何処かで見かけた下記方法ではアラートが現れ削除できず…
git rm
git ls-files --deleted
error: unknown option `deleted`'
usage: git rm [options] [--] <file>...
-n, --dry-run dry run
-q, --quiet do not list removed files
--cached only remove from the index
-f, --force override the up-to-date check
-r allow recursive removal
--ignore-unmatch exit with a zero status even if nothing matched
結局 xargs でOK。
git ls-files --deleted | xargs git rm -f
Ref: "gitの複数のブランチを一括で削除する"
http://qiita.com/satoshi03/items/c53aab17f3270477e33a