Write Cobra deprecation messages to stderr

We used to do the equivalent of `rootCmd.SetOut(os.Stdout)` because we
thought that Cobra's "Out" stream represents standard output. However,
upon closer inspection it turns out that this is Cobra's stream for
usage errors and deprecation warnings, and those we want written to
stderr as well. It is not clear to me why Cobra maintains a distinction
between "Out" and "Err" streams since both seem to go to sdterr by
default.

This change also ceases our usage of `command.Print()` functions in
favor of explicitly writing to `IOStreams.Out/ErrOut`.

pkg/cmd/repo/clone/clone_test.go

@@ -74,7 +74,7 @@ func TestNewCmdClone(t *testing.T) {
 			cmd.SetArgs(argv)
 
 			cmd.SetIn(stdin)
-			cmd.SetOut(stdout)
+			cmd.SetOut(stderr)
 			cmd.SetErr(stderr)
 
 			_, err = cmd.ExecuteC()
@@ -112,7 +112,7 @@ func runCloneCommand(httpClient *http.Client, cli string) (*test.CmdOut, error)
 	cmd.SetArgs(argv)
 
 	cmd.SetIn(stdin)
-	cmd.SetOut(stdout)
+	cmd.SetOut(stderr)
 	cmd.SetErr(stderr)
 
 	if err != nil {