autonomy contract.

Branch feature/clone-mitosis-agent, one commit e5aecc6: agents/conductors/clone/DESIGN.md (the design, in the conductor house shape, explicitly marked not-yet-implemented) + a design-stage entry in the Brain's conductor index.

Design highlights, per the prompt:

• Names: Clone Agent in engineering / CLI (pyauto-brain clone); Mitosis Agent in organism docs.
• Fundamental principle: the agent reasons about reproduction, never gives birth — CloneDecision on every run, writes only via --apply, and even then only by handing the generation plan to PyAutoBuild.
• The mandatory question: exact-clone / differentiated-sibling / lightweight-seed, asked before anything is generated (sibling expected as the normal mode).
• Organ boundary: Mind stores intent, Brain plans, Build executes, Heart validates the newborn, Memory is cited but never copied into a public assistant.
• Template seam: documentation-first — seeded from the reference assistant's modes/maintainer.md assistant-as-template partition (added there in autolens_assistant#34 for exactly this); unclassified files are reported back rather than guessed.
• Phasing: v0 decision-only (case study: PyAutoFit → autofit_assistant dry run) → v1 seed births via a Build primitive → v2 differentiated siblings + clone audit. Each phase is a future Mind prompt, filed as its predecessor nears shipping — not bulk-issued now.
• Open questions recorded for v0: repo-creation ownership, where clone audit lives, human-drafted example prompts.

Validation: Brain skill line-count guard passes (design doc is not a mandatory-load skill); no relative-link or CLI changes.

The question: approve opening the draft PR for this design? On approval it opens; merge stays human. Implementation (v0) is deliberately not started — it gets its own Mind prompt once this design is merged.

[Jammy2211]

Shipped. Design deliverable merged as #59 (squash 4af8a756): agents/conductors/clone/DESIGN.md + AGENTS.md pointer. Design-only per the prompt — no clone.sh/_clone.py/CLI wiring yet; those are the phased v0→v2 follow-ups filed as their predecessors near shipping. Prerequisite (autolens_assistant reference audit) was met. This clears the PyAutoBrain claim and unblocks the profiling-agent task.