Move the five sub-wikis under wiki/ with a shared schema at wiki/CLAUDE.md

wiki/lensing, wiki/smbh, wiki/cti, wiki/methods, wiki/galaxies replace the
root-level *_wiki folders (the _wiki suffix is redundant under wiki/). The
generic schema is promoted from lensing_wiki/CLAUDE.md to wiki/CLAUDE.md;
the lensing wiki keeps a slim scope-only CLAUDE.md like its siblings.
Relative links are rewritten for the new depth (append-only log.md files
are left as historical record); the citation validator's sources glob and
test fixture follow the layout.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Author: 2 people

AGENTS.md

@@ -15,13 +15,31 @@ packaging, tooling, and workflow tasks.
 When you do read:
 
 1. **Index first.** Start at [`index.md`](index.md), then the relevant
-   sub-wiki's own `index.md` (`lensing_wiki/`, `smbh_wiki/`, `cti_wiki/`,
-   `methods_wiki/`, `galaxies_wiki/`).
+   sub-wiki's own `index.md` (`wiki/lensing/`, `wiki/smbh/`, `wiki/cti/`,
+   `wiki/methods/`, `wiki/galaxies/`).
 2. **Then at most 2–3 pages.** Read only the concept/entity/source pages the
    index points you to. **Never bulk-load a sub-wiki.**
 3. **Do not couple to the internal layout** — reach pages through the indexes,
    not hard-coded paths.
 
+## The write contract (layout rules)
+
+The repo has exactly **two content homes**, enforced by
+`make validate-structure` (CI runs it on every push/PR):
+
+- **`wiki/<domain>/`** — every sub-wiki, following the shared schema in
+  [`wiki/CLAUDE.md`](wiki/CLAUDE.md). New sub-wikis are added beside the
+  existing ones, never at the repo root.
+- **`bibliography/`** — the *only* place BibTeX lives. One canonical file
+  (`pyautomemory.bib`) plus `bibkey_aliases.yaml`; never add loose `.bib`
+  files anywhere else.
+
+**Source PDFs live off-repo.** Never commit a paper (PDF/HTML, with or
+without a file extension) — read it, stub it in the right
+`wiki/<domain>/sources/*.md`, add its canonical entry to `bibliography/`,
+and run `make validate`. Unrecognised top-level files/folders fail the lint;
+the allowlist is in `scripts/validate_structure.py`.
+
 ## What does NOT live here
 
 - **Operational history** — what the organism *did* (prior tasks, decisions,

README.md

@@ -17,20 +17,20 @@ The sub-wikis (self-contained, shared schema):
 
 | Wiki | Covers |
 |------|--------|
-| [`lensing_wiki/`](lensing_wiki/index.md) | strong gravitational lensing (the primary wiki) |
-| [`smbh_wiki/`](smbh_wiki/index.md) | supermassive black holes, binaries, recoil, GW background |
-| [`cti_wiki/`](cti_wiki/index.md) | charge transfer inefficiency, Euclid VIS calibration |
-| [`methods_wiki/`](methods_wiki/index.md) | Bayesian inference, samplers, deep learning, simulations |
-| [`galaxies_wiki/`](galaxies_wiki/index.md) | galaxy formation and evolution |
+| [`wiki/lensing/`](wiki/lensing/index.md) | strong gravitational lensing (the primary wiki) |
+| [`wiki/smbh/`](wiki/smbh/index.md) | supermassive black holes, binaries, recoil, GW background |
+| [`wiki/cti/`](wiki/cti/index.md) | charge transfer inefficiency, Euclid VIS calibration |
+| [`wiki/methods/`](wiki/methods/index.md) | Bayesian inference, samplers, deep learning, simulations |
+| [`wiki/galaxies/`](wiki/galaxies/index.md) | galaxy formation and evolution |
 
 [`bibliography/`](bibliography/README.md) holds the canonical BibTeX
 metadata every wiki cites against; [`reading-queue.md`](reading-queue.md)
 is what's waiting to be read and filed. New knowledge updates the metadata
 and the claim support together, then passes
-`make validate-literature-citations`.
+`make validate`.
 
