fix: reconcile stale extraction artifacts safely

[Alexander Zaslonov (azaslonov)]

Summary

• add opt-in --remove-stale extraction cleanup and enable it in generated CI pipelines
• stage extraction output and reconcile only managed artifacts in the selected filter and workspace scope
• preserve stale artifacts after partial extraction and skip commits after fatal extraction
• propagate API, product, gateway, and workspace supplemental failures into cleanup gating
• use recoverable candidate/backup directory swaps with deterministic failure coverage
• reconcile specifications, policies, wikis, and association files while preserving unmanaged content

Validation

• npm run build
• npm run lint
• npm test (1,142 tests)
• git diff --check
• constitution review: approved with no findings

Related Issue(s)

Closes #106