docs: shareable science projects — fork/clone-and-continue + open-source-your-paper emphasis

[Jammy2211]

Overview

A science project created by start-new-project already becomes its own GitHub repo with a Create → Work → Collaborate → Publish lifecycle, a paper-hardening Publish gate, Zenodo/DOI minting and CITATION.cff. This task adds the missing user-facing emphasis: sharing as the default expectation — a collaborator forks or clones the project and continues the work with their own assistant — and an explicit pitch that the project repo is the natural open-source companion to a paper (data, results, every python script). The generated project currently has no README.md at all (the Publish gate references one that Create never scaffolds); that is the anchor gap.

Absorbs the retired PyAutoMind prompt science_project_collaborator_clone.md (its assistant-ref dependency — $AUTOLENS_ASSISTANT → sibling → clone-on-demand — is settled in start-new-project.md).

Plan

• Add the missing generated-project README.md template to the Create scaffold: standalone reproduction, fork/clone-and-continue with your own assistant, data-availability placeholder.
• Rework the Collaborate phase to actively encourage sharing and spell out a collaborator's fork-and-continue first session.
• Align the Publish phase wording so the published repo reads as the paper's open-source companion (data availability, results, every script).
• Add the open-source-your-paper pitch and share/fork example prompts to the assistant's top-level README "Science Project" section.

Detailed implementation plan

Affected Repositories

• autolens_assistant (primary, only)

Branch Survey

Repository	Current Branch	Dirty?
./autolens_assistant	main	clean (one untracked personal james.bib, untouched)

Suggested branch: feature/shareable-science-projects (in-place on the main checkout, no worktree)

Implementation Steps

1. skills/start-new-project.md — Phase 1 Create §5: add README.md to the generated lean project tree listing; insert a "Project README.md (generate)" template block after the thin AGENTS.md block with sections: title + description; Reproduce this analysis (env via activate.sh, code in scripts/, provenance in results/manifests/); Continue this work (fork or clone this repo, then point your own autolens_assistant at it — $AUTOLENS_ASSISTANT → sibling → clone-on-demand, see AGENTS.md); Data availability placeholder the Publish gate fills in; CITATION.cff pointer. Keep it short — detail lives in the thin AGENTS.md.
2. skills/start-new-project.md — Phase 3 Collaborate: actively encourage pushing + sharing; add "A collaborator's first session" flow (fork/clone → assistant resolves via refer-back → reads AGENTS.md + wiki/project/ journal → provenance-drift check fires → continues the work with journal entries). Phrase assistant safety via refer-back neutrally (the project-side API code-gate ships as a separate follow-up task).
3. skills/start-new-project.md — Phase 4 Publish: align the README data-availability gate item with the now-scaffolded section; one line framing the public repo as the paper's open-source companion. Frontmatter description:: add fork/clone-and-continue trigger phrases.
4. README.md (assistant top level, "Science Project" section): short pitch — share the project repo, a collaborator forks/clones and continues with their own assistant; open-source the entire project behind a paper (data or its availability statement, results, all python scripts) using the existing Publish gate / Zenodo DOI / CITATION.cff. Agentic-AI framing first-class; no llms.txt mechanics; add 1–2 example prompts.

Validation

• autoassistant path/citation checker (--check-citations mode) over the edited docs.
• Consistency read: Create tree ↔ README template ↔ Publish gate reference the same files.
• No personal content (repo is a generic public template).

Key Files

• skills/start-new-project.md — the science-project lifecycle skill (all three phases touched)
• README.md — user-facing Science Project pitch

Original Prompt

Click to expand starting prompt

I want it so that with autolens assistant a user can basically make a science project which becomes its own github repo, and then they should be encouraged to be able to easily share that project and another friend could come in, fork or clone it and cotinue the work with their own autolens assistant. Emphassie this aspect in the autolens_assistant design. Also make it clear this would be a wonderful way to put up the open-source repo that goes with a paper, so make sure autolens_assistant has user-facing aspects which make it clear its great for open sourceing a whole project (data, results, all python scripts).

[Jammy2211]

Shipped to PR-open: #46 (branch feature/shareable-science-projects, commit 58998e4).

All four planned steps landed:

1. ✅ Generated-project README.md template added to the Create scaffold (reproduce / continue-this-work / data-availability placeholder / citation) — the gap where the Publish gate referenced a README that Create never generated is closed.
2. ✅ Collaborate phase now opens with "built to be shared" and walks a collaborator's fork-and-continue first session end-to-end.
3. ✅ Publish phase framed as producing the paper's open-source companion; gate item aligned to the scaffolded section.
4. ✅ Top-level README "Built to be shared" pitch + new share/publish example prompts.

Validation: citation/path checker clean (388 citations, 0 missing); consistency read across Create tree ↔ README template ↔ Publish gate; no personal content. Heart YELLOW on the standing 6-reason set only (same set human-acked repeatedly today); docs-only, not on the release train.

Merge is a human act — awaiting sign-off on #46. Next in the batch queue after merge: science_project_api_gate.