Bioinfo-skills

Perform a non-destructive cross-artifact consistency and quality analysis across spec.md, plan.md, and tasks.md after task generation.

Generate a custom checklist for the current feature based on user requirements.

Identify underspecified areas in the current feature spec by asking up to 5 highly targeted clarification questions and encoding answers back into the spec.

Create or update the project constitution from interactive or provided principle inputs, ensuring all dependent templates stay in sync.

Create or refresh a current-understanding.md continuity report for a Bioinfo SDD feature or half-finished workflow by reviewing current specs, plans, tasks, section state, installed refs, selected packages/tools, wrappers, adapters, checks, evidence, and unresolved next steps.

Auto-commit changes after a BioKit command completes

Create a feature branch with sequential or timestamp numbering

Initialize a Git repository with an initial commit

Detect Git remote URL for GitHub integration

Validate current branch follows feature branch naming conventions

Execute the implementation plan by processing and executing all tasks defined in tasks.md

Execute the implementation planning workflow using the plan template to generate design artifacts.

Create or update the feature specification from a natural language feature description.

Generate an actionable, dependency-ordered tasks.md for the feature based on available design artifacts.

Convert existing tasks into actionable, dependency-ordered GitHub issues for the feature based on available design artifacts.

Create or revise Bioinfo-skills analysis section evidence reports.

Create or revise Bioinfo-skills analysis section implementation plans.

Create or revise Bioinfo-skills analysis section specifications and section.yml contracts.

Create or revise ordered Bioinfo-skills analysis section task lists.