speckit-implement

name	speckit-implement
description	Implement the current concise Spec Kit plan by executing the Work Checklist in plan.md.

Implement From Plan

Use plan.md as the source of truth. Separate tasks.md files are legacy and are not required.

Workflow

1. Run .specify/scripts/powershell/check-prerequisites.ps1 -Json and read the active plan.md, .specify/memory/constitution.md, and AGENTS.md.
2. Extract the Work Checklist, package surfaces, verification commands, and open questions from the plan.
3. If an open question blocks correctness, ask it before editing. Otherwise make conservative assumptions and proceed.
4. Implement checklist items in dependency order. Update the checkbox in plan.md as each item is completed.
5. Keep changes scoped to files named or implied by the plan and constitution.
6. For public API changes, apply openspecy-design-public-api before editing signatures.
7. Run staged verification with openspecy-run-quality-gates: focused tests, relevant benchmarks, toolchain preflight and documentation, full tests, then package check. Report skipped long-running, external-resource, optional backend, or CI-only checks precisely.
8. For reference-library or other long-running external workflows, run a small representative probe first, then isolated expensive stages with logs and temporary outputs before the full workflow. Compare rebuilt artifacts against available legacy identifiers, wavenumber axes, metadata shape, warnings, and representative OpenSpecy joins or matches before marking the work complete.
9. For bundled Shiny app work, keep app code/assets under inst/, audit and remove orphaned files, compress or downsample images, report package-size impact, test helpers and server/module logic headlessly where feasible, verify installed app paths/assets, and run a manual or CI-guarded app smoke test when relevant.
10. For hosted Shinylive/WebAssembly work, treat the bundled inst/ app and package source as canonical, fix and verify the "Build and deploy wasm R package repository" workflow when affected, keep the app on a hardcoded package version/commit pin plus pinned app dependency closure, stage only the small medoid/model libraries with guarded get_lib() workflows unless the plan says otherwise, avoid hand-editing generated web artifacts, and run a CI-guarded or manual smoke test that covers startup, assets, dependency resolution, and library matching.

Rules

• Tests cover current package behavior; old implementations used for speed comparisons belong in benchmarks/.
• Same-output function improvements need a benchmark update or a written reason in the plan. Short benchmarks need repeated measurements and must flag material regressions.
• Do not edit NAMESPACE, man/*.Rd, or generated pkgdown HTML directly.
• Do not regenerate documentation with a roxygen2 version that differs from the version configured in DESCRIPTION.
• Preserve OpenSpecy object structure, identifiers, metadata alignment, and relevant attributes through function flows.
• Treat logical metadata filters with possible NA values deliberately and verify spectra/metadata row-column alignment after filters, joins, reductions, and model-preparation steps.
• Shiny application code belongs under inst/; avoidable large, duplicate, raw, generated, or orphaned Shiny assets must not be bundled.
• Hosted Shinylive/WebAssembly app output and wasm package repository contents are generated deployment artifacts; update source app code, package code, workflow config, library staging, dependency closure, or pinned metadata instead of editing them directly.
• Do not run git push, git pull, or git pull --rebase unless the user explicitly authorizes that specific remote operation in the current request. Prior or standing permission does not carry forward; prepare a local handoff for maintainer synchronization by default.