Changelog

v0.8.0 (2026-10-02)

• The workbench kind. WORKBENCH.toml: one repo holding general tools/, sims/ and apps/ and one folder per study. scaffold new workbench creates one; new study --inside <workbench> creates a study that shares the repo's kit, agents, CI and licence; new tool|sim --inside <study or workbench> adds units to either. A workbench has no one stage or corpus project, may mount the corpus as a submodule, and declares its private folders, which requires a private repo. check on a workbench checks every study it lists.
• A study may hold its own tools ([[tools]] with a path); a tool inside a study is a unit, not a tool repo.
• A study inside a workbench carries no visibility of its own: the workbench decides it.
• Adopted units. A [[datasets]] or [[calculators]] entry with adopted = true predates the unit formats: check requires only that it exists, and warns that it owes its manifest when next worked on.
• Generated CI checks out v0.8.0.

v0.7.0 (2026-10-01)

• Pins scientific-research-agents v0.2.0, with provider-neutral role bodies and Claude Code subagent frontmatter retained as an adapter.
• Makes AGENTS.md the shared instruction surface for Claude, ChatGPT, Codex and other repository-aware assistants. Per-kind scientific rules now live in its scaffold-managed block; new CLAUDE.md files import it without duplication, while existing Claude customizations remain untouched.
• Packages new-study as a portable ChatGPT/Codex skills-only plugin and documents Claude and Codex skill installation separately.
• Generated CI checks out v0.7.0.

v0.6.0 (2026-10-01)

• Needs adaptive-preregistration v0.7.0 or later. Generated CI checks out v0.6.0.
• New tools start at 0.1.0, in preparation (an undated changelog heading), so release-check and check agree.
• Tools use kit v0.7.0. new tool installs tool-versioning (releases: annotated tags, outputs changed, consumers, release-check) in place of the profile's preregistration modules; prereg, a kit default, now scopes the tool claim first (tool-scope was merged into it). A tool's override experiments are preregistered in the research corpus. check warns while a tool with the scope protocol has no SCOPE.toml.

v0.5.1 (2026-09-30)

• Adopted repos stay adopted. .scaffold.lock records "adopted": true for a repo that took up the scaffold rather than being made by it, and update never adds a missing file to such a repo unasked. Before, a lock written by an adopting update made the next update treat the repo as scaffold-made and add its CI and Makefile.

v0.5.0 (2026-09-30)

• Needs adaptive-preregistration v0.5.0 or later, whose tool-scope applies to tool repositories.
• Generated CI checks out v0.5.0.
• Tools are scoped. new tool installs the profile's [prereg] tool_modules (tool-scope) in place of its preregistration modules, so a tool's claim, features and every scientific feature's evidence and decision are settled with the person first (SCOPE.toml at the root; kit tool-scope now applies to tool repositories). check warns while a scoped tool has no SCOPE.toml.

v0.4.0 (2026-09-30)

