Fix core bundle artifact apply handlers

[chubes4]

Summary

• Adds Data Machine-owned apply handling for approved pipeline and flow bundle artifacts.
• Updates the installed artifact registry after successful apply so rebased bundle upgrades can resolve cleanly.

Testing

• php -l inc/Engine/Bundle/AgentBundleUpgradeActionHandlers.php
• php tests/agent-bundle-pending-action-rebase-smoke.php
• php tests/agent-bundle-upgrade-planner-smoke.php
• vendor/bin/phpcs inc/Engine/Bundle/AgentBundleUpgradeActionHandlers.php

AI assistance

• AI assistance: Yes
• Tool(s): OpenCode (GPT-5.5)
• Used for: Ported and verified the core bundle artifact apply handler fix from a stale local worktree onto current main; Chris remains responsible for review and testing.

[homeboy-ci]

Homeboy Results — data-machine

Lint

❌ lint — failed

• yoda — 1 finding(s)
• Total: 1 finding(s)

ℹ️ Auto-fix: homeboy lint data-machine --path /home/runner/work/data-machine/data-machine --changed-since 68c4719 --fix (or homeboy refactor data-machine --path /home/runner/work/data-machine/data-machine --changed-since 68c4719 --from lint --write)
ℹ️ Some issues may require manual fixes
ℹ️ Full options: homeboy docs commands/lint
Deep dive: homeboy lint data-machine --changed-since 68c4719

Test

✅ test — passed

ℹ️ No impacted tests found for --changed-since 68c4719
ℹ️ Run full suite if needed: homeboy test data-machine
Deep dive: homeboy test data-machine --changed-since 68c4719

Audit

✅ audit — passed

• test_coverage — 1 finding(s)
• Total: 1 finding(s)

Deep dive: homeboy audit data-machine --changed-since 68c4719

Tooling versions

• Homeboy CLI: homeboy 0.182.0+a78f6a44
• Extension: wordpress from https://github.com/Extra-Chill/homeboy-extensions
• Extension revision: 9eb4c10
• Action: unknown@unknown