feature(pyautogut): register the Gut organ + condemned.md manifest

condemned.md

@@ -0,0 +1,77 @@
+# Condemned material
+
+The catalog of **condemned self-material** — stale branches, `git stash`
+entries, dead code and retired tests that a hygiene / `repo_cleanup` sweep is
+95%-but-not-100% sure is trash. Symmetric to `parked.md`: `parked.md` holds work
+that is *paused and will resume*; this file holds material that is *spent and
+awaiting elimination*, recoverable right up until it is voided.
+
+This is the **index**; the payload is durable **git refs**, not markdown. Fragile
+forms (local unmerged branches, stashes) are first materialised as real commits
+and pushed under the archive namespace `refs/heads/archive/condemned/<name>`
+(a branch prefix — GitHub only accepts pushes to `refs/heads/*` and
+`refs/tags/*`, so a custom `refs/archive/*` namespace is unpushable; filter with
+`git branch --list 'archive/condemned/*'`) into **PyAutoGut** as the attic remote
+— *before* the local copy is deleted. Recovery is a checkout. The organ (PyAutoGut) holds
+and voids; the Brain hygiene conductor drives (decides what to condemn, triggers
+a sweep), mirroring the Heart ↔ vitals template. See the decision:
+`research/pyautobrain/pyautogut_organ_decision.md`.
+
+## Lifecycle
+
+1. **Condemn** — the hygiene `tidy` pass files an entry here (async, no
+   synchronous per-item gate). Fragile forms are archived to a durable ref
+   first; merged branches and committed deletions need only a SHA recorded.
+2. **Transit** — the entry sits with a `sweep-after` date. Until then it is
+   recoverable (reabsorption): restore the branch/stash from its archive ref.
+3. **Void** — a batch `sweep` runs the existing `repo_cleanup` safety gates
+   against entries past `sweep-after` and eliminates them; the entry moves out
+   of this file (to a voided log or is deleted).
+
+## Entry schema
+
+One `##` block per item. Fields:
+
+- `type` — `branch` | `stash` | `file` | `test`
+- `locator` — the local name/path (e.g. `feature/old-thing`,
+  `stash@{2}`, `src/legacy/foo.py`)
+- `confidence` — how sure it is trash (e.g. `0.95`)
+- `reason` — why it is condemned
+- `merged` — `yes` | `no` (a merged branch is reachable from `main` forever →
+  skips the pen; near-zero risk)
+- `condemned` — date filed (YYYY-MM-DD)
+- `sweep-after` — earliest date it may be voided (the transit clock)
+- `breaks-if-wrong` — what is lost if this was a false positive (informs the
+  gate)
+- `archive-ref` — the durable ref + SHA to recover from
+  (`refs/heads/archive/condemned/<name>` @ `<sha>`), or `n/a` for a merged branch /
+  committed deletion whose bytes live in remote history (record the pre-delete
+  SHA instead)
+
+### Recoverability is not uniform
+
+- **Merged branches** — reachable from `main` forever; `archive-ref: n/a`, a note
+  is enough. The conductor recommends these straight to deletion without staging.
+- **Committed code / test deletions** — the old bytes live in remote history;
+  record only the pre-delete SHA.
+- **Local-only unmerged branches / stashes** — exist in one machine's reflog and
+  are gc-pruned. These **must** be materialised as an archive ref before deletion;
+  a manifest that merely *points* at a stash is worthless the moment it is dropped.
+
+<!-- Example entry (schema illustration only — not a live condemnation):
+
+## feature/abandoned-spike
+- type: branch
+- locator: feature/abandoned-spike
+- confidence: 0.95
+- reason: superseded by feature/real-approach; no unique commits worth keeping
+- merged: no
+- condemned: 2026-07-12
+- sweep-after: 2026-08-12
+- breaks-if-wrong: loses ~3 exploratory commits (delaunay prototype)
+- archive-ref: refs/heads/archive/condemned/abandoned-spike @ 0de4514
+-->
+
+<!-- No live condemned entries yet — the hygiene `tidy` drive seam
+     (feature/pyautobrain/hygiene_pyautogut_drive_seam.md) populates this file
+     once PyAutoGut exists as the attic remote. -->

