feat: per-project literature — project-local bibliography with deliberate upstream promotion

skills/README.md

@@ -48,7 +48,8 @@ them.
   sweep across skill recipes, wiki API pages, and pinned-source drift after a PyAuto\*
   upgrade or source refresh.
 - [`al_ingest_paper.md`](./al_ingest_paper.md) — add a strong-lensing paper (local PDF
-  or arxiv URL) to `wiki/literature/`: per-paper stub, concept cross-links, log entry.
+  or arxiv URL): project-local `wiki/project/bibliography.md` by default inside a science
+  project; shared `wiki/literature/` in the assistant clone or on explicit promotion.
 
 ### Project workflow
 

skills/al_ingest_paper.md

@@ -1,6 +1,6 @@
 ---
 name: al_ingest_paper
-description: Add a verified strong-lensing paper to the paired literature wiki and canonical BibTeX layer. Accepts a local PDF or public paper URL, resolves or adds canonical metadata, writes a compact claim-oriented `sources/*.md` entry, updates relevant concept/entity links, validates key consistency, and never records local PDF paths. Use when a user wants a paper added so future assistants can cite its supported claims reliably.
+description: Add a verified strong-lensing paper to the literature record — project-local (`wiki/project/bibliography.md`) by default when working inside a science project, or the shared literature wiki + canonical BibTeX layer when in the assistant clone or on explicit promotion. Accepts a local PDF or public paper URL, resolves or adds canonical metadata, writes a compact claim-oriented source entry, updates relevant concept/entity links, validates key consistency, and never records local PDF paths. Use when a user wants a paper added so future assistants can cite its supported claims reliably.
 ---
 
 # Ingesting a paper into the literature wiki
@@ -21,6 +21,25 @@ Ingestion makes a paper discoverable from scientific concepts while preserving a
 citation key. A normal addition changes the canonical `.bib`, one compact source section,
 relevant concept/entity links, and `log.md`.
 
+## Target — project-local or shared?
+
+Two destinations; pick before editing anything (the hybrid rule: general concepts stay
+shared, analysis-specific papers stay in the project):
+
+- **Inside a science project** (the working repo has `project.yaml` and a thin refer-back
+  `AGENTS.md`): the default target is the **project's** `wiki/project/bibliography.md` — one
+  `##` section per paper, exactly the "record claim support" shape below. Reuse the
+  assistant's canonical BibTeX key when the paper is already in `autolens_literature.bib`
+  (read-only lookup via refer-back); otherwise use a stable author-year key, aligned with the
+  project's own paper `.bib` if one exists. Do **not** edit the assistant clone's
+  `bibliography/` or `sources/` from a project session — that is promotion, below. The shared
+  quality gate does not run against a project page; keep it consistent by inspection.
+- **In the assistant clone, or on explicit promotion** of a generally-useful paper out of a
+  project: the shared `wiki/literature/` flow below — canonical `.bib`, `sources/<topic>.md`,
+  concept/entity links, `log.md`, `validate-citations`. Promotion is a deliberate act, never
+  the default, and is a verbatim copy of the project section into the right
+  `sources/<topic>.md` plus the canonical-metadata steps.
+
 ## Ask
 
 Establish only what is not already supplied:

skills/start-new-project.md

@@ -82,7 +82,8 @@ reproducible-science subset; generate the thin assistant layer; refer back for e
   data/  (datasets)
   results/{manifests,figures,tables}/.gitkeep   # manifests/figures/tables TRACKED
   paper/{figures,tables}/.gitkeep
-  wiki/project/             # journal — copy _profile_template.md + _template.md + README only
+  wiki/project/             # journal — copy _profile_template.md + _template.md + README;
+                            #   generate bibliography.md (below)
   environment.yml  CITATION.cff  .gitignore  .gitattributes
 ```
 
@@ -119,6 +120,9 @@ harness (Codex, Gemini, chat), self-enforce it: run
 
 ## This project
 - Context / decisions / results: `wiki/project/` (dated journal + `profile.md`).
+- Literature: general lensing concepts → the assistant's shared `wiki/literature/`
+  (refer-back); papers specific to this analysis → `wiki/project/bibliography.md`.
+  Promotion upstream is deliberate, via `al_ingest_paper` from the assistant clone.
 - Toolchain provenance: `project.yaml` (`assistant_ref`) + per-run `results/manifests/`.
 - Reproducibility: every meaningful run writes `results/manifests/<run_id>.json`.
 ```
@@ -195,6 +199,20 @@ The validator stays in the assistant — `validate_pyauto_code.py` resolves
 absolute paths. The cross-tool caveat (hooks are Claude Code-only; other harnesses
 self-enforce) is stated in the generated `AGENTS.md` "Code gate" section above.
 
+**`wiki/project/bibliography.md`** (generate — the project-local literature home; the hybrid
+rule stated once in its header):
+```markdown
+# Bibliography — papers specific to this analysis
+
+Papers that belong to this project's reference list live here, one `##` section per paper in
+the same shape as the assistant's `wiki/literature/sources/*.md` (canonical BibTeX key,
+reference, concepts, supported claims — public arXiv/DOI references only, never local PDF
+paths). General lensing concepts are NOT duplicated here: the assistant's shared
+`wiki/literature/` (resolved via refer-back) stays the one source of truth. A paper that
+proves generally useful can be promoted upstream by running `al_ingest_paper` from the
+assistant clone — promotion is deliberate, never the default.
+```
+
 **`.gitattributes`**: `* text=auto eol=lf` (+ `*.fits *.png *.npy *.pkl binary`).
 
 **`.gitignore`** (exclude data/output/secrets/cloned-assistant; **keep** manifests/figures/journal):