Fix clean handling for missing outputs

[hugosmoreira]

Summary

• check the previous output manifest before an if-file-deleted incremental run
• clean when outputs have changed so incremental tools cannot cache an incomplete result
• propagate manifest errors and document the expanded clean behavior
• add a regression covering a missing output with surviving incremental state

Fixes #1471

Validation

• npm run build
• focused regression test (including a failing negative control before the fix)
• Prettier check on changed files
• ESLint on changed TypeScript files
• git diff --check