• Generated CI checks out v0.4.0; update moves existing repos' CI to it, and UPGRADING.md says what else to do.
• Repos notice new releases. UPGRADING.md says, per release, what scaffold update does and what a session does by hand. scaffold version compares a repo's recorded release with the current one (and with GitHub's latest) and prints the steps in between; a session hook in .claude/settings.json runs it when a Claude Code session starts, beside the kit's hooks, and the AGENTS.md section tells Codex to. update adds the hook, and prints the upgrade notes with its plan.
• Work types replace experiments/. A study is built from apps, sims, datasets, calculators and tools (PROTOCOL.md § 5), each with its own folder, entry requirement and way of writing back to research. scaffold new dataset creates datasets/<slug>/ (a dataset-fetch reference pinned to a version, selection criteria, analysis/); scaffold new calculator creates calculators/<slug>/ (CALCULATOR.md, reference.csv). Preregistrations live in the unit they test, <unit>/preregistrations/<EID>/, listed in EXPERIMENTS.md; sims use preregistrations/ too. check enforces a selected dataset's pinned reference and licence, and calculator reference values from PROBE on; experiments/, data/manifest.json and unregistered unit folders are warnings. PROTOCOL.md sections from Apps on are renumbered.
• The agents moved to their own repo, scientific-research-agents, included as a submodule at agents/ pinned to v0.1.1: the briefs, the coordination protocol, discipline briefs, prices and the usage tool. scaffold usage passes through to its bin/agents usage. The new-study skill moved to skills/. Clone with --recurse-submodules.
• Agent coordination. agents/COORDINATION.md: one lead delegates, agents pass 150-word handoffs instead of transcripts, parallel work only for independent tasks (at most three, each in its own worktree), agent teams only for tight back-and-forth, and the science gate never skipped.
• Mathematician agent. Equations, constants, units and valid ranges; records each piece of maths with its source (BioNumbers style) and specifies calculators with reference values, handing code to the engineer.
• Model routing. Each agent's frontmatter now sets its starting model and effort (a new scout on Haiku; the others on Sonnet), overridable in a profile's [agents.routing]; the lead escalates a task on a clear signal.
• Codex. A marked scaffold section in AGENTS.md gives every assistant the roles, the coordination rules and Codex routing from the profile's [agents.codex]. update maintains it and leaves the rest of the file alone.
• scaffold usage. Tokens and API-equivalent cost per repo and model from Claude Code's and Codex's local logs, a monthly projection, and Codex's plan rate-limit windows. Prices are in agents/prices.toml. Each response is counted once: Claude Code writes one response as several transcript lines.

v0.3.0 (2026-09-30)

• The tool kind. A third kind of repo, for one job done for other repos with no research in it: TOOL.toml with a job in place of a question, a version, and [[consumers]] naming what each dependent repo uses. scaffold new tool <name> --job "..." creates one. check fails a tool that holds research (a question, [corpus], RESEARCH.md, EXPERIMENTS.md, experiments/), whose version differs across TOOL.toml, pyproject.toml, CITATION.cff and CHANGELOG.md, or whose consumers don't say what they use. Modelled on the TOOL.toml an existing tool repo already used; PROTOCOL.md § 7.
• scaffold status and scaffold update. status gives one line per repo: kind, stage, scaffold release, CI ref, check result and pending update. update brings a repo's scaffold-owned files (the CI workflow, Makefile, shared/workbench.py) up to this release. It replaces only files nobody edited, known from the new .scaffold.lock that new writes, or by matching what an earlier release wrote. In an edited workflow it moves only the scaffold ref:; other edited files are kept unless --adopted. A dry run unless --apply; refuses to overwrite uncommitted work; never commits. PROTOCOL.md § 12.
• Specialist agents. Every new repo gets Claude Code subagents in .claude/agents/: computational-engineer, designer, frontend-developer, researcher, analyst and science-writer (a sim has no UI agents), plus .claude/disciplines.md. A profile's new [agents] table chooses the discipline briefs (agents/disciplines/) and the code conventions written into the agents. The agents are scaffold-owned, so update keeps them current; --adopt now takes a folder, to add them to an existing repo. Generated CLAUDE.md says which agent takes which task, and in what order.
• Studies and sims list the tools they use under [[tools]], and check fails a tool pinned to a branch.
• PROTOCOL.md sections from Preregistration on are renumbered by one (Preregistration is now § 8).
• The built-in TOML parser (Python < 3.11) reads arrays that span lines, and decodes non-ASCII strings correctly; before, "µV" came back garbled.
• Generated CI checks out v0.3.0, and update moves existing repos' CI to it.

v0.2.0 (2026-09-29)

• No default profile. scaffold new takes --profile NAME or $SCAFFOLD_PROFILE, and fails with the list of profiles if neither is set. Before, it silently used polarizetech.
• Visibility is never defaulted. New manifests say visibility = "undecided" unless --visibility public|private is given, and scaffold check fails on undecided. Before, the template wrote "private" with today's date, which passed check without anyone deciding.
• Generated study and sim CI checks out v0.2.0.

v0.1.0 (2026-09-27)

First release.

• The study protocol, the adoption guide, study/sim/app templates, and scaffold (new, promote-sim, check, profiles), with the example and polarizetech profiles.
• Generated study and sim CI checks out this release (v0.1.0) rather than main.