biokit-plan

name	biokit-plan
description	Execute the implementation planning workflow using the plan template to generate design artifacts.
compatibility	Requires spec-kit project structure with .specify/ directory
metadata	{"author":"github-spec-kit","source":"templates/commands/plan.md"}

Bioinfo SDD Contract

This skill keeps the upstream Spec Kit-style Codex invocation, but the plan it generates must remain a Bioinfo SDD plan. Resolve the active feature from .specify/feature.json before branch fallback, and for analysis requests keep section.yml canonical, use section-local installed_refs/ for active package and bioinfo_tool context, treat tool_market/ as inactive source material, and preserve gates, wrappers, adapters, checks, evidence, and bounded claims.

User Input

$ARGUMENTS

You MUST consider the user input before proceeding (if not empty).

Pre-Execution Checks

Check for extension hooks (before planning):

• Check if .specify/extensions.yml exists in the project root.
• If it exists, read it and look for entries under the hooks.before_plan key
• If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
• Filter out hooks where enabled is explicitly false. Treat hooks without an enabled field as enabled by default.
• For each remaining hook, do not attempt to interpret or evaluate hook condition expressions:
  • If the hook has no condition field, or it is null/empty, treat the hook as executable
  • If the hook defines a non-empty condition, skip the hook and leave condition evaluation to the HookExecutor implementation
• When constructing slash commands from hook command names, replace dots (.) with hyphens (-). For example, biokit.git.commit → /biokit-git-commit.
• For each executable hook, output the following based on its optional flag:
  • Optional hook (optional: true):

    ## Extension Hooks
    
    **Optional Pre-Hook**: {extension}
    Command: `/{command}`
    Description: {description}
    
    Prompt: {prompt}
    To execute: `/{command}`
    

  • Mandatory hook (optional: false):

    ## Extension Hooks
    
    **Automatic Pre-Hook**: {extension}
    Executing: `/{command}`
    EXECUTE_COMMAND: {command}
    
    Wait for the result of the hook command before proceeding to the Outline.
    

• If no hooks are registered or .specify/extensions.yml does not exist, skip silently

Outline

1. Setup: Run .specify/scripts/bash/setup-plan.sh --json from repo root and parse JSON for FEATURE_SPEC, IMPL_PLAN, SPECS_DIR, BRANCH. For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'''m Groot' (or double-quote if possible: "I'm Groot").

2. Load context: Read FEATURE_SPEC and .specify/memory/constitution.md. Load IMPL_PLAN template (already copied).

3. Execute plan workflow: Follow the structure in IMPL_PLAN template to:

   • Fill Technical Context (mark unknowns as "NEEDS CLARIFICATION")
   • Fill Constitution Check section from constitution
   • Evaluate gates (ERROR if violations unjustified)
   • Phase 0: Generate research.md (resolve all NEEDS CLARIFICATION)
   • Phase 1: Generate data-model.md, contracts/, quickstart.md
   • Phase 1: Update agent context by running the agent script
   • Re-evaluate Constitution Check post-design

4. Stop and report: Command ends after Phase 2 planning. Report branch, IMPL_PLAN path, and generated artifacts.

5. Check for extension hooks: After reporting, check if .specify/extensions.yml exists in the project root.

   • If it exists, read it and look for entries under the hooks.after_plan key
   • If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
   • Filter out hooks where enabled is explicitly false. Treat hooks without an enabled field as enabled by default.
   • For each remaining hook, do not attempt to interpret or evaluate hook condition expressions:
     • If the hook has no condition field, or it is null/empty, treat the hook as executable
     • If the hook defines a non-empty condition, skip the hook and leave condition evaluation to the HookExecutor implementation
   • When constructing slash commands from hook command names, replace dots (.) with hyphens (-). For example, biokit.git.commit → /biokit-git-commit.
   • For each executable hook, output the following based on its optional flag:
     • Optional hook (optional: true):

       ## Extension Hooks
       
       **Optional Hook**: {extension}
       Command: `/{command}`
       Description: {description}
       
       Prompt: {prompt}
       To execute: `/{command}`
       

     • Mandatory hook (optional: false):

       ## Extension Hooks
       
       **Automatic Hook**: {extension}
       Executing: `/{command}`
       EXECUTE_COMMAND: {command}
       

   • If no hooks are registered or .specify/extensions.yml does not exist, skip silently

Phases

Phase 0: Outline & Research

1. Extract unknowns from Technical Context above:

   • For each NEEDS CLARIFICATION → research task
   • For each dependency → best practices task
   • For each integration → patterns task

2. Generate and dispatch research agents:

   For each unknown in Technical Context:
     Task: "Research {unknown} for {feature context}"
   For each technology choice:
     Task: "Find best practices for {tech} in {domain}"
   

3. Consolidate findings in research.md using format:

   • Decision: [what was chosen]
   • Rationale: [why chosen]
   • Alternatives considered: [what else evaluated]

Output: research.md with all NEEDS CLARIFICATION resolved

Phase 1: Design & Contracts

Prerequisites: research.md complete

1. Extract entities from feature spec → data-model.md:

   • Entity name, fields, relationships
   • Validation rules from requirements
   • State transitions if applicable

2. Define interface contracts (if project has external interfaces) → /contracts/:

   • Identify what interfaces the project exposes to users or other systems
   • Document the contract format appropriate for the project type
   • Examples: public APIs for libraries, command schemas for CLI tools, endpoints for web services, grammars for parsers, UI contracts for applications
   • Skip if project is purely internal (build scripts, one-off tools, etc.)

3. Agent context update:

   • Update the plan reference between the <!-- SPECKIT START --> and <!-- SPECKIT END --> markers in AGENTS.md to point to the plan file created in step 1 (the IMPL_PLAN path)

Output: data-model.md, /contracts/*, quickstart.md, updated agent context file

Key rules

• Use absolute paths for filesystem operations; use project-relative paths for references in documentation and agent context files
• ERROR on gate failures or unresolved clarifications