feat(clone): a sync mode, and the shared rename table birth and sync now both use

AGENTS.md

@@ -140,7 +140,7 @@ the `/<verb>` slash commands.
 | `eyes` | The perceptive function — the organism's sense of its own appearance: survey/review a visualization workspace's figure surface, critiques route to intake/start_dev — EyesSurvey/EyesReviewSurface (never renders, never edits) | `bin/pyauto-brain eyes` |
 | `profiling` | The proprioceptive function — the organism's sense of its own effort: campaign/ingest/triage plans over the autolens_profiling workspace — ProfilingDecision | `bin/pyauto-brain profiling` |
 | `hygiene` | The maintenance function — the organism's sense of its own upkeep: code-quality debt (dev-loop cost + tidiness), delegating fixes — HygieneDecision | `bin/pyauto-brain hygiene` |
-| `clone` | The Mitosis Agent: partition the reference assistant, analyze the domain, emit the CloneDecision; --apply --mode lightweight-seed delegates the seed birth to Build | `bin/pyauto-brain clone` |
+| `clone` | The Mitosis Agent: partition the reference assistant, analyze the domain, emit the CloneDecision; --apply --mode lightweight-seed delegates the seed birth to Build; 'clone sync' patches the reference's generic-file diff onto the born siblings (dry run by default; rejected hunks are a human decision) | `bin/pyauto-brain clone` |
 | `build` | Coordinate execution: consult the vitals faculty, then delegate to PyAutoHands | `bin/pyauto-brain build` |
 | `release` | Release door → the Build Agent release mode (single gate); 'release rehearse'/'release validate' drive release validation; 'release nightly' is the scheduled-nightly driver | `bin/pyauto-brain release` |
 | `health` | The organism's clinician: run the health loop with a human, dispatch by dispatch, toward green | `bin/pyauto-brain health` |

agents/conductors/clone/AGENTS.md

@@ -17,6 +17,9 @@ bin/pyauto-brain clone <library> --workspace <repo> [--reference <repo>] [--json
 # give birth (the mode is the human's answer to the clone-mode question):
 bin/pyauto-brain clone <library> --workspace <repo> --apply --mode lightweight-seed
 #   ... add --no-push to build the seed tree in scratch without creating a repo
+# keep the already-born siblings from drifting (dry run by default):
+bin/pyauto-brain clone sync [--reference <repo>] [--target <repo>]... \
+                            [--since <rev>] [--until <rev>] [--apply] [--json]
 ```
 
 What analyze does: domain analysis (library public API via `ast`, workspace
@@ -39,13 +42,69 @@ instead of `main`, so paired PRs can both be green before the ordered merge
 (PyAutoBrain#186); new cells inherit this from the reference's
 `clone-boundary.yml`.
 
+## `sync` — the second mode (drift, not birth)
+
+Birth copies the reference **once**. Nothing re-synced afterwards, so the four
+copies of `skills/start-new-project.md` and `wiki/project/*` grew four distinct
+hashes and the `autofit_assistant` copy diverged by ~343 lines. `sync` closes
+that loop for the files the boundary already calls **generic** — and only
+those; a domain file the reference changed never crosses.
+
+**It is not an overwrite.** It takes the *reference's own diff* over a commit
+range, restricted to that reference's `generic` pattern set, rewrites the names
+in it for the target (`name_substitutions` — the one rename table birth and
+sync share), and applies it with GNU `patch`. Per file, per sibling it reports
+one of:
+
+| result | meaning |
+|--------|---------|
+| `applied` / `created` | the hunks fit; on `--apply` the file is written |
+| `already-applied` | the sibling already carries the change |
+| `rejected` | one or more hunks no longer fit — **listed by number**; on `--apply` they land as a `.rej` file |
+| `absent` | the reference changed a file this sibling does not have |
+| `skipped` | the reference *added* a file the sibling already has — compare by hand |
+| `unsupported` | a rename/delete in the reference — do it by hand |
+
+### The rename table (`name_substitutions`)
+
+One table, used by **both** birth and sync, so a generic file reads the same
+whichever route brought it into a sibling. Most specific first: the assistant
+name, the `al_` → `ac_` skill prefix (word-anchored), the library repo name,
+the **UPPERCASE** package form, the lowercase package, then the **domain noun**
+(`DOMAIN_NOUNS`: lensing / galaxy / CTI / model-fitting, each with its longer
+phrase, word-anchored so `microlensing` survives).
+
+The last two rules were missing at the first births, and both are still visible
+in `autocti_assistant` (PyAutoBrain#315): its generated project scaffold points
+at `$AUTOLENS_ASSISTANT`, and its profile template heads its first section
+"Lensing background". Neither is reachable by the identity rules — `AUTOLENS`
+is not `autolens`, and "lensing" is not a package at all. A target whose
+package is not in `DOMAIN_NOUNS` gets **no** domain rule and a printed warning;
+a science's own noun is never guessed.
+
+Apply is **per hunk**, the way `patch` has always worked: what fits lands, what
+does not is written out for a human. A sibling's domain adaptation outranks the
+reference's prose, and a conflict is never resolved silently — that judgement
+is the human's, which is the whole reason this mode is a patch and not a copy.
+
+**Dry run is the default.** `--apply` writes. Exit `1` means at least one file
+had rejected hunks (in either mode), so a caller can gate on it.
+
+**"Since the sibling's last sync"** is read from the sibling's *own* history:
+a sync commit carries the trailer `Clone-sync: <reference>@<sha>`, and the next
+run diffs the reference from there. No state file, and the pointer travels with
+the commit that consumed the patch. The first sync of a sibling therefore needs
+an explicit `--since <rev>`; without one the run reports that and exits 1
+rather than guessing a range.
+
 Hard rules (from DESIGN.md): never writes repos/files/GitHub state itself
 (birth is Build's — this agent hands over a plan); never copies domain content
 across domains; never modifies the reference; never embeds PyAutoMemory content
 in a public assistant; a newborn is born private and is not flipped public or
 announced before its Heart validation legs pass
 (`PyAutoHeart/docs/newborn_validation.md`).
 
-Exit codes: `0` decision · `4` inputs unresolvable (incl. an unclassified
+Exit codes: `0` decision / clean sync · `1` a sync completed with rejected
+hunks · `4` inputs unresolvable (incl. an unclassified
 boundary, or Build's birth failing) · `5` bad usage (`--apply` without
 `--mode lightweight-seed` — the v2 modes are refused here).