feature/pyautobrain/hygiene_pyautogut_drive_seam.md

@@ -0,0 +1,42 @@
+# Add the hygiene → PyAutoGut drive seam
+
+Type: feature
+Target: PyAutoBrain
+Repos:
+- PyAutoBrain
+- PyAutoGut
+- PyAutoMind
+Difficulty: medium
+Autonomy: supervised
+Priority: normal
+Status: formalised
+
+Add the drive seam that lets the hygiene conductor use **@PyAutoGut** — the
+second build follow-up from `research/pyautobrain/pyautogut_organ_decision.md`.
+Depends on the repo skeleton (`feature/pyautogut/repo_skeleton.md`) existing
+first.
+
+The seam mirrors the **Heart ↔ vitals** template exactly: the organ *holds and
+voids*; the @PyAutoBrain hygiene conductor *drives* it (decides what to condemn,
+triggers a sweep) and owns none of the storage.
+
+- **PyAutoGut-aware `tidy` mode.** Instead of the synchronous, one-item-at-a-time
+  `repo_cleanup` interrogation (the decision doc's pain #1 — decision fatigue at
+  the point of least context), `tidy` *files candidates into `condemned.md`*
+  asynchronously, with no per-item gate. This gives the 95%-confident-but-not-
+  certain items a home (pain #2) and captures the fragile forms' bytes as durable
+  archive refs before deletion (pain #3).
+- **Batch `sweep` mode.** Runs the *existing* `repo_cleanup` safety gates
+  (`yes, force delete <name>`; stash keep/apply/drop) in batch against the
+  manifest, at a time the user chooses — the transit-window clock: items with a
+  past `sweep-after` date are voided; anything still wanted is reabsorbed
+  (recovered) before then.
+
+No second gate implementation — reuse `repo_cleanup`'s gates. The conductor
+reasons and delegates; @PyAutoGut performs the actual deletion (elimination is a
+gut function).
+
+<!-- formalised 2026-07-12 from ideas.md by intake review; provenance:
+     research pyautogut-organ-decision · research/pyautobrain/pyautogut_organ_decision.md.
+     Work-type corrected to feature/ per the decision doc's named follow-up
+     (the deterministic classifier guessed refactor from surface keywords). -->

feature/pyautogut/repo_skeleton.md

@@ -0,0 +1,54 @@
+# Stand up the PyAutoGut repo skeleton
+
+Type: feature
+Target: PyAutoGut
+Repos:
+- PyAutoGut
+- PyAutoMind
+- PyAutoBrain
+Difficulty: medium
+Autonomy: supervised
+Priority: normal
+Status: formalised
+
+Stand up **@PyAutoGut**, the new peer organ repo that owns the lifecycle of
+*condemned self-material* — decided in
+`research/pyautobrain/pyautogut_organ_decision.md`. This is the first of that
+decision's two build follow-ups (the Brain-side drive seam is the sibling
+`feature/pyautobrain/hygiene_pyautogut_drive_seam.md`).
+
+Scope — the storage substrate only (organ holds + voids; the reasoning stays in
+the Brain conductor):
+
+- **Attic remote + archive-ref convention.** Fragile forms (local unmerged
+  branches, `git stash` entries) are materialised as real commits and pushed
+  under an archive namespace — `refs/archive/condemned/<name>` — which stays out
+  of `git branch -a`, into PyAutoGut as the attic remote, *before* the local
+  copy is deleted. Recovery is a checkout; a stash becomes a branch/commit via
+  `git stash branch` or a tagged stash commit.
+- **The `condemned.md` manifest schema** (lands in @PyAutoMind, symmetric to
+  `parked.md`): one entry per item — `type` (branch/stash/file/test), `locator`,
+  `confidence`, `reason`, `merged?`, `condemned` date, `sweep-after` date,
+  `breaks-if-wrong`, and the archive ref/SHA to recover from. The `.md` is the
+  index; the git refs are the payload. Merged branches skip the pen (reachable
+  from `main` forever); committed code/test deletions need only the pre-delete
+  SHA recorded.
+- **Register PyAutoGut as a peer organ**: add it to @PyAutoMind `repos.yaml` and
+  to @PyAutoBrain `ORGANISM.md` (then `python3 scripts/repos_sync.py --write`),
+  as a body organ peer to Heart/Memory/Hands — the storage mirror of Memory
+  (Memory keeps; Gut sheds, recoverable until voided).
+
+Boundaries to settle in PyAutoGut's `AGENTS.md` (from the decision doc): vs
+Immune/`bug` (self+spent, not foreign+pathological), vs the hygiene conductor
+(Heart↔vitals template — the conductor drives, the organ stores/voids), vs
+Memory (retention vs release), vs Heart/profiling (no verdict, no compute
+measure).
+
+Note: creating the GitHub repo itself is a human-required step; the rest of the
+skeleton (conventions, manifest schema, doctrine wiring) is the supervised work.
+
+<!-- formalised 2026-07-12 from ideas.md by intake review; provenance:
+     research pyautogut-organ-decision · research/pyautobrain/pyautogut_organ_decision.md.
+     Target PyAutoGut is a new repo not yet in repos.yaml, so the deterministic
+     classifier could not resolve it — corrected to feature/pyautogut per the
+     decision doc's named follow-up. -->

