Use Cobra flag helpers for better shell completion

Cobra has a helper methods which can make shell completion a little nicer:

- [`MarkFlagFilename`](https://pkg.go.dev/github.com/spf13/cobra#MarkFlagFilename) tells Cobra that the flag represents a filename. This tells the `ko completion` logic to generate helpers to match filenames. (e.g., `ko apply -f `)
- [`MarkFlagRequired`](https://pkg.go.dev/github.com/spf13/cobra#MarkFlagRequired) tells Cobra that the flag is required, and prioritizes in completion if it's unset (e.g., `ko apply ` prioritizes `-f` over `--preserve-import-paths`).

Audit flags we configure and see if there are any that would benefit from being marked this way. Check that the expected behavior is actually observed when shell completion is configured.