 The wiki schema is defined in
-[`lensing_wiki/CLAUDE.md`](lensing_wiki/CLAUDE.md) and inherited by every
+[`wiki/CLAUDE.md`](wiki/CLAUDE.md) and inherited by every
 sub-wiki. How agents should read this repo: [AGENTS.md](AGENTS.md). The
 organism this repo is the Memory of:
 [PyAutoBrain/ORGANISM.md](https://github.com/PyAutoLabs/PyAutoBrain/blob/main/ORGANISM.md),

bibliography/README.md

@@ -1,6 +1,6 @@
 # Canonical PyAutoMemory bibliography
 
-`pyautomemory.bib` is the canonical metadata layer shared by every `*_wiki/` in this
+`pyautomemory.bib` is the canonical metadata layer shared by every sub-wiki under `../wiki/` in this
 repository. Wiki source entries explain which claims papers support; the BibTeX file records
 citation metadata and canonical keys. Keep PDFs, local paths, abstracts, and long paper
 summaries out of both layers.
@@ -20,8 +20,8 @@ added elsewhere in the repo.
 1. Verify the paper from an authoritative public record or the paper itself.
 2. Search `pyautomemory.bib` by DOI, arXiv ID, and title. Reuse the existing canonical key;
    otherwise add verified metadata under a unique, stable author-year key.
-3. Add a compact section to the relevant `<domain>_wiki/sources/*.md` using the inherited
-   schema in [`../lensing_wiki/CLAUDE.md`](../lensing_wiki/CLAUDE.md).
+3. Add a compact section to the relevant `../wiki/<domain>/sources/*.md` using the inherited
+   schema in [`../wiki/CLAUDE.md`](../wiki/CLAUDE.md).
 4. Add concept/entity links only where the paper materially supports existing text.
 5. Run `make validate-literature-citations`.
 

index.md

@@ -3,25 +3,25 @@
 The PyAuto organism's long-term knowledge: a multi-domain knowledge base of
 accumulated scientific and project knowledge, organised as several
 Karpathy-style LLM wikis over a shared canonical bibliography. Each sub-wiki uses
-the schema in [`lensing_wiki/CLAUDE.md`](lensing_wiki/CLAUDE.md).
+the schema in [`wiki/CLAUDE.md`](wiki/CLAUDE.md).
 
 ## Sub-wikis
 
-- [`lensing_wiki/`](lensing_wiki/index.md) — **strong gravitational
+- [`wiki/lensing/`](wiki/lensing/index.md) — **strong gravitational
   lensing.** The primary sub-wiki. Lens equation, mass models, source
   reconstruction, degeneracies, time-delay cosmography, dark-matter
   substructure, surveys (SLACS, BELLS, H0liCOW, TDCOSMO, Euclid Q1,
   HFF), software (PyAutoLens, lenstronomy).
-- [`smbh_wiki/`](smbh_wiki/index.md) — **supermassive black holes.**
+- [`wiki/smbh/`](wiki/smbh/index.md) — **supermassive black holes.**
   Binaries, recoil, scouring, mass functions, GW background
   (NANOGrav), seeds and growth.
-- [`cti_wiki/`](cti_wiki/index.md) — **Charge Transfer Inefficiency.**
+- [`wiki/cti/`](wiki/cti/index.md) — **Charge Transfer Inefficiency.**
   CCD trap physics, forward-model correction (`arctic`), trap pumping,
   Euclid VIS calibration, HST ACS, Gaia.
-- [`methods_wiki/`](methods_wiki/index.md) — **statistical and
+- [`wiki/methods/`](wiki/methods/index.md) — **statistical and
   computational methods.** Bayesian inference, samplers, deep learning,
   probabilistic programming, NUFFT, simulations, scientific software.
-- [`galaxies_wiki/`](galaxies_wiki/index.md) — **galaxy formation and
+- [`wiki/galaxies/`](wiki/galaxies/index.md) — **galaxy formation and
   evolution.** Massive ellipticals (MASSIVE survey), bulge/disk
   decomposition, IFU spectroscopy, stellar halos, COSMOS,
   high-redshift, halo-galaxy connection, galaxy-scale DM geometry.
@@ -38,7 +38,7 @@ the schema in [`lensing_wiki/CLAUDE.md`](lensing_wiki/CLAUDE.md).
 ## Schema
 
 The schema is defined once in
-[`lensing_wiki/CLAUDE.md`](lensing_wiki/CLAUDE.md) and inherited by
+[`wiki/CLAUDE.md`](wiki/CLAUDE.md) and inherited by
 all sub-wikis. Each sub-wiki has its own `CLAUDE.md` that diverges
 only on the `## Scope` section. Per-page frontmatter, naming
 conventions, `[[wiki-links]]`, status flags (`stub | drafted |

reading-queue.md

@@ -6,7 +6,7 @@ became the unified knowledge repo. Section headers below match topic folders
 in this repo (Strong Lensing, SMBHs, Galaxy Formation, Dark Matter,
 Stats, …) — when a paper here is acquired as a PDF, it should be
 filed under the matching folder and stubbed in the relevant
-`<sub>_wiki/sources/*.md` page.
+the matching `wiki/<domain>/sources/*.md` page.
 
