# PPI/KaKs Integration Commit and Push Plan

> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking.

**Goal:** Commit the validated PPI → owner-specific Ortholog → Ka/Ks workflow and push it to the main PlantAI repository without including runtime data.

**Architecture:** Preserve the tested cross-layer change as one functional integration: frontend orchestration, API/backend identity resolution, owner-namespaced Ortholog materialization, contracts, and their tests. Keep input, workspace, downloaded bundles, logs, caches, and shared data outside Git.

**Tech Stack:** Vue 3 single-page frontend, FastAPI, Celery, Python, pytest, Git.

## Global Constraints

- Push must be a normal fast-forward update; never force-push.
- Do not stage `input/`, `workspace/`, `final/`, downloaded reference bundles, logs, PID files, caches, or shared `data` content.
- Preserve standalone, PPI-owner, and KaKs-owner Ortholog namespaces.
- Verify the relevant regression suite before committing and re-check the committed tree before pushing.

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### Task 1: Clean the commit boundary

**Files:** All currently modified tracked source, contract, and test files; the three PPI/KaKs plan/spec documents.

- [ ] Remove whitespace errors without changing runtime behavior.
- [ ] Update stale source-contract assertions to the current unified dialog and producer variable names.
- [ ] Confirm no runtime outputs are staged.

### Task 2: Verify the integrated workflow

**Files:** `tests/unit/test_ppi*.py`, reference-bundle tests, handoff/snapshot tests, and the affected production files.

- [ ] Run JavaScript syntax validation for `apps/web/vue3/index.html`.
- [ ] Run the focused PPI/KaKs, reference download, owner identity, and context regression tests.
- [ ] Run `git diff --check` and inspect the final staged file list.

### Task 3: Commit and push

**Files:** Only the verified source, contracts, tests, and documentation from Tasks 1–2.

- [ ] Fetch `origin/master` and verify the push remains fast-forward.
- [ ] Commit with a PPI/KaKs integration message.
- [ ] Push the committed branch to `origin/master` without force.
- [ ] Verify the remote master commit ID equals the local committed ID.