Fix improper elision of -J flags

Currently if we use a command like `apply default -f
components/whatever.yaml`, kubecfg will fail to emit flags that add
ksonnet-lib to the -J paths. This means that, while a command like
`apply default` will correctly linke against (e.g.) `k.libsonnet`,
adding the `-f` flag will not.

This commit will correct this problem for all commands of this form.