 ---
 

scripts/validate_literature_citations.py

@@ -82,7 +82,7 @@ def extract_canonical_keys(
 
 
 def source_directories(root: Path) -> tuple[Path, ...]:
-    return tuple(sorted(path for path in root.glob("*_wiki/sources") if path.is_dir()))
+    return tuple(sorted(path for path in root.glob("wiki/*/sources") if path.is_dir()))
 
 
 def collect_source_citations(directories: tuple[Path, ...]) -> tuple[SourceCitation, ...]:

tests/test_validate_literature_citations.py

@@ -44,7 +44,7 @@ def test_extract_canonical_keys_from_source_markdown():
 def _fixture_paths(tmp_path: Path) -> tuple[Path, Path, Path]:
     bibliography = tmp_path / "literature.bib"
     bibliography.write_text("@article{Alpha2024,\n}\n", encoding="utf-8")
-    sources = tmp_path / "example_wiki" / "sources"
+    sources = tmp_path / "wiki" / "example" / "sources"
     sources.mkdir(parents=True)
     aliases = tmp_path / "aliases.yaml"
     aliases.write_text("", encoding="utf-8")

lensing_wiki/CLAUDE.md wiki/CLAUDE.mdlensing_wiki/CLAUDE.md renamed to wiki/CLAUDE.md

@@ -1,36 +1,41 @@
-# PyAutoLens AI Assistant — Strong Lensing Wiki
+# PyAutoMemory wikis — shared schema + usage rules
 
-This wiki gives a PyAutoLens AI assistant broad scientific context for strong
-gravitational lensing. It follows Karpathy's "LLM Wiki" pattern: concise,
+Every sub-wiki under `wiki/` gives an AI assistant broad scientific context
+for one domain. They follow Karpathy's "LLM Wiki" pattern: concise,
 cross-linked pages are read at query time, while canonical citation metadata
-lives separately in `../bibliography/`.
+lives separately in [`../bibliography/`](../bibliography/README.md). This
+file defines the schema once; each sub-wiki's own `CLAUDE.md` diverges only
+on scope.
 
 ## Layout
 
 ```
 PyAutoMemory/                  # repo root
-├── lensing_wiki/             # this folder — the compiled wiki (in git)
+├── wiki/                     # all sub-wikis (in git)
 │   ├── CLAUDE.md             # this file — schema + usage rules
-│   ├── index.md              # top-level navigation
-│   ├── log.md                # append-only compilation log
-│   ├── concepts/             # one topic per page — the science
-│   ├── entities/             # specific surveys, lenses, collaborations, software
-│   └── sources/              # compact claim support (one paper = one section)
-└── bibliography/             # canonical BibTeX, aliases, citation instructions
+│   └── <domain>/             # one domain per sub-wiki, e.g. lensing/
+│       ├── CLAUDE.md         # the sub-wiki's scope notes
+│       ├── index.md          # the sub-wiki's own navigation
+│       ├── log.md            # append-only compilation log
+│       ├── concepts/         # one topic per page — the science
+│       ├── entities/         # named things: surveys, instruments, software
+│       └── sources/          # compact claim support (one paper = one section)
+└── bibliography/             # canonical BibTeX, aliases, citation tooling
 ```
 
 Papers are the ground truth; wiki pages are syntheses. If they disagree, update
-the wiki and note the change in `log.md`.
+the wiki and note the change in the sub-wiki's `log.md`.
 
 ## References and citation metadata
 
 - `sources/*.md` records compact guidance about what claims a paper supports.
 - `../bibliography/pyautomemory.bib` records canonical metadata and keys.
 - `../bibliography/bibkey_aliases.yaml` maps known alternate keys to canonical keys.
 
-Never record local PDF paths or fabricate metadata. A canonical key is local to
-PyAutoMemory: resolve it against a target project's `.bib` before patching LaTeX.
-See [`../bibliography/README.md`](../bibliography/README.md) for the workflow.
+Never record local PDF paths or fabricate metadata — source PDFs live
+off-repo. A canonical key is local to PyAutoMemory: resolve it against a
+target project's `.bib` before patching LaTeX. See
+[`../bibliography/README.md`](../bibliography/README.md) for the workflow.
 
 ## Page types
 
@@ -87,8 +92,8 @@ One paragraph an assistant can quote back to a user.
 ## What it is
 The physics / definition.
 
-## Why it matters for PyAutoLens
-How this concept shows up in lens-modeling decisions a PyAutoLens user makes.
+## Why it matters
+How this concept shows up in the decisions the domain's software users make.
 
