Manage GitHub work
Use gh CLI when authenticated; otherwise produce the exact proposed issue or PR update and state that it was not applied.
Create an issue when work
- spans sessions or multiple steps;
- changes code, analyses, outputs, or manuscript artifacts;
- needs review, acceptance criteria, discussion, or provenance; or
- implements a recorded decision.
Keep quick personal actions in tasks.md. Search open and closed issues before creating one.
Issue content
## Why
[Research or project context]
## Scope
- [work]
## Acceptance criteria
- [observable result or validation]
## Links
- Aim:
- Decision:
- Source meeting/task:
- Affected files/outputs:
Update issues when evidence changes, not merely because code was edited. Close only when acceptance criteria are satisfied. Link PRs to their issue and summarize scientific impact, validation, changed outputs, and remaining uncertainty. Never create, close, or materially rewrite remote items without explicit user intent.