fix: detect orphan diffs in check mode

[dyoshikawa-claw]

Summary

• fix generate --check so orphan-only diffs are not treated as up to date when no files are written
• detect orphan diffs for non-deletable/shared-config targets during deletion scans
• add/update processor tests covering the new behavior

Test

• pnpm test:e2e

[dyoshikawa-claw]

Supersedes #1436.

This PR covers the same check-mode/orphan-diff issue, but expands the fix across processor-level orphan detection (including non-deletable/shared-config targets) and is validated with full pnpm test:e2e.

Closing #1436 to keep the discussion on a single PR.