Use case:
git ls-tree -r master --name-only | xargs fix-whitespace --config fix-whitespace.yaml
or simply
git ls-tree -r master --name-only | xargs fix-whitespace
This should filter the FILES given to fix-whitespace through the configuration given in fix-whitespace.yaml.
A new flag, like --config - could be used if really all of the given FILES should be processed.