biokit-constitution

name	biokit-constitution
description	Create or update the project constitution from interactive or provided principle inputs, ensuring all dependent templates stay in sync.
compatibility	Requires spec-kit project structure with .specify/ directory
metadata	{"author":"github-spec-kit","source":"templates/commands/constitution.md"}

Bioinfo SDD Contract

This skill keeps the upstream Spec Kit-style Codex invocation, but the constitution it creates or amends is the Bioinfo SDD constitution. Treat generic Spec Kit behavior as ergonomics only: Bioinfo section scope, section.yml, review gates, tool_market/, section-local installed_refs/, wrappers, adapters, deterministic checks, and evidence remain authoritative. For non-analysis infrastructure, explicitly mark the section as N/A instead of weakening analysis-section requirements.

User Input

$ARGUMENTS

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

Pre-Execution Checks

Check for extension hooks (before constitution update):

• Check if .specify/extensions.yml exists in the project root.
• If it exists, read it and look for entries under the hooks.before_constitution 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

You are updating the project constitution at .specify/memory/constitution.md. This file is a TEMPLATE containing placeholder tokens in square brackets (e.g. [PROJECT_NAME], [PRINCIPLE_1_NAME]). Your job is to (a) collect/derive concrete values, (b) fill the template precisely, and (c) propagate any amendments across dependent artifacts.

Note: If .specify/memory/constitution.md does not exist yet, it should have been initialized from .specify/templates/constitution-template.md during project setup. If it's missing, copy the template first.

Follow this execution flow:

1. Load the existing constitution at .specify/memory/constitution.md.

   • Identify every placeholder token of the form [ALL_CAPS_IDENTIFIER]. IMPORTANT: The user might require less or more principles than the ones used in the template. If a number is specified, respect that - follow the general template. You will update the doc accordingly.

2. Collect/derive values for placeholders:

   • If user input (conversation) supplies a value, use it.
   • Otherwise infer from existing repo context (README, docs, prior constitution versions if embedded).
   • For governance dates: RATIFICATION_DATE is the original adoption date (if unknown ask or mark TODO), LAST_AMENDED_DATE is today if changes are made, otherwise keep previous.
   • CONSTITUTION_VERSION must increment according to semantic versioning rules:
     • MAJOR: Backward incompatible governance/principle removals or redefinitions.
     • MINOR: New principle/section added or materially expanded guidance.
     • PATCH: Clarifications, wording, typo fixes, non-semantic refinements.
   • If version bump type ambiguous, propose reasoning before finalizing.

3. Draft the updated constitution content:

   • Replace every placeholder with concrete text (no bracketed tokens left except intentionally retained template slots that the project has chosen not to define yet—explicitly justify any left).
   • Preserve heading hierarchy and comments can be removed once replaced unless they still add clarifying guidance.
   • Ensure each Principle section: succinct name line, paragraph (or bullet list) capturing non‑negotiable rules, explicit rationale if not obvious.
   • Ensure Governance section lists amendment procedure, versioning policy, and compliance review expectations.

4. Consistency propagation checklist (convert prior checklist into active validations):

   • Read .specify/templates/plan-template.md and ensure any "Constitution Check" or rules align with updated principles.
   • Read .specify/templates/spec-template.md for scope/requirements alignment—update if constitution adds/removes mandatory sections or constraints.
   • Read .specify/templates/tasks-template.md and ensure task categorization reflects new or removed principle-driven task types (e.g., observability, versioning, testing discipline).
   • Read each command file in .specify/templates/commands/*.md (including this one) to verify no outdated references (agent-specific names like CLAUDE only) remain when generic guidance is required.
   • Read any runtime guidance docs (e.g., README.md, docs/quickstart.md, or agent-specific guidance files if present). Update references to principles changed.

5. Produce a Sync Impact Report (prepend as an HTML comment at top of the constitution file after update):

   • Version change: old → new
   • List of modified principles (old title → new title if renamed)
   • Added sections
   • Removed sections
   • Templates requiring updates (✅ updated / ⚠ pending) with file paths
   • Follow-up TODOs if any placeholders intentionally deferred.

6. Validation before final output:

   • No remaining unexplained bracket tokens.
   • Version line matches report.
   • Dates ISO format YYYY-MM-DD.
   • Principles are declarative, testable, and free of vague language ("should" → replace with MUST/SHOULD rationale where appropriate).

7. Write the completed constitution back to .specify/memory/constitution.md (overwrite).

8. Output a final summary to the user with:

   • New version and bump rationale.
   • Any files flagged for manual follow-up.
   • Suggested commit message (e.g., docs: amend constitution to vX.Y.Z (principle additions + governance update)).

Formatting & Style Requirements:

• Use Markdown headings exactly as in the template (do not demote/promote levels).
• Wrap long rationale lines to keep readability (<100 chars ideally) but do not hard enforce with awkward breaks.
• Keep a single blank line between sections.
• Avoid trailing whitespace.

If the user supplies partial updates (e.g., only one principle revision), still perform validation and version decision steps.

If critical info missing (e.g., ratification date truly unknown), insert TODO(<FIELD_NAME>): explanation and include in the Sync Impact Report under deferred items.

Do not create a new template; always operate on the existing .specify/memory/constitution.md file.

Post-Execution Checks

Check for extension hooks (after constitution update): Check if .specify/extensions.yml exists in the project root.

• If it exists, read it and look for entries under the hooks.after_constitution 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