fix(sync): stop editor-theme scaffold-once outputs from flapping as stale files

[JustAGhosT]

Problem

Local retort:sync can alternate editor-theme scaffold-once outputs between regenerated and deleted-as-stale on consecutive runs. The observed files include .cursor/settings.json and .windsurf/settings.json.

This is related to, but distinct from, #246. #246 covers path normalization for scaffold-once checks; this issue covers manifest/stale-clean behavior when scaffold-once outputs are skipped and therefore never registered in the new manifest.

Root cause sketch

• When all editor-theme outputs already exist, sync skips writing them to the temp output tree.
• Per-output scaffold-once skips can also continue without copying existing content into the temp tree.
• Manifest carry-forward only sees files that pass through the temp tree or skipped-file list.
• cleanStaleFiles can delete previously managed editor-theme files because they are absent from the new manifest.

Acceptance criteria

• Running sync twice does not delete existing editor-theme scaffold-once outputs.
• Existing project-root files are carried into the manifest when scaffold-once skips generation.
• Regression test covers clean sync, second sync with previous manifest, and stale-file list behavior.
• Behavior remains safe for genuinely stale managed outputs.

Source

Created during Baton/GitHub consolidation on 2026-07-07 from Baton task 376cacd9-c92d-4aa3-8b44-7ce041e201cb.