Overview
wiki/literature/ is the assistant's shared, self-contained strong-lensing reference; spun-off science projects refer back to it. Open question resolved (hybrid): general concepts stay shared (refer-back, one source of truth); papers specific to one analysis live in the project, so niche references never pollute the global wiki. A generally-useful paper can still be promoted upstream — a deliberate act, not the default.
Plan
- Project-local home:
wiki/project/bibliography.md, scaffolded at Create (user decision 2026-07-10: single page, not a literature/ tree) — one H2 per paper in the same section shape as shared sources/*.md (canonical key / reference / concepts / supports; public refs only, never PDF paths), so promotion upstream is a verbatim copy.
al_ingest_paper.md: target-selection step — inside a science project (detect project.yaml + refer-back AGENTS.md) default to the project's bibliography.md; shared wiki/literature/ only on explicit promotion run from the assistant clone (full canonical-key + validate-citations flow).start-new-project.md: scaffold the page; thin AGENTS.md gains a "Literature" bullet explaining the hybrid rule.- Guided paper-intake at project creation stays deferred (evidence-gated): validate through real assistant usage first — when users naturally supply papers, how much literature searching they want at setup, whether creation is even the right moment. Revisit with evidence.
Detailed implementation plan
Affected Repositories
- autolens_assistant (primary, only)
Branch Survey
| Repository |
Current Branch |
Dirty? |
| ./autolens_assistant |
main (post-#48) |
clean (untracked personal james.bib, untouched) |
Suggested branch: feature/per-project-literature (in-place, no worktree)
Implementation Steps
skills/start-new-project.md Create §5: add wiki/project/bibliography.md to the scaffold (tree comment on the wiki/project line + a short generated-header template block: hybrid rule, section shape pointer, public-refs-only rule).- Thin
AGENTS.md template: "Literature" bullet under "## This project": general lensing concepts → the assistant's shared wiki/literature/ via refer-back; papers specific to this analysis → wiki/project/bibliography.md; promotion upstream = al_ingest_paper run from the assistant clone, deliberate only.
skills/al_ingest_paper.md: new target-selection subsection in Ask/Branch — detect project context; project-local default (same H2 shape; reuse the assistant's canonical key when the paper is already in autolens_literature.bib, else stable author-year key + the project's own paper .bib if present; do NOT edit the assistant clone's .bib/sources/ from a project session); explicit promotion = full shared flow incl. validate-citations + log.md row. Frontmatter description updated for the two targets.
Validation
--check-citations clean; consistency read across the three files; markdown-only change, no personal content.
Key Files
skills/al_ingest_paper.md, skills/start-new-project.md
Original Prompt
Click to expand starting prompt
wiki/literature/ is the assistant's shared, self-contained base reference for strong-lensing science (decoupled from any external paper repo). Spun-off science projects refer back to it rather than copying it. Open question: when a paper is ingested for a specific project, where does it go? Decision (lean: hybrid): general concepts — refer back to shared wiki/literature/, one source of truth. Papers specific to this analysis — the project's own bibliography, kept in the project, NOT pushed into the shared wiki. A generally useful paper can be contributed upstream via al_ingest_paper from the assistant clone — deliberate promotion, not the default. Implement: define the project-local literature location and shape; teach al_ingest_paper to choose its target (project-local by default inside a project, shared only on explicit promotion); have start-new-project scaffold the project-local bibliography home and explain the hybrid rule. Deferred (validate through real usage first): a guided "Scientific context and papers" step at project creation — prompt for papers, inspect existing wiki coverage, search externally, present a reviewable shortlist, ingest approved selections project-locally with provenance; promotion stays the only route into the shared wiki.
Overview
wiki/literature/is the assistant's shared, self-contained strong-lensing reference; spun-off science projects refer back to it. Open question resolved (hybrid): general concepts stay shared (refer-back, one source of truth); papers specific to one analysis live in the project, so niche references never pollute the global wiki. A generally-useful paper can still be promoted upstream — a deliberate act, not the default.Plan
wiki/project/bibliography.md, scaffolded at Create (user decision 2026-07-10: single page, not a literature/ tree) — one H2 per paper in the same section shape as sharedsources/*.md(canonical key / reference / concepts / supports; public refs only, never PDF paths), so promotion upstream is a verbatim copy.al_ingest_paper.md: target-selection step — inside a science project (detectproject.yaml+ refer-backAGENTS.md) default to the project'sbibliography.md; sharedwiki/literature/only on explicit promotion run from the assistant clone (full canonical-key +validate-citationsflow).start-new-project.md: scaffold the page; thinAGENTS.mdgains a "Literature" bullet explaining the hybrid rule.Detailed implementation plan
Affected Repositories
Branch Survey
Suggested branch:
feature/per-project-literature(in-place, no worktree)Implementation Steps
skills/start-new-project.mdCreate §5: addwiki/project/bibliography.mdto the scaffold (tree comment on the wiki/project line + a short generated-header template block: hybrid rule, section shape pointer, public-refs-only rule).AGENTS.mdtemplate: "Literature" bullet under "## This project": general lensing concepts → the assistant's sharedwiki/literature/via refer-back; papers specific to this analysis →wiki/project/bibliography.md; promotion upstream =al_ingest_paperrun from the assistant clone, deliberate only.skills/al_ingest_paper.md: new target-selection subsection in Ask/Branch — detect project context; project-local default (same H2 shape; reuse the assistant's canonical key when the paper is already inautolens_literature.bib, else stable author-year key + the project's own paper.bibif present; do NOT edit the assistant clone's.bib/sources/from a project session); explicit promotion = full shared flow incl.validate-citations+log.mdrow. Frontmatter description updated for the two targets.Validation
--check-citationsclean; consistency read across the three files; markdown-only change, no personal content.Key Files
skills/al_ingest_paper.md,skills/start-new-project.mdOriginal Prompt
Click to expand starting prompt
wiki/literature/ is the assistant's shared, self-contained base reference for strong-lensing science (decoupled from any external paper repo). Spun-off science projects refer back to it rather than copying it. Open question: when a paper is ingested for a specific project, where does it go? Decision (lean: hybrid): general concepts — refer back to shared wiki/literature/, one source of truth. Papers specific to this analysis — the project's own bibliography, kept in the project, NOT pushed into the shared wiki. A generally useful paper can be contributed upstream via al_ingest_paper from the assistant clone — deliberate promotion, not the default. Implement: define the project-local literature location and shape; teach al_ingest_paper to choose its target (project-local by default inside a project, shared only on explicit promotion); have start-new-project scaffold the project-local bibliography home and explain the hybrid rule. Deferred (validate through real usage first): a guided "Scientific context and papers" step at project creation — prompt for papers, inspect existing wiki coverage, search externally, present a reviewable shortlist, ingest approved selections project-locally with provenance; promotion stays the only route into the shared wiki.