docs: register PyAutoGut (Gut organ) in README and PyAutoScientist docs

Add the Gut organ to the hand-maintained organ tables and PyAutoScientist
docs now that PyAutoGut exists: README organ table, the organism concept
page (organ row + five→six count + instance-organ list), the docs index
(repo count + organ toctree), and a new organs/gut.md page. The canonical
ORGANISM.md/AGENTS.md generated tables already carry Gut.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Author: 2 people

README.md

@@ -17,6 +17,7 @@ version:
 | Heart | PyAutoHeart | is it healthy — the release-readiness verdict |
 | Hands | PyAutoBuild | do it — packaging, tagging, PyPI releases |
 | Memory | PyAutoMemory | what we know — long-term scientific knowledge |
+| Gut | PyAutoGut | what we shed — condemned branches, stashes and dead code, held recoverably then voided |
 
 Agents live under `agents/` in two tiers: **conductors** (front doors a
 human drives; they decide and act) and **faculties** (read-only judgments

docs/concepts/organism.md

@@ -14,6 +14,7 @@ it and adds the framework/instance distinction an adopter needs.
 | **Heart** | PyAutoHeart | Decides whether the organism is *healthy*. `pyauto-heart readiness` is the authoritative GREEN/YELLOW/RED release gate. An observer: never writes into other repos, never triggers a build. |
 | **Hands** | PyAutoBuild | *Does* — packaging, tagging, notebook generation, PyPI releases. A pure executor: never re-derives a gate decision. |
 | **Memory** | PyAutoMemory | *Knows* — long-term domain knowledge: literature wikis, concepts, bibliographies. Pull-only; consulted, never load-bearing at runtime. |
+| **Gut** | PyAutoGut | *Sheds* — the lifecycle of condemned self-material (stale branches, stashes, dead code/tests): holds each as a durable, recoverable git ref through a transit window, then **voids** it on a sweep. The storage mirror of Memory (retention ↔ release); the hygiene conductor drives it, as vitals reads Heart. |
 
 Everything else — the libraries being developed, their example workspaces,
 test suites, tutorials — is a **satellite**: a capability the organism works
@@ -33,15 +34,16 @@ organ has to be trusted to police itself.
 
 ## Framework vs instance
 
-The five organs split on one line that matters for adoption:
+The six organs split on one line that matters for adoption:
 
 - **Framework organs — Brain, Heart, Hands.** Code, agents, checks,
   pipelines. Domain facts appear only in declared config surfaces (tables
   and policy files, not logic), and a drift check — the
   {ref}`tenant firewall <tenant-firewall>` — keeps it that way.
-- **Instance organs — Mind, Memory.** Committed state and knowledge. These
-  are *inherently yours*: an adopter never forks the upstream Mind or Memory
-  content, they create their own repos with the same documented shape.
+- **Instance organs — Mind, Memory, Gut.** Committed state, knowledge, and
+  shed material. These are *inherently yours*: an adopter never forks the
+  upstream Mind, Memory or Gut content, they create their own repos with the
+  same documented shape.
 
 One more principle worth knowing before you read anything else:
 **one canonical page per fact.** Organ boundaries live in ORGANISM.md;

docs/index.md

@@ -2,8 +2,8 @@
 
 PyAutoScientist is a working, opinionated reference implementation of an
 **AI-agent development organism** for human-led, natural-language software
-development: a set of five git repositories — Mind, Brain, Heart, Hands,
-Memory — through which you lead a multi-repo project in plain English. You
+development: a set of six git repositories — Mind, Brain, Heart, Hands,
+Memory, Gut — through which you lead a multi-repo project in plain English. You
 describe what you want; AI agents plan, implement, test, gate and release
 it; you make every judgment call.
 
@@ -57,6 +57,7 @@ organs/brain
 organs/heart
 organs/build
 organs/memory
+organs/gut
 ```
 
 ```{toctree}

docs/organs/gut.md

@@ -0,0 +1,57 @@
+# Gut — PyAutoGut
+
+**What it owns:** the lifecycle of *condemned self-material* — the stale
+branches, `git stash` entries, dead code and retired tests a hygiene sweep is
+95%-but-not-100% sure is trash. Code that is not *wrong*, just *done*. Gut is
+the storage mirror of Memory: Memory holds what the organism **keeps**, Gut
+holds what it **sheds** — retention ↔ release.
+
+**Repo:** [PyAutoLabs/PyAutoGut](https://github.com/PyAutoLabs/PyAutoGut)
+
+## The defining function: elimination
+
+Gut is a storage organ that ends in **deletion** — it performs the final void
+itself. (An organ that only filtered and handed waste downstream would be a
+spleen; the one that *voids* is the gut.) Between condemnation and deletion it
+holds each item in a **transit window**: a staging state that is neither "keep"
+nor "delete now", with a clock on it.
+
+## Lifecycle: condemn → transit → void
+
+- **Condemn** — the Brain's hygiene conductor files an entry into the
+  `condemned.md` manifest in the Mind (symmetric to `parked.md`). Fragile forms
+  — local unmerged branches, stashes — are archived to a durable ref here
+  *first*.
+- **Transit** — the entry carries a `sweep-after` date. Until then it is
+  **recoverable**: restore the branch or stash from its archive ref. The
+  holding window *is* the gut's transit time, with a clock on it.
+- **Void** — a batch `sweep` runs the existing `repo_cleanup` safety gates
+  against entries past their date and eliminates them.
+
+## Storage model
+
+- **Payload = durable git refs, never lossy markdown.** Fragile forms are
+  materialised as real commits and pushed under the
+  `refs/heads/archive/condemned/<name>` prefix into this repo — the *attic
+  remote* — before the local copy is deleted. Recovery is a checkout. (It is a
+  branch prefix, not a custom `refs/archive/*` namespace: GitHub only accepts
+  pushes to `refs/heads/*` and `refs/tags/*`.)
+- **Catalog = `condemned.md` in the Mind** (symmetric to `parked.md`). The
+  `.md` is the index; the refs here are the payload. Merged branches skip the
+  pen entirely — reachable from `main` forever, so the conductor recommends them
+  straight to deletion.
+
+## The driver split
+
+Gut *holds and voids*; it decides nothing. The Brain's hygiene conductor decides
+what to condemn and when to sweep — the same split as **Heart ↔ vitals**: the
+organ does the work, the conductor reasons. The `bin/pyauto-gut` entrypoint
+provides the mechanics: `archive`, `recover`, `list`, `void`.
+
+## For an adopter
+
+You do not fork this repo's contents — the condemned refs are your organism's
+own shed material. You create your own Gut with the same shape: an attic remote
+that accepts `archive/condemned/*` refs, the `condemned.md` catalog in your
+Mind, and the hygiene conductor wired to drive it. Like Mind and Memory, Gut is
+an **instance organ** — inherently yours.