ideas.md

@@ -26,3 +26,5 @@
 - [from: PyAutoBuild/to_do_list] Workspace tagging.
 - [from: PyAutoBuild/to_do_list] Remove annoying report.log and root.log once and for all.
 - [from: pyautoscientist-3b-smoke, 2026-07-10] Extend spawn --stamp-family to stamp the smoke thin-caller workflow + a starter smoke_install.sh into the template family (spec-gated on the reusable smoke workflow, which is now live).
+- [formalised -> feature/pyautogut/repo_skeleton.md] [from: research pyautogut-organ-decision · research/pyautobrain/pyautogut_organ_decision.md] Stand up the PyAutoGut repo skeleton — the new peer organ repo owning condemned self-material: the attic remote, the `refs/archive/condemned/<name>` archive-ref convention (stays out of `git branch -a`), and the `condemned.md` Mind manifest schema (type/locator/confidence/reason/merged?/condemned/sweep-after/breaks-if-wrong/archive-ref+SHA). Work-type feature/pyautogut; also adds PyAutoGut to repos.yaml + ORGANISM.md as a peer organ.
+- [formalised -> feature/pyautobrain/hygiene_pyautogut_drive_seam.md] [from: research pyautogut-organ-decision · research/pyautobrain/pyautogut_organ_decision.md] Add the hygiene→PyAutoGut drive seam in the Brain — a PyAutoGut-aware hygiene `tidy` mode that files condemned candidates into `condemned.md` async (no synchronous per-item gate, replacing the mid-sweep repo_cleanup interrogation), plus a batch `sweep` mode that runs the existing repo_cleanup safety gates against the manifest at a user-chosen time. Mirrors the Heart↔vitals template: the organ holds+voids, the conductor drives. Work-type feature/pyautobrain.

repos.yaml

@@ -72,6 +72,11 @@ repos:
     category: organ
     organ: Memory
     role: "Long-term scientific/software/project knowledge (see science pointer below)."
+  PyAutoGut:
+    github: PyAutoLabs/PyAutoGut
+    category: organ
+    organ: Gut
+    role: "Owns the lifecycle of condemned self-material (stale branches, stashes, dead code/tests): holds it as durable, recoverable git refs through a transit window and voids it on a sweep. The storage mirror of Memory (retention vs release)."
 
   # --- scientific libraries ----------------------------------------------
   PyAutoConf:

research/pyautobrain/pyautogut_organ_decision.md

@@ -96,10 +96,19 @@ and ecosystem-scale answers converge on one place.
 
 - **Payload = durable git refs, never markdown.** Fragile forms (local unmerged
   branches, stashes) are first materialised as real commits on a remote — pushed
-  under an archive namespace (e.g. `refs/archive/condemned/<name>`, which stays
-  out of `git branch -a`) into PyAutoGut as the attic remote — *before* the
+  under an archive namespace into PyAutoGut as the attic remote — *before* the
   local copy is deleted. Recovery is a checkout. A stash becomes a branch/commit
   via `git stash branch` or a tagged stash commit.
+  <!-- Implementation revision (2026-07-12, during the repo_skeleton build): the
+       namespace is `refs/heads/archive/condemned/<name>` (a branch prefix), NOT
+       a custom `refs/archive/condemned/*`. GitHub only accepts pushes to
+       refs/heads/* and refs/tags/*, so the custom namespace is unpushable. The
+       "out of git branch -a" nicety is relaxed to "filter with
+       `git branch --list 'archive/condemned/*'`". Tags (refs/tags/condemned/*)
+       were the alternative — hidden + immutable — but rejected: immutability
+       blocks re-pointing, and they were unusable in the cloud session's git
+       proxy. -->
+
 - **Catalog = a manifest in the Mind** (`condemned.md`, symmetric to
   `parked.md`): one entry per item — `type` (branch/stash/file/test), `locator`,
   `confidence`, `reason`, `merged?`, `condemned` date, `sweep-after` date,