 ## Key results from the literature
 Bullet list. Each bullet ends with `([[author-year-stub]])` so the LLM can
@@ -102,7 +107,7 @@ follow the link to the per-paper section.
 ## Entity page structure
 
 Same idea but the headings are "What it is / Key facts / Papers / See also".
-Use entity pages for: surveys (SLACS, BELLS, H0liCOW), specific lenses
+Use entity pages for: surveys (SLACS, BELLS, H0liCOW), specific objects
 (Abell 1201, the Cosmic Horseshoe), software (PyAutoLens, lenstronomy),
 collaborations (TDCOSMO, Space Warps).
 
@@ -134,27 +139,17 @@ Papers covering this topic. Each paper has its own H2 section; cross-link with
 Keep entries short: normally 2–5 support bullets and no long prose. Do not copy
 abstracts or infer claims from filenames. Add a TODO when support is unverified.
 
-## How the assistant should use this wiki
+## How the assistant should use a wiki
 
-1. On a user question, first open `index.md`.
+1. On a user question, first open the sub-wiki's `index.md`.
 2. Follow the relevant `concepts/` or `entities/` page.
 3. Follow the source entry for claim scope and its canonical key for metadata.
 4. Resolve that key against downstream `.bib` files before changing LaTeX.
 5. If support or metadata is unclear, read the public paper and add a TODO
    rather than guessing. Log verified upgrades.
 
-## Scope
+## Adding a sub-wiki
 
-In-scope folders for the current wiki build:
-
-- `Strong_Lens/`           — primary
-- `Substructure/`
-- `StrongLensCluster/`
-- `Dark_Matter_Detection/`
-- `DarkMatterModels/`
-
-Other folders (`WeakLensing/`, `Ellipticals/`, `Deep Learning/`, etc.)
-contain papers that touch lensing tangentially but are out of scope until
-explicitly added — see `log.md` for the decision.
-
-This is the **lensing** sub-wiki. Sibling domain wikis inherit this schema.
+Create `wiki/<domain>/` with its own `CLAUDE.md` (scope notes only — this
+schema is inherited, not copied), `index.md`, `log.md`, and the three page
+folders. Give it a row in the repo-root `index.md` and `README.md` tables.

cti_wiki/AGENTS.md wiki/cti/AGENTS.mdcti_wiki/AGENTS.md renamed to wiki/cti/AGENTS.md

@@ -4,13 +4,13 @@ This sub-wiki gives an AI assistant the scientific context of Charge
 Transfer Inefficiency (CTI) in CCDs — the physics of charge trapping
 and release in silicon, its impact on astronomical imaging, the
 forward-model correction algorithms (`arctic`), and the Euclid VIS
-detector calibration programme. Sibling of `lensing_wiki/` under
+detector calibration programme. Sibling of `../lensing/` under
 `PyAutoMemory/`, same Karpathy "LLM Wiki" pattern.
 
 ## Layout
 
 ```
-cti_wiki/
+cti/
 ├── CLAUDE.md           # this file — schema + scope
 ├── index.md            # top-level navigation
 ├── log.md              # append-only compilation log
@@ -21,7 +21,7 @@ cti_wiki/
 
 ## Schema
 
-Inherits verbatim from [`../lensing_wiki/CLAUDE.md`](../lensing_wiki/CLAUDE.md)
+Inherits verbatim from [`../CLAUDE.md`](../CLAUDE.md)
 — page types, naming, `[[wiki-links]]`, frontmatter, concept-page
 structure, source-collection structure, `status: stub|drafted|reviewed`.
 This file only diverges on scope.
@@ -33,16 +33,16 @@ injection, the Euclid VIS detector and calibration pipeline, and the
 Hall-Shockley-Read trap-emission theory underlying CTI. Source PDFs live
 off-repo (the wiki was compiled from an off-repo CTI/Euclid paper corpus);
 what's here is the durable knowledge plus canonical citation metadata in
-`../bibliography/`.
+`../../bibliography/`.
 
 Adjacent topics that link out:
 - Sampling / Bayesian inference of trap-density posteriors —
-  `../methods_wiki/`.
+  `../methods/`.
 - Cosmological weak-lensing shape biases from residual CTI —
-  `../lensing_wiki/` ([[weak-lensing]] when written).
+  `../lensing/` ([[weak-lensing]] when written).
 
 ## How the assistant should use this wiki
 
-Same protocol as `../lensing_wiki/CLAUDE.md`: follow concepts/entities to
-compact source claims, use canonical metadata from `../bibliography/`, resolve
+Same protocol as `../CLAUDE.md`: follow concepts/entities to
+compact source claims, use canonical metadata from `../../bibliography/`, resolve
 downstream keys before editing LaTeX, and never fabricate.