fix: discover worktree-backed workspace primaries

[chubes4]

Summary

• Treat primary workspace checkouts with a .git file as valid git repositories during worktree inventory scans.
• Add smoke coverage for linked primary checkouts so inventory refresh does not mark existing paths missing.

Testing

• php tests/smoke-worktree-lifecycle-metadata.php

AI assistance

• AI assistance: Yes
• Tool(s): OpenCode (GPT-5.5)
• Used for: Diagnosed the workspace inventory regression, drafted the minimal fix and smoke-test coverage, and ran targeted verification. Chris remains responsible for review and merge.

[homeboy-ci]

Homeboy Results — data-machine-code

Lint

✅ lint — passed

ℹ️ Full options: homeboy docs commands/lint
ℹ️ Save lint baseline: homeboy lint data-machine-code --baseline
Deep dive: homeboy lint data-machine-code --changed-since 32c71e9

Artifacts and drill-down

• CI results artifact: homeboy-ci-results-data-machine-code-lint-quality-Linux-node24 contains immediate command JSON for this action invocation.
• Observation artifact: homeboy-observations-data-machine-code-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-code/actions/runs/27110188666

Test

✅ test — passed

ℹ️ Auto-fix lint issues: homeboy refactor data-machine-code --from lint --write
ℹ️ Collect coverage: homeboy test data-machine-code --coverage
ℹ️ Pass args to test runner: homeboy test -- [args]
ℹ️ Full options: homeboy docs commands/test
Deep dive: homeboy test data-machine-code --changed-since 32c71e9

Artifacts and drill-down

• CI results artifact: homeboy-ci-results-data-machine-code-test-quality-Linux-node24 contains immediate command JSON for this action invocation.
• Observation artifact: homeboy-observations-data-machine-code-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-code/actions/runs/27110188666

Audit

✅ audit — passed

• audit — 20 finding(s)
• Total: 20 finding(s)

Deep dive: homeboy audit data-machine-code --changed-since 32c71e9

Artifacts and drill-down

• CI results artifact: homeboy-ci-results-data-machine-code-audit-quality-Linux-node24 contains immediate command JSON for this action invocation.
• Observation artifact: homeboy-observations-data-machine-code-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-code/actions/runs/27110188666

Tooling versions

• Homeboy CLI: homeboy 0.222.12+d696383
• Extension: wordpress from https://github.com/Extra-Chill/homeboy-extensions
• Extension revision: 5b66afcb
• Action: unknown@unknown