BUG: WriteCLI should write the prefix and data as separate strings

PARSE_ARGS seems to be able to deal with a string
"--flag x,y,z"
but else where in the CLI module logic it's producing command lines with:
"--flag"
"x,y,z"
so update the WriteCLI methods to separate out the prefix flag and the values.

Added a warning message in the Annotation control point node for when there's
an annotation with multiple points and the multiple flag is false.

Issue #1910