Separate flow runtime overlay drift

[chubes4]

Summary

• Adds normalized flow runtime_overlays payloads so bundle queue, schedule, and burn-in seed drift is visible without treating live runtime state as package source drift.
• Preserves site-local queue state, _queue_consume_revision, scheduling, and handler max_items on normal upgrades while keeping --reconcile-runtime able to replace them with bundle seeds.
• Extends runtime drift/planner smoke coverage for config_patch_queue, queue_mode, _queue_consume_revision, max_items, and paused/manual scheduling examples.

Fixes #1844.

Verification

• vendor/bin/phpcs inc/Core/Agents/AgentBundler.php inc/Engine/Bundle/AgentBundleRuntimeDrift.php inc/Cli/Commands/AgentBundleCommand.php tests/agent-bundle-runtime-drift-smoke.php tests/agent-bundle-upgrade-planner-smoke.php tests/Unit/Core/Agents/AgentBundlerImportTest.php
• php -l inc/Core/Agents/AgentBundler.php
• php -l inc/Engine/Bundle/AgentBundleRuntimeDrift.php
• php -l inc/Cli/Commands/AgentBundleCommand.php
• php -l tests/Unit/Core/Agents/AgentBundlerImportTest.php
• php tests/agent-bundle-runtime-drift-smoke.php && php tests/agent-bundle-upgrade-planner-smoke.php && php tests/agent-bundle-artifact-rebase-smoke.php
• git diff --check

Notes

• homeboy test --path /Users/chubes/Developer/data-machine@issue-1844-runtime-overlays --extension wordpress --force-hot -- --filter=AgentBundlerImportTest still exits from WP Codebox with an unclassified failure after discovering 100 test files and without stderr/details.
• homeboy lint --path /Users/chubes/Developer/data-machine@issue-1844-runtime-overlays --extension wordpress --force-hot reports existing unrelated ESLint findings in admin React files outside this change; changed PHP files pass PHPCS directly.

AI assistance

• AI assistance: Yes
• Tool(s): OpenCode (GPT-5.5)
• Used for: implementing and testing the focused Separate bundle flow seeds from live runtime overlays #1844 runtime overlay slice; Chris remains responsible for review.

[homeboy-ci]

Homeboy Results — data-machine

Lint

✅ lint — passed

ℹ️ Full options: homeboy docs commands/lint
Deep dive: homeboy lint data-machine --changed-since 9caa8a9

Artifacts and drill-down

• CI results artifact: homeboy-ci-results-data-machine-lint-quality-Linux-node24 contains immediate command JSON for this action invocation.
• Observation artifact: homeboy-observations-data-machine-lint-quality-Linux-node24 contains exported Homeboy run history for deeper queries.
• Drill-down: download the observation artifact, then run homeboy runs import <dir>, homeboy runs list, and homeboy runs findings <run-id>.
• Artifacts are attached to the workflow run: https://github.com/Extra-Chill/data-machine/actions/runs/26334935887

Test

✅ test — passed

• 220 passed
• 3 skipped

ℹ️ Auto-fix lint issues: homeboy refactor data-machine --from lint --write
ℹ️ Collect coverage: homeboy test data-machine --coverage
ℹ️ Save test baseline: homeboy test data-machine --baseline
ℹ️ Pass args to test runner: homeboy test -- [args]
ℹ️ Full options: homeboy docs commands/test
Deep dive: homeboy test data-machine --changed-since 9caa8a9

Artifacts and drill-down

• CI results artifact: homeboy-ci-results-data-machine-test-quality-Linux-node24 contains immediate command JSON for this action invocation.
• Observation artifact: homeboy-observations-data-machine-test-quality-Linux-node24 contains exported Homeboy run history for deeper queries.
• Drill-down: download the observation artifact, then run homeboy runs import <dir>, homeboy runs list, and homeboy runs findings <run-id>.
• Artifacts are attached to the workflow run: https://github.com/Extra-Chill/data-machine/actions/runs/26334935887

Audit

✅ audit — passed

• requested_detectors — 26 finding(s)
• intra-method-duplication — 8 finding(s)
• dead_code — 6 finding(s)
• parallel-implementation — 6 finding(s)
• Directives — 1 finding(s)
• Retention — 1 finding(s)
• structural — 1 finding(s)
• Total: 49 finding(s)

Deep dive: homeboy audit data-machine --changed-since 9caa8a9

Artifacts and drill-down

• CI results artifact: homeboy-ci-results-data-machine-audit-quality-Linux-node24 contains immediate command JSON for this action invocation.
• Observation artifact: homeboy-observations-data-machine-audit-quality-Linux-node24 contains exported Homeboy run history for deeper queries.
• Drill-down: download the observation artifact, then run homeboy runs import <dir>, homeboy runs list, and homeboy runs findings <run-id>.
• Artifacts are attached to the workflow run: https://github.com/Extra-Chill/data-machine/actions/runs/26334935887

Tooling versions

• Homeboy CLI: homeboy 0.197.2+69c9e7d1
• Extension: wordpress from https://github.com/Extra-Chill/homeboy-extensions
• Extension revision: dd23ee80
• Action: unknown@unknown

[chubes4]

Follow-up pushed in 69c9e7d.\n\nFixed the scoped WP Codebox failure by normalizing flow artifact hashes so package-source comparison ignores install-time flow step IDs and live runtime scheduling overlays while keeping bundle seed drift visible in runtime_overlays. Also fixed the PHPCS assignment alignment warning.\n\nVerified:\n- homeboy lint --path /Users/chubes/Developer/data-machine@issue-1844-runtime-overlays --extension wordpress --changed-since 9caa8a9\n- homeboy test --path /Users/chubes/Developer/data-machine@issue-1844-runtime-overlays --extension wordpress --changed-since 9caa8a9\n\nBoth pass locally; test result was 223 total, 220 passed, 3 skipped.