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repository_files() listed every path `git ls-files` returns, including tracked files the worktree has already deleted. Every content scan that reads the listing then reported "[Errno 2] No such file or directory" as a finding: in a worktree that removed roles/web-app-nextcloud/filter_plugins/nextcloud_janus.py and its test but had not committed the removal yet, test_no_rsync_backup_flag failed on exactly those two paths and turned the whole lint target red. No scan can read such a file until the deletion is committed. The listing now subtracts `git ls-files --deleted`. A clean checkout, as in CI, has no deleted entries, so the listing there is unchanged. The rsync lint is green again on the same worktree. The unit tests stub the extra git call and cover a file deleted in the worktree. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>